Starting phenix.real_space_refine on Fri Mar 22 03:40:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upl_26669/03_2024/7upl_26669.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upl_26669/03_2024/7upl_26669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upl_26669/03_2024/7upl_26669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upl_26669/03_2024/7upl_26669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upl_26669/03_2024/7upl_26669.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upl_26669/03_2024/7upl_26669.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.075 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 141 5.16 5 C 20472 2.51 5 N 5252 2.21 5 O 6280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32145 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 8224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8224 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 57, 'TRANS': 992} Chain breaks: 5 Chain: "B" Number of atoms: 8249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8249 Classifications: {'peptide': 1053} Link IDs: {'PTRANS': 57, 'TRANS': 995} Chain breaks: 5 Chain: "C" Number of atoms: 8224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8224 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 57, 'TRANS': 992} Chain breaks: 5 Chain: "D" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1662 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "E" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1684 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "F" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1684 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "I" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1662 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "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: "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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" 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: 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 14.97, per 1000 atoms: 0.47 Number of scatterers: 32145 At special positions: 0 Unit cell: (150.7, 133.1, 242, 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 141 16.00 O 6280 8.00 N 5252 7.00 C 20472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.04 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=2.05 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 135 " - pdb=" SG CYS I 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=1, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG h 1 " - " NAG h 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 2 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 61 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1098 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B1074 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1134 " " NAG C1306 " - " ASN C1098 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 603 " " NAG C1310 " - " ASN C 657 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN C 801 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 282 " " NAG M 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN B 282 " " NAG Z 1 " - " ASN B 717 " " NAG a 1 " - " ASN B 801 " " NAG h 1 " - " ASN C 234 " " NAG o 1 " - " ASN C 717 " " NAG q 1 " - " ASN C1074 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.24 Conformation dependent library (CDL) restraints added in 5.6 seconds 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7546 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 60 sheets defined 21.7% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.628A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.836A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.674A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.789A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.740A pdb=" N ILE A 624 " --> pdb=" O PRO A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.818A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.644A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.650A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.306A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.529A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 853 removed outlier: 3.969A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 848 through 853' Processing helix chain 'A' and resid 854 through 856 No H-bonds generated for 'chain 'A' and resid 854 through 856' Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.617A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.882A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.063A pdb=" N TYR A 917 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 938 removed outlier: 3.846A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.631A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.871A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.933A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.594A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.758A pdb=" N ASN B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.785A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 637 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.911A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 Processing helix chain 'B' and resid 758 through 760 No H-bonds generated for 'chain 'B' and resid 758 through 760' Processing helix chain 'B' and resid 761 through 783 removed outlier: 4.402A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN B 777 " --> pdb=" O GLU B 773 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.752A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 833 removed outlier: 3.718A pdb=" N GLY B 832 " --> pdb=" O ALA B 829 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 833 " --> pdb=" O ASP B 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 829 through 833' Processing helix chain 'B' and resid 835 through 841 removed outlier: 3.993A pdb=" N LEU B 841 " --> pdb=" O TYR B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.777A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.870A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.695A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.981A pdb=" N TYR B 917 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 933 removed outlier: 3.677A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 removed outlier: 3.517A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.390A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.269A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1034 removed outlier: 4.482A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B1034 " --> pdb=" O SER B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.773A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.103A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.674A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 623 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.730A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 removed outlier: 4.265A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 4.269A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.838A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 838 through 842 removed outlier: 3.527A pdb=" N GLY C 842 " --> pdb=" O ASP C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.906A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 879 " --> pdb=" O SER C 875 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.794A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 918 Processing helix chain 'C' and resid 919 through 932 removed outlier: 3.827A pdb=" N GLN C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 941 removed outlier: 4.302A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 956 removed outlier: 4.352A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 966 removed outlier: 3.698A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.290A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.722A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.573A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 184 through 188 removed outlier: 3.633A pdb=" N GLU D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 184 through 188' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.948A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.997A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 Processing helix chain 'I' and resid 122 through 129 Processing helix chain 'I' and resid 213 through 215 No H-bonds generated for 'chain 'I' and resid 213 through 215' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.995A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.911A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.305A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.542A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.884A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.753A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP A 586 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.676A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.507A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.992A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.884A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.725A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.436A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.193A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 63 through 64 removed outlier: 3.662A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.705A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 313 Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.629A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.825A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.598A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.789A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 6.495A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.762A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.027A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.596A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.883A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.977A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.963A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.963A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE5, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AE7, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.990A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 116 through 119 removed outlier: 4.003A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN D 139 " --> pdb=" O TYR D 174 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER D 175 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR D 179 " --> pdb=" O GLN D 161 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN D 161 " --> pdb=" O THR D 179 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 146 through 151 Processing sheet with id=AF1, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AF2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.795A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AF4, first strand: chain 'E' and resid 127 through 130 removed outlier: 4.911A pdb=" N ALA E 143 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL E 190 " --> pdb=" O ALA E 143 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLY E 145 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL E 188 " --> pdb=" O GLY E 145 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU E 147 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER E 186 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LYS E 149 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU E 184 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER E 183 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA E 174 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N SER E 185 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE E 172 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 187 " --> pdb=" O HIS E 170 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 156 through 160 removed outlier: 4.600A pdb=" N TYR E 200 " --> pdb=" O VAL E 217 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.781A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AF8, first strand: chain 'F' and resid 58 through 60 removed outlier: 3.765A pdb=" N ARG F 59 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE F 50 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG F 98 " --> pdb=" O TYR F 108 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR F 108 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 127 through 130 removed outlier: 4.077A pdb=" N ASP F 150 " --> pdb=" O TYR F 182 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N TYR F 182 " --> pdb=" O ASP F 150 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU F 181 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU F 176 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER F 183 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA F 174 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER F 185 " --> pdb=" O PHE F 172 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 157 through 159 Processing sheet with id=AG2, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AG4, first strand: chain 'I' and resid 45 through 48 removed outlier: 6.895A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 115 through 119 removed outlier: 3.932A pdb=" N VAL I 134 " --> pdb=" O PHE I 119 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU I 180 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 145 through 151 1089 hydrogen bonds defined for protein. 2847 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: 14.25 Time building geometry restraints manager: 12.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10175 1.35 - 1.47: 8311 1.47 - 1.59: 14226 1.59 - 1.72: 0 1.72 - 1.84: 175 Bond restraints: 32887 Sorted by residual: bond pdb=" C GLU B 214 " pdb=" N PRO B 214A" ideal model delta sigma weight residual 1.335 1.361 -0.026 8.70e-03 1.32e+04 8.77e+00 bond pdb=" C7 NAG G 1 " pdb=" O7 NAG G 1 " ideal model delta sigma weight residual 1.222 1.278 -0.056 2.00e-02 2.50e+03 7.89e+00 bond pdb=" C1 NAG q 2 " pdb=" O5 NAG q 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.41e+00 bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.02e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 ... (remaining 32882 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.22: 865 106.22 - 113.19: 18000 113.19 - 120.16: 11312 120.16 - 127.13: 14258 127.13 - 134.10: 322 Bond angle restraints: 44757 Sorted by residual: angle pdb=" C THR A1100 " pdb=" N HIS A1101 " pdb=" CA HIS A1101 " ideal model delta sigma weight residual 122.87 113.06 9.81 1.61e+00 3.86e-01 3.71e+01 angle pdb=" N GLY A 311 " pdb=" CA GLY A 311 " pdb=" C GLY A 311 " ideal model delta sigma weight residual 110.20 116.78 -6.58 1.32e+00 5.74e-01 2.48e+01 angle pdb=" N PRO B 214A" pdb=" CA PRO B 214A" pdb=" C PRO B 214A" ideal model delta sigma weight residual 110.21 116.26 -6.05 1.64e+00 3.72e-01 1.36e+01 angle pdb=" C SER E 209 " pdb=" N ASN E 210 " pdb=" CA ASN E 210 " ideal model delta sigma weight residual 121.54 127.70 -6.16 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C SER D 30 " pdb=" N ASN D 31 " pdb=" CA ASN D 31 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.76e+00 ... (remaining 44752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.45: 18824 20.45 - 40.89: 1249 40.89 - 61.34: 205 61.34 - 81.79: 58 81.79 - 102.24: 22 Dihedral angle restraints: 20358 sinusoidal: 8618 harmonic: 11740 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual 93.00 5.24 87.76 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 5.48 87.52 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual 93.00 175.90 -82.90 1 1.00e+01 1.00e-02 8.41e+01 ... (remaining 20355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4527 0.076 - 0.152: 679 0.152 - 0.228: 11 0.228 - 0.305: 7 0.305 - 0.381: 1 Chirality restraints: 5225 Sorted by residual: chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 5222 not shown) Planarity restraints: 5735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 97 " -0.030 2.00e-02 2.50e+03 2.25e-02 1.27e+01 pdb=" CG TRP I 97 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP I 97 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP I 97 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP I 97 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I 97 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 97 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 97 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 97 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP I 97 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE F 152 " -0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO F 153 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO F 153 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 153 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 214 " -0.049 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO B 214A" 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 214A" -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 214A" -0.043 5.00e-02 4.00e+02 ... (remaining 5732 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 431 2.65 - 3.21: 29646 3.21 - 3.77: 43898 3.77 - 4.34: 57381 4.34 - 4.90: 95231 Nonbonded interactions: 226587 Sorted by model distance: nonbonded pdb=" OG SER F 159 " pdb=" OD1 ASN F 203 " model vdw 2.086 2.440 nonbonded pdb=" OG1 THR A 393 " pdb=" OE1 GLU A 516 " model vdw 2.091 2.440 nonbonded pdb=" OG SER D 7 " pdb=" OG1 THR D 22 " model vdw 2.097 2.440 nonbonded pdb=" OG1 THR D 165 " pdb=" OG SER D 175 " model vdw 2.119 2.440 nonbonded pdb=" OH TYR A 91 " pdb=" OE2 GLU A 191 " model vdw 2.170 2.440 ... (remaining 226582 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 1147 or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 678 or resid 689 through 1147 or resid 1301 thr \ ough 1308)) selection = (chain 'C' and (resid 27 through 1147 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'a' selection = chain 'h' selection = chain 'o' selection = chain 'q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.160 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 78.920 Find NCS groups from input model: 2.260 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32887 Z= 0.279 Angle : 0.681 10.308 44757 Z= 0.356 Chirality : 0.049 0.381 5225 Planarity : 0.005 0.082 5694 Dihedral : 14.030 102.237 12668 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.42 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3987 helix: -0.68 (0.19), residues: 707 sheet: 0.13 (0.16), residues: 1013 loop : -1.40 (0.13), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP I 97 HIS 0.009 0.001 HIS F 206 PHE 0.030 0.002 PHE B 906 TYR 0.043 0.002 TYR C 873 ARG 0.008 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 3.537 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: A 265 TYR cc_start: 0.8503 (p90) cc_final: 0.8264 (p90) REVERT: A 634 ARG cc_start: 0.7351 (ttm-80) cc_final: 0.7130 (tpt90) REVERT: A 985 ASP cc_start: 0.7126 (t0) cc_final: 0.6444 (m-30) REVERT: B 191 GLU cc_start: 0.8028 (tt0) cc_final: 0.7715 (mm-30) REVERT: B 428 ASP cc_start: 0.8828 (m-30) cc_final: 0.8593 (p0) REVERT: B 516 GLU cc_start: 0.8026 (tp30) cc_final: 0.7811 (tp30) REVERT: B 564 GLN cc_start: 0.8178 (tp40) cc_final: 0.7406 (tp40) REVERT: B 572 THR cc_start: 0.8604 (m) cc_final: 0.8137 (p) REVERT: B 578 ASP cc_start: 0.8144 (t0) cc_final: 0.7779 (t0) REVERT: C 568 ASP cc_start: 0.7360 (t0) cc_final: 0.6572 (p0) REVERT: C 968 SER cc_start: 0.9494 (m) cc_final: 0.9278 (p) REVERT: F 111 GLN cc_start: 0.6612 (pm20) cc_final: 0.6029 (pm20) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.4355 time to fit residues: 212.1763 Evaluate side-chains 132 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 338 optimal weight: 8.9990 chunk 303 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 314 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 233 optimal weight: 0.7980 chunk 364 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 207 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN A 907 ASN A 935 GLN B 99 ASN B 343 ASN B 542 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1101 HIS B1142 GLN C 207 HIS C 334 ASN C 370 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN C 965 GLN D 53 ASN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN I 53 ASN I 125 GLN ** I 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32887 Z= 0.195 Angle : 0.604 14.340 44757 Z= 0.312 Chirality : 0.047 0.311 5225 Planarity : 0.005 0.064 5694 Dihedral : 8.068 77.410 5453 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.68 % Rotamer: Outliers : 0.14 % Allowed : 4.49 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 3987 helix: -0.28 (0.19), residues: 726 sheet: 0.14 (0.16), residues: 1022 loop : -1.39 (0.13), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 97 HIS 0.006 0.001 HIS A1083 PHE 0.023 0.001 PHE A 823 TYR 0.029 0.001 TYR C 873 ARG 0.008 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 199 time to evaluate : 3.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.8343 (p90) cc_final: 0.8039 (p90) REVERT: A 634 ARG cc_start: 0.7590 (ttm-80) cc_final: 0.7186 (tpt90) REVERT: B 191 GLU cc_start: 0.8051 (tt0) cc_final: 0.7838 (mm-30) REVERT: B 197 ILE cc_start: 0.8315 (tp) cc_final: 0.8064 (tp) REVERT: B 516 GLU cc_start: 0.7998 (tp30) cc_final: 0.7779 (tp30) REVERT: B 564 GLN cc_start: 0.8174 (tp40) cc_final: 0.7392 (tp40) REVERT: B 572 THR cc_start: 0.8056 (m) cc_final: 0.7715 (p) REVERT: B 578 ASP cc_start: 0.8131 (t0) cc_final: 0.7787 (t0) REVERT: C 568 ASP cc_start: 0.7222 (t0) cc_final: 0.6575 (p0) REVERT: C 968 SER cc_start: 0.9506 (m) cc_final: 0.9262 (p) REVERT: E 93 MET cc_start: 0.5503 (ttt) cc_final: 0.5225 (ttp) REVERT: F 48 MET cc_start: 0.7157 (mtt) cc_final: 0.6589 (tpp) REVERT: F 55 ASP cc_start: 0.6736 (p0) cc_final: 0.6511 (p0) REVERT: F 111 GLN cc_start: 0.6363 (pm20) cc_final: 0.5616 (pm20) outliers start: 5 outliers final: 1 residues processed: 204 average time/residue: 0.4103 time to fit residues: 140.8710 Evaluate side-chains 131 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 202 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 303 optimal weight: 0.0570 chunk 247 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 chunk 364 optimal weight: 2.9990 chunk 394 optimal weight: 0.9980 chunk 324 optimal weight: 3.9990 chunk 361 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 HIS ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C 992 GLN I 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32887 Z= 0.188 Angle : 0.585 16.447 44757 Z= 0.299 Chirality : 0.046 0.388 5225 Planarity : 0.004 0.061 5694 Dihedral : 7.582 68.462 5453 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 3987 helix: -0.05 (0.20), residues: 723 sheet: 0.14 (0.16), residues: 1028 loop : -1.37 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 97 HIS 0.009 0.001 HIS I 190 PHE 0.022 0.001 PHE A 981 TYR 0.025 0.001 TYR C 873 ARG 0.006 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 199 time to evaluate : 3.726 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: A 265 TYR cc_start: 0.8274 (p90) cc_final: 0.8018 (p90) REVERT: A 634 ARG cc_start: 0.7591 (ttm-80) cc_final: 0.7205 (tpt90) REVERT: A 1029 MET cc_start: 0.8647 (tpp) cc_final: 0.8409 (tpp) REVERT: B 101 ILE cc_start: 0.8271 (pt) cc_final: 0.7842 (pt) REVERT: B 516 GLU cc_start: 0.7943 (tp30) cc_final: 0.7712 (tp30) REVERT: B 572 THR cc_start: 0.8136 (m) cc_final: 0.7754 (p) REVERT: B 578 ASP cc_start: 0.8092 (t0) cc_final: 0.7793 (t0) REVERT: B 869 MET cc_start: 0.8438 (mpp) cc_final: 0.7732 (mpp) REVERT: C 131 CYS cc_start: 0.4862 (p) cc_final: 0.4597 (t) REVERT: C 233 ILE cc_start: 0.8391 (mt) cc_final: 0.8065 (mm) REVERT: C 568 ASP cc_start: 0.7307 (t0) cc_final: 0.6568 (p0) REVERT: C 968 SER cc_start: 0.9514 (m) cc_final: 0.9294 (p) REVERT: E 93 MET cc_start: 0.5679 (ttt) cc_final: 0.5303 (ttp) REVERT: F 48 MET cc_start: 0.7409 (mtt) cc_final: 0.7047 (tpp) REVERT: F 59 ARG cc_start: 0.7339 (mtt-85) cc_final: 0.7047 (mtm-85) REVERT: I 62 PHE cc_start: 0.5682 (m-80) cc_final: 0.4649 (m-80) outliers start: 2 outliers final: 1 residues processed: 201 average time/residue: 0.4043 time to fit residues: 138.2157 Evaluate side-chains 136 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 3.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 360 optimal weight: 9.9990 chunk 274 optimal weight: 3.9990 chunk 189 optimal weight: 0.0370 chunk 40 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 366 optimal weight: 0.7980 chunk 387 optimal weight: 20.0000 chunk 191 optimal weight: 0.8980 chunk 346 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1101 HIS ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN I 53 ASN I 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32887 Z= 0.243 Angle : 0.608 17.320 44757 Z= 0.312 Chirality : 0.047 0.391 5225 Planarity : 0.004 0.066 5694 Dihedral : 7.330 60.595 5453 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.26 % Rotamer: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.13), residues: 3987 helix: -0.03 (0.20), residues: 729 sheet: 0.10 (0.16), residues: 1001 loop : -1.41 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 97 HIS 0.008 0.001 HIS A1101 PHE 0.036 0.002 PHE A 823 TYR 0.027 0.001 TYR C 873 ARG 0.006 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.8291 (p90) cc_final: 0.8055 (p90) REVERT: A 634 ARG cc_start: 0.7662 (ttm-80) cc_final: 0.7277 (tpt90) REVERT: B 516 GLU cc_start: 0.7985 (tp30) cc_final: 0.7765 (tp30) REVERT: B 564 GLN cc_start: 0.8211 (tp40) cc_final: 0.7301 (tp-100) REVERT: B 572 THR cc_start: 0.8208 (m) cc_final: 0.7846 (p) REVERT: B 578 ASP cc_start: 0.8083 (t0) cc_final: 0.7752 (t0) REVERT: C 568 ASP cc_start: 0.7336 (t0) cc_final: 0.6518 (p0) REVERT: I 62 PHE cc_start: 0.5855 (m-80) cc_final: 0.4938 (m-80) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.3883 time to fit residues: 122.6720 Evaluate side-chains 126 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 3.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 322 optimal weight: 9.9990 chunk 220 optimal weight: 0.0470 chunk 5 optimal weight: 8.9990 chunk 288 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 330 optimal weight: 7.9990 chunk 267 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 chunk 347 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1101 HIS ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32887 Z= 0.206 Angle : 0.586 17.433 44757 Z= 0.300 Chirality : 0.046 0.405 5225 Planarity : 0.004 0.072 5694 Dihedral : 7.035 58.715 5453 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 3987 helix: 0.06 (0.20), residues: 728 sheet: 0.09 (0.16), residues: 1027 loop : -1.40 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP D 97 HIS 0.011 0.001 HIS A1101 PHE 0.023 0.001 PHE C 981 TYR 0.019 0.001 TYR C 873 ARG 0.005 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 4.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8344 (mt-10) REVERT: A 265 TYR cc_start: 0.8316 (p90) cc_final: 0.8054 (p90) REVERT: A 634 ARG cc_start: 0.7534 (ttm-80) cc_final: 0.7210 (tpt90) REVERT: B 572 THR cc_start: 0.8266 (m) cc_final: 0.7914 (p) REVERT: B 578 ASP cc_start: 0.8063 (t0) cc_final: 0.7753 (t0) REVERT: C 568 ASP cc_start: 0.7324 (t0) cc_final: 0.6523 (p0) REVERT: C 697 MET cc_start: 0.8058 (mtp) cc_final: 0.7850 (tpp) REVERT: C 884 SER cc_start: 0.9323 (m) cc_final: 0.8880 (t) REVERT: F 93 MET cc_start: 0.6503 (tpt) cc_final: 0.6155 (mmm) REVERT: I 62 PHE cc_start: 0.6015 (m-80) cc_final: 0.5170 (m-80) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.3697 time to fit residues: 114.5126 Evaluate side-chains 126 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 130 optimal weight: 4.9990 chunk 349 optimal weight: 0.0070 chunk 76 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 387 optimal weight: 20.0000 chunk 322 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 32 optimal weight: 0.0670 chunk 128 optimal weight: 0.7980 chunk 203 optimal weight: 4.9990 overall best weight: 2.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32887 Z= 0.288 Angle : 0.641 17.587 44757 Z= 0.328 Chirality : 0.047 0.378 5225 Planarity : 0.004 0.058 5694 Dihedral : 7.110 57.521 5453 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.85 % Favored : 93.13 % Rotamer: Outliers : 0.03 % Allowed : 2.62 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.13), residues: 3987 helix: -0.10 (0.20), residues: 732 sheet: 0.01 (0.16), residues: 1022 loop : -1.46 (0.13), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 97 HIS 0.007 0.001 HIS B1064 PHE 0.033 0.002 PHE B 906 TYR 0.024 0.001 TYR C 873 ARG 0.007 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 3.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8366 (mt-10) REVERT: A 634 ARG cc_start: 0.7536 (ttm-80) cc_final: 0.7182 (tpt90) REVERT: A 983 ARG cc_start: 0.8010 (ttt180) cc_final: 0.7669 (mmm-85) REVERT: B 529 LYS cc_start: 0.8456 (mmmt) cc_final: 0.7973 (mmmt) REVERT: B 564 GLN cc_start: 0.8234 (tp40) cc_final: 0.7368 (tp-100) REVERT: B 572 THR cc_start: 0.8328 (m) cc_final: 0.7968 (p) REVERT: B 578 ASP cc_start: 0.8137 (t0) cc_final: 0.7815 (t0) REVERT: D 86 TYR cc_start: 0.7288 (m-80) cc_final: 0.6824 (m-80) REVERT: I 62 PHE cc_start: 0.6051 (m-80) cc_final: 0.5261 (m-80) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.3981 time to fit residues: 111.4241 Evaluate side-chains 114 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 4.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 374 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 283 optimal weight: 0.0370 chunk 219 optimal weight: 2.9990 chunk 326 optimal weight: 0.6980 chunk 216 optimal weight: 5.9990 chunk 386 optimal weight: 50.0000 chunk 241 optimal weight: 8.9990 chunk 235 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 317 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN D 139 ASN ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 GLN ** I 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32887 Z= 0.167 Angle : 0.579 16.229 44757 Z= 0.295 Chirality : 0.046 0.414 5225 Planarity : 0.004 0.057 5694 Dihedral : 6.794 56.316 5453 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 0.03 % Allowed : 1.22 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 3987 helix: 0.08 (0.20), residues: 733 sheet: 0.15 (0.16), residues: 999 loop : -1.41 (0.13), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 97 HIS 0.004 0.001 HIS F 206 PHE 0.033 0.001 PHE A 823 TYR 0.021 0.001 TYR F 200 ARG 0.008 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8339 (mt-10) REVERT: A 634 ARG cc_start: 0.7505 (ttm-80) cc_final: 0.7182 (tpt90) REVERT: B 529 LYS cc_start: 0.8478 (mmmt) cc_final: 0.7956 (mmmt) REVERT: B 578 ASP cc_start: 0.8168 (t0) cc_final: 0.7817 (t0) REVERT: B 592 PHE cc_start: 0.6115 (t80) cc_final: 0.5468 (t80) REVERT: C 568 ASP cc_start: 0.7386 (t0) cc_final: 0.6526 (p0) REVERT: C 884 SER cc_start: 0.9263 (m) cc_final: 0.8878 (t) REVERT: D 86 TYR cc_start: 0.7167 (m-80) cc_final: 0.6686 (m-80) REVERT: F 93 MET cc_start: 0.6286 (tpt) cc_final: 0.5869 (tpp) REVERT: I 62 PHE cc_start: 0.6092 (m-80) cc_final: 0.5341 (m-80) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.4001 time to fit residues: 116.1757 Evaluate side-chains 114 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 239 optimal weight: 8.9990 chunk 154 optimal weight: 0.5980 chunk 230 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 75 optimal weight: 0.0070 chunk 74 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 303 optimal weight: 3.9990 overall best weight: 2.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN B 317 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 32887 Z= 0.306 Angle : 0.656 17.311 44757 Z= 0.337 Chirality : 0.048 0.439 5225 Planarity : 0.005 0.063 5694 Dihedral : 6.987 57.947 5453 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.50 % Favored : 92.48 % Rotamer: Outliers : 0.03 % Allowed : 1.31 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3987 helix: -0.07 (0.20), residues: 730 sheet: -0.03 (0.16), residues: 1005 loop : -1.45 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 97 HIS 0.007 0.001 HIS C 625 PHE 0.030 0.002 PHE C 906 TYR 0.025 0.001 TYR C 873 ARG 0.009 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 3.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8380 (mt-10) REVERT: B 529 LYS cc_start: 0.8455 (mmmt) cc_final: 0.7973 (mmmt) REVERT: B 564 GLN cc_start: 0.8270 (tp40) cc_final: 0.7398 (tp-100) REVERT: B 578 ASP cc_start: 0.8259 (t0) cc_final: 0.7908 (t0) REVERT: B 592 PHE cc_start: 0.6030 (t80) cc_final: 0.5295 (t80) REVERT: C 690 GLN cc_start: 0.6995 (pm20) cc_final: 0.6772 (pm20) REVERT: C 981 PHE cc_start: 0.7576 (t80) cc_final: 0.7364 (t80) REVERT: I 62 PHE cc_start: 0.6101 (m-80) cc_final: 0.5390 (m-80) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.3636 time to fit residues: 97.9947 Evaluate side-chains 110 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 3.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 351 optimal weight: 30.0000 chunk 370 optimal weight: 1.9990 chunk 337 optimal weight: 0.9990 chunk 360 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 282 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 325 optimal weight: 6.9990 chunk 340 optimal weight: 0.9990 chunk 358 optimal weight: 7.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN D 53 ASN ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32887 Z= 0.184 Angle : 0.585 15.918 44757 Z= 0.299 Chirality : 0.046 0.373 5225 Planarity : 0.004 0.059 5694 Dihedral : 6.706 57.452 5453 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.96 % Rotamer: Outliers : 0.06 % Allowed : 0.68 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 3987 helix: 0.05 (0.20), residues: 731 sheet: 0.10 (0.16), residues: 1008 loop : -1.38 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 97 HIS 0.004 0.001 HIS F 206 PHE 0.028 0.001 PHE A 823 TYR 0.014 0.001 TYR A 501 ARG 0.005 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 3.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8351 (mt-10) REVERT: B 529 LYS cc_start: 0.8438 (mmmt) cc_final: 0.7934 (mmmt) REVERT: B 578 ASP cc_start: 0.8171 (t0) cc_final: 0.7803 (t0) REVERT: B 592 PHE cc_start: 0.6359 (t80) cc_final: 0.5448 (t80) REVERT: C 884 SER cc_start: 0.9275 (m) cc_final: 0.8848 (t) REVERT: C 981 PHE cc_start: 0.7566 (t80) cc_final: 0.7237 (t80) REVERT: I 62 PHE cc_start: 0.6088 (m-80) cc_final: 0.5390 (m-80) outliers start: 2 outliers final: 0 residues processed: 153 average time/residue: 0.3918 time to fit residues: 104.2162 Evaluate side-chains 116 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 4.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 236 optimal weight: 50.0000 chunk 380 optimal weight: 8.9990 chunk 232 optimal weight: 1.9990 chunk 180 optimal weight: 0.4980 chunk 264 optimal weight: 0.9990 chunk 399 optimal weight: 7.9990 chunk 367 optimal weight: 20.0000 chunk 318 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN D 53 ASN ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 32887 Z= 0.321 Angle : 0.670 17.366 44757 Z= 0.346 Chirality : 0.048 0.393 5225 Planarity : 0.005 0.080 5694 Dihedral : 6.990 58.655 5453 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.90 % Favored : 92.07 % Rotamer: Outliers : 0.06 % Allowed : 0.28 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3987 helix: -0.16 (0.20), residues: 730 sheet: 0.03 (0.16), residues: 970 loop : -1.53 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 97 HIS 0.007 0.002 HIS A1058 PHE 0.042 0.002 PHE A 906 TYR 0.026 0.002 TYR C 873 ARG 0.006 0.000 ARG C 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8324 (mt-10) REVERT: B 529 LYS cc_start: 0.8453 (mmmt) cc_final: 0.7969 (mmmt) REVERT: B 578 ASP cc_start: 0.8291 (t0) cc_final: 0.7875 (t0) REVERT: C 981 PHE cc_start: 0.7608 (t80) cc_final: 0.7266 (t80) REVERT: I 62 PHE cc_start: 0.6173 (m-80) cc_final: 0.5494 (m-80) outliers start: 2 outliers final: 0 residues processed: 144 average time/residue: 0.3815 time to fit residues: 97.3895 Evaluate side-chains 112 residues out of total 3518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 252 optimal weight: 5.9990 chunk 338 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 293 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 318 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 327 optimal weight: 0.4980 chunk 40 optimal weight: 0.0770 chunk 58 optimal weight: 2.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1011 GLN D 53 ASN ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.124444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082038 restraints weight = 90628.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.081975 restraints weight = 70951.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.081484 restraints weight = 56627.435| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32887 Z= 0.157 Angle : 0.575 15.578 44757 Z= 0.293 Chirality : 0.046 0.345 5225 Planarity : 0.004 0.074 5694 Dihedral : 6.536 58.612 5453 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.03 % Allowed : 0.23 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 3987 helix: 0.05 (0.20), residues: 737 sheet: 0.13 (0.16), residues: 1010 loop : -1.38 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 97 HIS 0.004 0.001 HIS C1048 PHE 0.031 0.001 PHE C 906 TYR 0.012 0.001 TYR A 265 ARG 0.004 0.000 ARG F 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4814.64 seconds wall clock time: 89 minutes 39.71 seconds (5379.71 seconds total)