Starting phenix.real_space_refine on Thu Feb 22 12:20:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgl_34741/02_2024/8hgl_34741.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgl_34741/02_2024/8hgl_34741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgl_34741/02_2024/8hgl_34741.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgl_34741/02_2024/8hgl_34741.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgl_34741/02_2024/8hgl_34741.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgl_34741/02_2024/8hgl_34741.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 21669 2.51 5 N 5631 2.21 5 O 6723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34170 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7784 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 54, 'TRANS': 946} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1668 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "B" Number of atoms: 7784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7784 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 54, 'TRANS': 946} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1668 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "D" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "E" Number of atoms: 7784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7784 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 54, 'TRANS': 946} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1668 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "G" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: 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: "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: "S" 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 17.07, per 1000 atoms: 0.50 Number of scatterers: 34170 At special positions: 0 Unit cell: (138.414, 138.414, 260.406, 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 147 16.00 O 6723 8.00 N 5631 7.00 C 21669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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 H 20 " - pdb=" SG CYS H 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 99 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 20 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 204 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 20 " - pdb=" SG CYS F 94 " distance=2.04 Simple disulfide: pdb=" SG CYS F 99 " - pdb=" SG CYS F 104 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 204 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.04 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 BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A1098 " " NAG A1312 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B1098 " " NAG B1312 " - " ASN B1134 " " NAG E1301 " - " ASN E 282 " " NAG E1302 " - " ASN E 61 " " NAG E1303 " - " ASN E 122 " " NAG E1304 " - " ASN E 165 " " NAG E1305 " - " ASN E 234 " " NAG E1306 " - " ASN E 603 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1310 " - " ASN E1074 " " NAG E1311 " - " ASN E1098 " " NAG E1312 " - " ASN E1134 " " NAG I 1 " - " ASN A 331 " " NAG J 1 " - " ASN A 343 " " NAG K 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN B 331 " " NAG O 1 " - " ASN B 343 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN E 331 " " NAG S 1 " - " ASN E 343 " " NAG T 1 " - " ASN E 717 " " NAG U 1 " - " ASN E 801 " Time building additional restraints: 12.50 Conformation dependent library (CDL) restraints added in 5.7 seconds 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8046 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 77 sheets defined 20.0% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.04 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.718A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.020A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.709A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.609A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.879A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.557A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.506A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.706A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.765A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'H' and resid 26 through 29 removed outlier: 3.820A pdb=" N TYR H 29 " --> pdb=" O THR H 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 26 through 29' Processing helix chain 'H' and resid 85 through 89 Processing helix chain 'H' and resid 164 through 166 No H-bonds generated for 'chain 'H' and resid 164 through 166' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.994A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 184 through 189 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: 4.001A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.774A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.563A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.889A 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: 3.563A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.552A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.541A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.667A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.787A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.974A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.738A pdb=" N LYS D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.697A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 370 removed outlier: 4.008A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 390 removed outlier: 3.506A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.555A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.863A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 825 Processing helix chain 'E' and resid 866 through 885 removed outlier: 3.516A pdb=" N ILE E 870 " --> pdb=" O THR E 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 890 removed outlier: 3.559A pdb=" N ALA E 890 " --> pdb=" O THR E 887 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 913 through 919 Processing helix chain 'E' and resid 919 through 941 removed outlier: 4.011A pdb=" N SER E 939 " --> pdb=" O GLN E 935 " (cutoff:3.500A) Processing helix chain 'E' and resid 946 through 967 removed outlier: 3.891A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL E 952 " --> pdb=" O LEU E 948 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN E 955 " --> pdb=" O VAL E 951 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 956 " --> pdb=" O VAL E 952 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.511A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.738A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE E 993 " --> pdb=" O ALA E 989 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP E 994 " --> pdb=" O GLU E 990 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG E 995 " --> pdb=" O VAL E 991 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 996 " --> pdb=" O GLN E 992 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR E1006 " --> pdb=" O GLN E1002 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR E1007 " --> pdb=" O SER E1003 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1145 Processing helix chain 'F' and resid 85 through 89 Processing helix chain 'F' and resid 164 through 166 No H-bonds generated for 'chain 'F' and resid 164 through 166' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.968A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 128 Processing helix chain 'G' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.778A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.325A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 51 removed outlier: 4.124A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.605A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.939A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.286A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.741A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.519A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.925A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.576A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.642A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.227A 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=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.638A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.611A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'H' and resid 2 through 4 Processing sheet with id=AC2, first strand: chain 'H' and resid 8 through 10 removed outlier: 6.782A pdb=" N VAL H 32 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP H 48 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP H 34 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 8 through 10 Processing sheet with id=AC4, first strand: chain 'H' and resid 128 through 132 removed outlier: 3.774A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 128 through 132 removed outlier: 3.774A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 159 through 162 Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.133A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.615A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN L 161 " --> pdb=" O THR L 179 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 154 through 155 Processing sheet with id=AD2, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.561A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.170A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AD5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.572A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 119 through 122 removed outlier: 3.547A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.935A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.304A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP B 574 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.689A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.269A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AE5, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.660A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.049A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.648A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AF1, first strand: chain 'C' and resid 8 through 10 removed outlier: 6.799A pdb=" N VAL C 32 " --> pdb=" O TRP C 48 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TRP C 48 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TRP C 34 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 8 through 10 Processing sheet with id=AF3, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.773A pdb=" N GLY C 147 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.773A pdb=" N GLY C 147 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 159 through 162 Processing sheet with id=AF6, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.171A pdb=" N LEU D 11 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.638A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN D 161 " --> pdb=" O THR D 179 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AG1, first strand: chain 'E' and resid 28 through 30 removed outlier: 7.912A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 93 " --> pdb=" O TYR E 266 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL E 90 " --> pdb=" O PHE E 194 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE E 203 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL E 227 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 47 through 51 removed outlier: 4.180A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AG4, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.607A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 241 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASN E 121 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU E 118 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL E 130 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 311 through 319 removed outlier: 6.969A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.767A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AG8, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AG9, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.255A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 711 through 713 removed outlier: 3.670A pdb=" N THR E1076 " --> pdb=" O SER E1097 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 718 through 728 removed outlier: 3.516A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.668A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AH5, first strand: chain 'F' and resid 2 through 4 Processing sheet with id=AH6, first strand: chain 'F' and resid 8 through 10 removed outlier: 6.793A pdb=" N VAL F 32 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP F 48 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TRP F 34 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 8 through 10 removed outlier: 3.500A pdb=" N LEU F 110 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 128 through 132 removed outlier: 3.771A pdb=" N GLY F 147 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR F 184 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 128 through 132 removed outlier: 3.771A pdb=" N GLY F 147 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR F 184 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 159 through 162 removed outlier: 3.506A pdb=" N THR F 159 " --> pdb=" O ASN F 207 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AI3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.141A pdb=" N LEU G 11 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 115 through 119 removed outlier: 3.626A pdb=" N VAL G 134 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR G 174 " --> pdb=" O ASN G 139 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN G 161 " --> pdb=" O THR G 179 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 154 through 155 1363 hydrogen bonds defined for protein. 3633 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: 16.16 Time building geometry restraints manager: 13.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10766 1.34 - 1.46: 7769 1.46 - 1.58: 16220 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 34935 Sorted by residual: bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.83e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.34e+00 bond pdb=" C1 NAG E1304 " pdb=" O5 NAG E1304 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.58e+00 ... (remaining 34930 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.34: 971 106.34 - 113.27: 19296 113.27 - 120.21: 11804 120.21 - 127.14: 15144 127.14 - 134.07: 344 Bond angle restraints: 47559 Sorted by residual: angle pdb=" C ASN E 122 " pdb=" CA ASN E 122 " pdb=" CB ASN E 122 " ideal model delta sigma weight residual 111.68 103.48 8.20 1.68e+00 3.54e-01 2.38e+01 angle pdb=" C ASN E 234 " pdb=" CA ASN E 234 " pdb=" CB ASN E 234 " ideal model delta sigma weight residual 110.74 118.02 -7.28 1.61e+00 3.86e-01 2.05e+01 angle pdb=" C LYS F 151 " pdb=" N ASP F 152 " pdb=" CA ASP F 152 " ideal model delta sigma weight residual 122.46 128.47 -6.01 1.41e+00 5.03e-01 1.82e+01 angle pdb=" C LYS C 151 " pdb=" N ASP C 152 " pdb=" CA ASP C 152 " ideal model delta sigma weight residual 122.46 128.47 -6.01 1.41e+00 5.03e-01 1.81e+01 angle pdb=" C LYS H 151 " pdb=" N ASP H 152 " pdb=" CA ASP H 152 " ideal model delta sigma weight residual 122.82 128.51 -5.69 1.42e+00 4.96e-01 1.61e+01 ... (remaining 47554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.06: 20300 22.06 - 44.12: 1092 44.12 - 66.18: 184 66.18 - 88.24: 55 88.24 - 110.31: 26 Dihedral angle restraints: 21657 sinusoidal: 9132 harmonic: 12525 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.87 66.87 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS E 538 " pdb=" SG CYS E 538 " pdb=" SG CYS E 590 " pdb=" CB CYS E 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.33 66.33 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.30 63.30 1 1.00e+01 1.00e-02 5.29e+01 ... (remaining 21654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4830 0.077 - 0.154: 722 0.154 - 0.231: 21 0.231 - 0.308: 2 0.308 - 0.384: 2 Chirality restraints: 5577 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C1 NAG E1303 " pdb=" ND2 ASN E 122 " pdb=" C2 NAG E1303 " pdb=" O5 NAG E1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 5574 not shown) Planarity restraints: 6114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 122 " -0.006 2.00e-02 2.50e+03 5.11e-02 3.26e+01 pdb=" CG ASN E 122 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN E 122 " 0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN E 122 " -0.061 2.00e-02 2.50e+03 pdb=" C1 NAG E1303 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " 0.003 2.00e-02 2.50e+03 4.63e-02 2.68e+01 pdb=" CG ASN E 234 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " 0.055 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " -0.046 2.00e-02 2.50e+03 pdb=" C1 NAG E1305 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 717 " 0.004 2.00e-02 2.50e+03 4.22e-02 2.23e+01 pdb=" CG ASN B 717 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN B 717 " 0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN B 717 " -0.051 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.044 2.00e-02 2.50e+03 ... (remaining 6111 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 2072 2.73 - 3.27: 33123 3.27 - 3.81: 52689 3.81 - 4.36: 61870 4.36 - 4.90: 110122 Nonbonded interactions: 259876 Sorted by model distance: nonbonded pdb=" OD1 ASN L 139 " pdb=" OG1 THR L 173 " model vdw 2.181 2.440 nonbonded pdb=" OD1 ASN D 139 " pdb=" OG1 THR D 173 " model vdw 2.182 2.440 nonbonded pdb=" OD1 ASN G 139 " pdb=" OG1 THR G 173 " model vdw 2.196 2.440 nonbonded pdb=" OG SER D 66 " pdb=" OG1 THR D 73 " model vdw 2.198 2.440 nonbonded pdb=" OG SER L 66 " pdb=" OG1 THR L 73 " model vdw 2.201 2.440 ... (remaining 259871 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' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 20.170 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 86.480 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.390 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: 0.010 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 : 0.006 0.052 34935 Z= 0.417 Angle : 0.672 8.195 47559 Z= 0.358 Chirality : 0.050 0.384 5577 Planarity : 0.004 0.047 6066 Dihedral : 14.180 110.306 13449 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 4257 helix: 1.28 (0.20), residues: 699 sheet: 0.26 (0.14), residues: 1311 loop : -1.09 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 886 HIS 0.007 0.001 HIS B1064 PHE 0.064 0.002 PHE E 906 TYR 0.044 0.002 TYR B 160 ARG 0.007 0.000 ARG E 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 4.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 111 TRP cc_start: 0.2761 (m100) cc_final: 0.1056 (m100) REVERT: D 174 TYR cc_start: 0.5804 (m-80) cc_final: 0.5564 (m-80) REVERT: F 29 TYR cc_start: 0.6080 (m-80) cc_final: 0.5745 (m-10) REVERT: G 174 TYR cc_start: 0.5838 (m-80) cc_final: 0.5597 (m-80) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 1.4449 time to fit residues: 471.7460 Evaluate side-chains 146 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 0.9980 chunk 325 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 chunk 111 optimal weight: 50.0000 chunk 219 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 336 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 204 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 389 optimal weight: 40.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 38 GLN B 66 HIS B 211 ASN B 388 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B1071 GLN C 113 GLN D 27 GLN E 196 ASN E 388 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN G 32 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 34935 Z= 0.310 Angle : 0.639 9.843 47559 Z= 0.325 Chirality : 0.048 0.273 5577 Planarity : 0.005 0.051 6066 Dihedral : 9.003 79.814 5889 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.30 % Favored : 95.68 % Rotamer: Outliers : 1.13 % Allowed : 7.19 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.13), residues: 4257 helix: 1.42 (0.20), residues: 708 sheet: 0.38 (0.14), residues: 1308 loop : -1.05 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 64 HIS 0.004 0.001 HIS B1088 PHE 0.032 0.002 PHE E 906 TYR 0.026 0.002 TYR D 141 ARG 0.014 0.001 ARG D 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 158 time to evaluate : 4.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 MET cc_start: 0.4862 (mpm) cc_final: 0.4626 (mpm) REVERT: H 111 TRP cc_start: 0.3520 (m100) cc_final: 0.1563 (m100) REVERT: B 675 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7997 (pp30) REVERT: D 174 TYR cc_start: 0.5992 (m-80) cc_final: 0.5731 (m-80) REVERT: E 160 TYR cc_start: 0.4905 (t80) cc_final: 0.4452 (t80) REVERT: F 29 TYR cc_start: 0.6052 (m-80) cc_final: 0.5639 (m-10) REVERT: G 174 TYR cc_start: 0.5770 (m-80) cc_final: 0.5565 (m-80) outliers start: 42 outliers final: 18 residues processed: 183 average time/residue: 1.4003 time to fit residues: 313.8969 Evaluate side-chains 150 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 3.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 0.7980 chunk 120 optimal weight: 30.0000 chunk 324 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 390 optimal weight: 8.9990 chunk 421 optimal weight: 40.0000 chunk 347 optimal weight: 2.9990 chunk 387 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 313 optimal weight: 10.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 360 ASN A 493 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 32 ASN B 66 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 27 GLN D 32 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 360 ASN E 388 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN G 27 GLN G 32 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 34935 Z= 0.469 Angle : 0.681 9.156 47559 Z= 0.351 Chirality : 0.049 0.247 5577 Planarity : 0.005 0.056 6066 Dihedral : 8.008 59.177 5889 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.19 % Favored : 94.79 % Rotamer: Outliers : 1.96 % Allowed : 9.88 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.13), residues: 4257 helix: 1.24 (0.19), residues: 708 sheet: 0.13 (0.14), residues: 1335 loop : -1.06 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 64 HIS 0.008 0.001 HIS B1064 PHE 0.026 0.002 PHE E 86 TYR 0.026 0.002 TYR A1067 ARG 0.016 0.001 ARG L 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 141 time to evaluate : 4.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6614 (p90) REVERT: A 464 PHE cc_start: 0.7347 (m-80) cc_final: 0.6823 (m-80) REVERT: A 869 MET cc_start: 0.8732 (mtt) cc_final: 0.8175 (mtt) REVERT: H 72 MET cc_start: 0.4660 (mpm) cc_final: 0.2466 (mmt) REVERT: L 106 GLU cc_start: 0.3176 (pt0) cc_final: 0.2693 (tt0) REVERT: L 124 GLU cc_start: 0.4756 (pp20) cc_final: 0.4019 (pm20) REVERT: C 72 MET cc_start: 0.6628 (mpp) cc_final: 0.4411 (mmt) REVERT: D 174 TYR cc_start: 0.5816 (m-80) cc_final: 0.5608 (m-80) REVERT: G 174 TYR cc_start: 0.5662 (m-80) cc_final: 0.5408 (m-80) outliers start: 73 outliers final: 42 residues processed: 193 average time/residue: 1.2424 time to fit residues: 298.7006 Evaluate side-chains 172 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 129 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 3.9990 chunk 293 optimal weight: 8.9990 chunk 202 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 chunk 391 optimal weight: 40.0000 chunk 414 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 371 optimal weight: 0.7980 chunk 111 optimal weight: 50.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 32 ASN L 167 GLN B 66 HIS B 115 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN D 6 GLN D 27 GLN D 32 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN G 27 GLN G 90 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 34935 Z= 0.296 Angle : 0.603 7.997 47559 Z= 0.309 Chirality : 0.046 0.222 5577 Planarity : 0.004 0.051 6066 Dihedral : 7.439 59.931 5889 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 1.85 % Allowed : 11.89 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 4257 helix: 1.45 (0.20), residues: 711 sheet: 0.23 (0.14), residues: 1353 loop : -1.02 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 64 HIS 0.004 0.001 HIS A1064 PHE 0.048 0.002 PHE B 168 TYR 0.020 0.001 TYR A1067 ARG 0.006 0.000 ARG G 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 133 time to evaluate : 4.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 PHE cc_start: 0.7415 (m-80) cc_final: 0.6854 (m-80) REVERT: H 72 MET cc_start: 0.4603 (mpm) cc_final: 0.2329 (mmt) REVERT: L 106 GLU cc_start: 0.3197 (pt0) cc_final: 0.2665 (tt0) REVERT: L 124 GLU cc_start: 0.4765 (pp20) cc_final: 0.4044 (pm20) REVERT: L 162 GLU cc_start: 0.3534 (tp30) cc_final: 0.2856 (mm-30) REVERT: B 492 LEU cc_start: 0.7930 (mp) cc_final: 0.7525 (tp) REVERT: C 72 MET cc_start: 0.6631 (mpp) cc_final: 0.4580 (mmt) REVERT: D 174 TYR cc_start: 0.5721 (m-80) cc_final: 0.5508 (m-80) REVERT: E 1002 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8378 (tp40) outliers start: 69 outliers final: 32 residues processed: 184 average time/residue: 1.1817 time to fit residues: 275.0323 Evaluate side-chains 160 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 3.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain E residue 1002 GLN Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 308 optimal weight: 0.8980 chunk 171 optimal weight: 0.0970 chunk 353 optimal weight: 1.9990 chunk 286 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 211 optimal weight: 0.9980 chunk 372 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 GLN L 6 GLN L 32 ASN B 66 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 200 GLN D 6 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 606 ASN E 762 GLN E 955 ASN F 200 GLN G 6 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 34935 Z= 0.152 Angle : 0.550 8.069 47559 Z= 0.278 Chirality : 0.044 0.247 5577 Planarity : 0.004 0.041 6066 Dihedral : 6.982 59.516 5889 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.44 % Favored : 95.54 % Rotamer: Outliers : 1.74 % Allowed : 12.59 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 4257 helix: 1.80 (0.20), residues: 714 sheet: 0.36 (0.14), residues: 1350 loop : -0.92 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 64 HIS 0.003 0.000 HIS E1088 PHE 0.029 0.001 PHE A 168 TYR 0.016 0.001 TYR E1067 ARG 0.005 0.000 ARG D 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 133 time to evaluate : 3.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 PHE cc_start: 0.7160 (m-80) cc_final: 0.6871 (m-80) REVERT: H 72 MET cc_start: 0.4555 (mpm) cc_final: 0.2378 (mmt) REVERT: L 106 GLU cc_start: 0.3015 (pt0) cc_final: 0.2567 (tt0) REVERT: L 124 GLU cc_start: 0.4988 (pp20) cc_final: 0.4164 (pm20) REVERT: L 162 GLU cc_start: 0.3655 (tp30) cc_final: 0.3236 (mm-30) REVERT: B 492 LEU cc_start: 0.7934 (mp) cc_final: 0.7591 (tp) REVERT: C 72 MET cc_start: 0.6803 (mpp) cc_final: 0.4699 (mmt) REVERT: D 174 TYR cc_start: 0.5758 (m-80) cc_final: 0.5497 (m-10) REVERT: F 32 VAL cc_start: 0.6999 (OUTLIER) cc_final: 0.6754 (p) REVERT: F 72 MET cc_start: 0.4819 (mpm) cc_final: 0.2848 (mmt) outliers start: 65 outliers final: 24 residues processed: 182 average time/residue: 1.2092 time to fit residues: 277.0638 Evaluate side-chains 144 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 50.0000 chunk 373 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 243 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 chunk 415 optimal weight: 40.0000 chunk 344 optimal weight: 4.9990 chunk 192 optimal weight: 0.0270 chunk 34 optimal weight: 20.0000 chunk 137 optimal weight: 40.0000 chunk 217 optimal weight: 3.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN B 66 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN D 27 GLN D 32 ASN E 66 HIS E 196 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 34935 Z= 0.323 Angle : 0.611 10.887 47559 Z= 0.312 Chirality : 0.047 0.446 5577 Planarity : 0.004 0.046 6066 Dihedral : 7.036 58.870 5889 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.14 % Favored : 94.83 % Rotamer: Outliers : 1.93 % Allowed : 13.29 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.13), residues: 4257 helix: 1.60 (0.20), residues: 714 sheet: 0.35 (0.14), residues: 1338 loop : -0.99 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.006 0.001 HIS B1064 PHE 0.037 0.002 PHE B 168 TYR 0.034 0.002 TYR A 453 ARG 0.006 0.000 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 120 time to evaluate : 3.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 PHE cc_start: 0.7152 (m-80) cc_final: 0.6940 (m-80) REVERT: A 869 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8126 (mtt) REVERT: H 72 MET cc_start: 0.4380 (mpm) cc_final: 0.2459 (mmt) REVERT: L 106 GLU cc_start: 0.2980 (pt0) cc_final: 0.2552 (tt0) REVERT: L 110 THR cc_start: 0.3721 (OUTLIER) cc_final: 0.3467 (t) REVERT: L 124 GLU cc_start: 0.4769 (pp20) cc_final: 0.4002 (pm20) REVERT: B 492 LEU cc_start: 0.7929 (mp) cc_final: 0.7590 (tp) REVERT: C 72 MET cc_start: 0.6945 (mpp) cc_final: 0.4728 (mmt) REVERT: E 117 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8055 (tt) REVERT: F 32 VAL cc_start: 0.6831 (OUTLIER) cc_final: 0.6607 (p) REVERT: F 72 MET cc_start: 0.4568 (mpm) cc_final: 0.2531 (mmt) outliers start: 72 outliers final: 38 residues processed: 178 average time/residue: 1.1130 time to fit residues: 254.8220 Evaluate side-chains 159 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 117 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain E residue 1043 CYS Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 30.0000 chunk 46 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 303 optimal weight: 9.9990 chunk 234 optimal weight: 0.0770 chunk 349 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 413 optimal weight: 30.0000 chunk 258 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 32 ASN B 66 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN D 27 GLN D 32 ASN E 66 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN F 172 HIS G 27 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 34935 Z= 0.231 Angle : 0.568 7.799 47559 Z= 0.289 Chirality : 0.046 0.515 5577 Planarity : 0.004 0.047 6066 Dihedral : 6.875 59.505 5889 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.37 % Favored : 95.61 % Rotamer: Outliers : 1.66 % Allowed : 13.79 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.13), residues: 4257 helix: 1.72 (0.20), residues: 714 sheet: 0.39 (0.14), residues: 1338 loop : -0.98 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 48 HIS 0.004 0.001 HIS B1064 PHE 0.028 0.001 PHE B 168 TYR 0.023 0.001 TYR A 453 ARG 0.004 0.000 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 117 time to evaluate : 3.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 MET cc_start: 0.4426 (mpm) cc_final: 0.2457 (mmt) REVERT: L 110 THR cc_start: 0.3497 (OUTLIER) cc_final: 0.3231 (t) REVERT: B 492 LEU cc_start: 0.7955 (mp) cc_final: 0.7607 (tp) REVERT: B 1113 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8394 (mt0) REVERT: C 72 MET cc_start: 0.6918 (mpp) cc_final: 0.4620 (mmt) REVERT: E 117 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8011 (tt) REVERT: E 492 LEU cc_start: 0.8231 (mp) cc_final: 0.7797 (tp) REVERT: F 32 VAL cc_start: 0.6878 (OUTLIER) cc_final: 0.6654 (p) REVERT: F 72 MET cc_start: 0.4347 (mpm) cc_final: 0.2523 (mmt) outliers start: 62 outliers final: 34 residues processed: 166 average time/residue: 1.0772 time to fit residues: 230.7967 Evaluate side-chains 150 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 112 time to evaluate : 3.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 754 LEU Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain E residue 1043 CYS Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain G residue 33 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 246 optimal weight: 30.0000 chunk 124 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 262 optimal weight: 0.0070 chunk 281 optimal weight: 30.0000 chunk 204 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 325 optimal weight: 0.9980 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 32 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN E 66 HIS ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 34935 Z= 0.172 Angle : 0.546 7.907 47559 Z= 0.277 Chirality : 0.044 0.390 5577 Planarity : 0.004 0.043 6066 Dihedral : 6.685 59.554 5889 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.51 % Favored : 95.47 % Rotamer: Outliers : 1.50 % Allowed : 14.12 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.13), residues: 4257 helix: 1.86 (0.20), residues: 714 sheet: 0.54 (0.14), residues: 1314 loop : -0.98 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 48 HIS 0.004 0.001 HIS E 66 PHE 0.030 0.001 PHE A 168 TYR 0.029 0.001 TYR E 160 ARG 0.006 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 117 time to evaluate : 4.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8013 (mtt) REVERT: H 72 MET cc_start: 0.4451 (mpm) cc_final: 0.2663 (mmt) REVERT: L 110 THR cc_start: 0.3856 (OUTLIER) cc_final: 0.3547 (t) REVERT: B 492 LEU cc_start: 0.8176 (mp) cc_final: 0.7735 (tp) REVERT: B 1113 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8383 (mt0) REVERT: C 72 MET cc_start: 0.6583 (mpp) cc_final: 0.4547 (mmt) REVERT: E 117 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7921 (tt) REVERT: E 492 LEU cc_start: 0.8376 (mp) cc_final: 0.7886 (tp) REVERT: F 32 VAL cc_start: 0.6847 (OUTLIER) cc_final: 0.6626 (p) REVERT: F 72 MET cc_start: 0.4377 (mpm) cc_final: 0.2536 (mmt) outliers start: 56 outliers final: 37 residues processed: 157 average time/residue: 1.0710 time to fit residues: 219.1535 Evaluate side-chains 154 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 112 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 160 TYR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 754 LEU Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain E residue 1043 CYS Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 1.9990 chunk 396 optimal weight: 9.9990 chunk 361 optimal weight: 0.5980 chunk 385 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 302 optimal weight: 0.7980 chunk 118 optimal weight: 50.0000 chunk 348 optimal weight: 3.9990 chunk 364 optimal weight: 2.9990 chunk 383 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN B 422 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 200 GLN D 32 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 34935 Z= 0.219 Angle : 0.560 10.207 47559 Z= 0.283 Chirality : 0.045 0.333 5577 Planarity : 0.004 0.041 6066 Dihedral : 6.646 59.106 5889 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.63 % Favored : 95.35 % Rotamer: Outliers : 1.58 % Allowed : 14.22 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.13), residues: 4257 helix: 1.85 (0.20), residues: 714 sheet: 0.54 (0.14), residues: 1314 loop : -0.96 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 97 HIS 0.004 0.001 HIS B1064 PHE 0.030 0.001 PHE B 168 TYR 0.026 0.001 TYR E 160 ARG 0.004 0.000 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 116 time to evaluate : 3.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8065 (mtt) REVERT: H 72 MET cc_start: 0.4559 (mpm) cc_final: 0.2902 (mmt) REVERT: L 110 THR cc_start: 0.3892 (OUTLIER) cc_final: 0.3551 (t) REVERT: B 492 LEU cc_start: 0.8146 (mp) cc_final: 0.7646 (tp) REVERT: B 1113 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8391 (mt0) REVERT: C 72 MET cc_start: 0.6629 (mpp) cc_final: 0.4508 (mmt) REVERT: E 117 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7951 (tt) REVERT: E 492 LEU cc_start: 0.8409 (mp) cc_final: 0.7906 (tp) REVERT: F 71 ASP cc_start: 0.4265 (OUTLIER) cc_final: 0.3997 (p0) REVERT: F 72 MET cc_start: 0.4457 (mpm) cc_final: 0.2578 (mmt) outliers start: 59 outliers final: 39 residues processed: 162 average time/residue: 1.0872 time to fit residues: 226.8848 Evaluate side-chains 154 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 110 time to evaluate : 3.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 754 LEU Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain E residue 1043 CYS Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 50.0000 chunk 407 optimal weight: 10.0000 chunk 248 optimal weight: 40.0000 chunk 193 optimal weight: 2.9990 chunk 283 optimal weight: 9.9990 chunk 427 optimal weight: 5.9990 chunk 393 optimal weight: 20.0000 chunk 340 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 262 optimal weight: 0.0020 chunk 208 optimal weight: 1.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN ** H 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 GLN L 32 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 32 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 34935 Z= 0.373 Angle : 0.620 10.816 47559 Z= 0.316 Chirality : 0.047 0.315 5577 Planarity : 0.004 0.049 6066 Dihedral : 6.773 59.125 5889 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.38 % Favored : 94.60 % Rotamer: Outliers : 1.50 % Allowed : 14.33 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.13), residues: 4257 helix: 1.61 (0.20), residues: 714 sheet: 0.53 (0.14), residues: 1296 loop : -1.08 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 64 HIS 0.006 0.001 HIS B1064 PHE 0.026 0.002 PHE L 210 TYR 0.028 0.002 TYR B 160 ARG 0.005 0.000 ARG A 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 112 time to evaluate : 3.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8151 (mtt) REVERT: H 72 MET cc_start: 0.4873 (mpm) cc_final: 0.3103 (mmt) REVERT: B 410 ILE cc_start: 0.8493 (mt) cc_final: 0.8253 (mt) REVERT: B 492 LEU cc_start: 0.8227 (mp) cc_final: 0.7702 (tp) REVERT: B 1113 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8424 (mt0) REVERT: C 72 MET cc_start: 0.6714 (mpp) cc_final: 0.4437 (mmt) REVERT: E 117 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8056 (tt) REVERT: E 492 LEU cc_start: 0.8346 (mp) cc_final: 0.7922 (tp) REVERT: F 72 MET cc_start: 0.4309 (mpm) cc_final: 0.2431 (mmt) outliers start: 56 outliers final: 44 residues processed: 156 average time/residue: 1.0977 time to fit residues: 220.9504 Evaluate side-chains 156 residues out of total 3753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 109 time to evaluate : 3.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain E residue 1043 CYS Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 40.0000 chunk 362 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 313 optimal weight: 0.4980 chunk 50 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 340 optimal weight: 2.9990 chunk 142 optimal weight: 20.0000 chunk 350 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN H 172 HIS H 200 GLN L 27 GLN L 32 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 32 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.133189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.069109 restraints weight = 88644.351| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.00 r_work: 0.2842 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34935 Z= 0.195 Angle : 0.562 10.693 47559 Z= 0.283 Chirality : 0.045 0.282 5577 Planarity : 0.004 0.044 6066 Dihedral : 6.604 59.358 5889 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.37 % Favored : 95.61 % Rotamer: Outliers : 1.37 % Allowed : 14.52 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.13), residues: 4257 helix: 1.80 (0.20), residues: 714 sheet: 0.57 (0.14), residues: 1308 loop : -0.97 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 97 HIS 0.003 0.001 HIS B1064 PHE 0.033 0.001 PHE B 168 TYR 0.028 0.001 TYR B 160 ARG 0.004 0.000 ARG A 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9483.31 seconds wall clock time: 172 minutes 27.43 seconds (10347.43 seconds total)