Starting phenix.real_space_refine on Mon Mar 25 00:56:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rie_4890/03_2024/6rie_4890.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rie_4890/03_2024/6rie_4890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rie_4890/03_2024/6rie_4890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rie_4890/03_2024/6rie_4890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rie_4890/03_2024/6rie_4890.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rie_4890/03_2024/6rie_4890.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8814 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 42 5.49 5 Mg 2 5.21 5 S 161 5.16 5 C 23319 2.51 5 N 6104 2.21 5 O 6951 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 30": "OD1" <-> "OD2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ASP 547": "OD1" <-> "OD2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A ASP 615": "OD1" <-> "OD2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A ARG 751": "NH1" <-> "NH2" Residue "A ASP 799": "OD1" <-> "OD2" Residue "A ARG 872": "NH1" <-> "NH2" Residue "A ARG 897": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A GLU 903": "OE1" <-> "OE2" Residue "A TYR 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 950": "OE1" <-> "OE2" Residue "A GLU 963": "OE1" <-> "OE2" Residue "A ASP 984": "OD1" <-> "OD2" Residue "A GLU 1002": "OE1" <-> "OE2" Residue "A ARG 1010": "NH1" <-> "NH2" Residue "A GLU 1038": "OE1" <-> "OE2" Residue "A ARG 1043": "NH1" <-> "NH2" Residue "A GLU 1061": "OE1" <-> "OE2" Residue "A GLU 1079": "OE1" <-> "OE2" Residue "A TYR 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1126": "OE1" <-> "OE2" Residue "A GLU 1132": "OE1" <-> "OE2" Residue "A GLU 1165": "OE1" <-> "OE2" Residue "A ARG 1211": "NH1" <-> "NH2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ARG 181": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B GLU 367": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B GLU 598": "OE1" <-> "OE2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B ARG 648": "NH1" <-> "NH2" Residue "B ASP 659": "OD1" <-> "OD2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "B ARG 792": "NH1" <-> "NH2" Residue "B ARG 821": "NH1" <-> "NH2" Residue "B ASP 841": "OD1" <-> "OD2" Residue "B ARG 856": "NH1" <-> "NH2" Residue "B GLU 860": "OE1" <-> "OE2" Residue "B GLU 874": "OE1" <-> "OE2" Residue "B ARG 876": "NH1" <-> "NH2" Residue "B GLU 901": "OE1" <-> "OE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 923": "NH1" <-> "NH2" Residue "B TYR 943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 948": "OE1" <-> "OE2" Residue "B ARG 950": "NH1" <-> "NH2" Residue "B GLU 983": "OE1" <-> "OE2" Residue "B GLU 984": "OE1" <-> "OE2" Residue "B PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1055": "OE1" <-> "OE2" Residue "B ASP 1080": "OD1" <-> "OD2" Residue "B ARG 1105": "NH1" <-> "NH2" Residue "B ASP 1119": "OD1" <-> "OD2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E ASP 43": "OD1" <-> "OD2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ASP 55": "OD1" <-> "OD2" Residue "E ASP 75": "OD1" <-> "OD2" Residue "E ASP 76": "OD1" <-> "OD2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ASP 132": "OD1" <-> "OD2" Residue "E ARG 138": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F GLU 107": "OE1" <-> "OE2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "F TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ASP 103": "OD1" <-> "OD2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "J GLU 17": "OE1" <-> "OE2" Residue "J ASP 30": "OD1" <-> "OD2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L ASP 67": "OD1" <-> "OD2" Residue "L GLU 72": "OE1" <-> "OE2" Residue "L ARG 92": "NH1" <-> "NH2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L ASP 187": "OD1" <-> "OD2" Residue "L ASP 207": "OD1" <-> "OD2" Residue "L GLU 247": "OE1" <-> "OE2" Residue "L ARG 280": "NH1" <-> "NH2" Residue "O ASP 2": "OD1" <-> "OD2" Residue "O ASP 16": "OD1" <-> "OD2" Residue "O ARG 28": "NH1" <-> "NH2" Residue "O PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 128": "NH1" <-> "NH2" Residue "O ASP 133": "OD1" <-> "OD2" Residue "O ARG 142": "NH1" <-> "NH2" Residue "O ASP 199": "OD1" <-> "OD2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "O ARG 217": "NH1" <-> "NH2" Residue "O ASP 246": "OD1" <-> "OD2" Residue "O ASP 262": "OD1" <-> "OD2" Residue "O ASP 343": "OD1" <-> "OD2" Residue "O ARG 344": "NH1" <-> "NH2" Residue "O GLU 396": "OE1" <-> "OE2" Residue "O ARG 408": "NH1" <-> "NH2" Residue "O GLU 413": "OE1" <-> "OE2" Residue "O ARG 493": "NH1" <-> "NH2" Residue "O GLU 552": "OE1" <-> "OE2" Residue "O GLU 612": "OE1" <-> "OE2" Residue "O ASP 657": "OD1" <-> "OD2" Residue "O GLU 665": "OE1" <-> "OE2" Residue "O PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 793": "OE1" <-> "OE2" Residue "O ASP 807": "OD1" <-> "OD2" Residue "O PHE 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 38": "OE1" <-> "OE2" Residue "S GLU 42": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S GLU 77": "OE1" <-> "OE2" Residue "S ARG 89": "NH1" <-> "NH2" Residue "S GLU 114": "OE1" <-> "OE2" Residue "S ARG 119": "NH1" <-> "NH2" Residue "S GLU 133": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36583 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 10330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10330 Classifications: {'peptide': 1285} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1240} Chain: "B" Number of atoms: 9089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9089 Classifications: {'peptide': 1129} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1076} Chain breaks: 3 Chain: "C" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2475 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1024 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "L" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2345 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 9, 'TRANS': 277} Chain: "N" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 143 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "O" Number of atoms: 6661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 822, 6661 Classifications: {'peptide': 822} Link IDs: {'PTRANS': 30, 'TRANS': 791} Chain breaks: 3 Chain: "P" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 350 Unusual residues: {'GDP': 1} Classifications: {'RNA': 15, 'undetermined': 1} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna3p': 14, None: 1} Not linked: pdbres="GDP P 1 " pdbres=" A P 2 " Chain breaks: 1 Chain: "S" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 929 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Chain: "T" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 360 SG CYS A 49 46.599 90.788 91.537 1.00 46.07 S ATOM 382 SG CYS A 52 47.166 94.376 91.096 1.00 43.17 S ATOM 434 SG CYS A 59 50.256 91.904 91.542 1.00 35.72 S ATOM 694 SG CYS A 90 55.449 79.269 138.557 1.00 74.88 S ATOM 718 SG CYS A 93 53.704 81.396 139.996 1.00 76.26 S ATOM 1016 SG CYS A 130 55.980 80.765 141.620 1.00 79.81 S ATOM 1059 SG CYS A 135 52.147 78.381 141.745 1.00 85.90 S ATOM 18828 SG CYS B1087 50.073 102.080 104.692 1.00 33.26 S ATOM 18851 SG CYS B1090 50.138 98.552 106.128 1.00 33.48 S ATOM 18940 SG CYS B1103 48.206 99.170 103.052 1.00 36.59 S ATOM 18965 SG CYS B1106 47.455 100.482 106.899 1.00 38.67 S ATOM 25310 SG CYS J 7 111.266 77.088 57.165 1.00 16.99 S ATOM 25329 SG CYS J 10 112.892 79.280 54.749 1.00 19.49 S ATOM 25566 SG CYS J 39 114.497 78.750 58.418 1.00 21.87 S ATOM 25572 SG CYS J 40 114.158 76.737 55.147 1.00 20.15 S Time building chain proxies: 19.30, per 1000 atoms: 0.53 Number of scatterers: 36583 At special positions: 0 Unit cell: (148.05, 163.8, 174.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 161 16.00 P 42 15.00 Mg 2 11.99 O 6951 8.00 N 6104 7.00 C 23319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.60 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 135 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 40 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 39 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " Number of angles added : 21 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8440 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 50 sheets defined 38.2% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.726A pdb=" N ARG A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 118 " --> pdb=" O HIS A 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 118' Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 218 through 230 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 250 through 253 removed outlier: 3.754A pdb=" N ILE A 253 " --> pdb=" O ILE A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 253' Processing helix chain 'A' and resid 261 through 266 removed outlier: 3.575A pdb=" N TYR A 264 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.610A pdb=" N SER A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 321 through 330 removed outlier: 3.669A pdb=" N VAL A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 409 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 458 through 471 removed outlier: 4.467A pdb=" N VAL A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 500 through 509 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 572 Processing helix chain 'A' and resid 585 through 615 removed outlier: 3.694A pdb=" N TYR A 609 " --> pdb=" O ALA A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 656 removed outlier: 3.844A pdb=" N LEU A 637 " --> pdb=" O MET A 633 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 653 " --> pdb=" O MET A 649 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 654 " --> pdb=" O ARG A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 668 Processing helix chain 'A' and resid 672 through 681 removed outlier: 3.678A pdb=" N TYR A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 700 removed outlier: 3.560A pdb=" N ARG A 700 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 764 Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 809 through 821 removed outlier: 3.612A pdb=" N LYS A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 removed outlier: 3.817A pdb=" N VAL A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 875 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.685A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 removed outlier: 3.834A pdb=" N TYR A 913 " --> pdb=" O PHE A 909 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 944 Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.588A pdb=" N PHE A 964 " --> pdb=" O GLY A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 996 removed outlier: 3.556A pdb=" N SER A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN A 994 " --> pdb=" O SER A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1004 removed outlier: 3.542A pdb=" N ASN A1004 " --> pdb=" O GLY A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1033 through 1047 removed outlier: 3.663A pdb=" N VAL A1037 " --> pdb=" O THR A1033 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1093 removed outlier: 3.768A pdb=" N SER A1083 " --> pdb=" O GLU A1079 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Proline residue: A1090 - end of helix removed outlier: 3.626A pdb=" N ALA A1093 " --> pdb=" O LEU A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1136 removed outlier: 4.560A pdb=" N GLU A1132 " --> pdb=" O ASN A1129 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A1136 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1154 Processing helix chain 'A' and resid 1155 through 1170 removed outlier: 3.611A pdb=" N THR A1170 " --> pdb=" O ALA A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1207 through 1215 Processing helix chain 'A' and resid 1218 through 1227 removed outlier: 3.646A pdb=" N ASN A1222 " --> pdb=" O LYS A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1241 Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'A' and resid 1264 through 1282 Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.695A pdb=" N PHE B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 81 through 88 Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.535A pdb=" N VAL B 261 " --> pdb=" O PRO B 257 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 298 Processing helix chain 'B' and resid 303 through 313 Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.543A pdb=" N ASN B 320 " --> pdb=" O PRO B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.701A pdb=" N LYS B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 392 removed outlier: 3.874A pdb=" N TYR B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 413 removed outlier: 3.906A pdb=" N ALA B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 498 through 516 removed outlier: 3.585A pdb=" N TYR B 516 " --> pdb=" O TYR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 521 removed outlier: 4.113A pdb=" N ILE B 521 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 544 removed outlier: 3.543A pdb=" N MET B 544 " --> pdb=" O ASN B 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 541 through 544' Processing helix chain 'B' and resid 545 through 557 removed outlier: 3.973A pdb=" N ASP B 551 " --> pdb=" O ASP B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 610 removed outlier: 3.712A pdb=" N GLU B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.584A pdb=" N PHE B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 649 Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.769A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 682 removed outlier: 3.642A pdb=" N ASN B 682 " --> pdb=" O ILE B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 695 removed outlier: 4.098A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 731 Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 898 through 902 removed outlier: 3.796A pdb=" N LEU B 902 " --> pdb=" O GLU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 923 removed outlier: 3.732A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 941 removed outlier: 3.512A pdb=" N ILE B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 977 removed outlier: 3.579A pdb=" N TYR B 965 " --> pdb=" O SER B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 990 removed outlier: 3.532A pdb=" N LEU B 985 " --> pdb=" O SER B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1065 removed outlier: 3.575A pdb=" N GLY B1065 " --> pdb=" O LEU B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1075 Processing helix chain 'B' and resid 1103 through 1109 Processing helix chain 'B' and resid 1121 through 1133 removed outlier: 3.527A pdb=" N LYS B1125 " --> pdb=" O THR B1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.604A pdb=" N TRP C 52 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.603A pdb=" N VAL C 155 " --> pdb=" O ASN C 151 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 151 through 157' Processing helix chain 'C' and resid 162 through 174 removed outlier: 3.602A pdb=" N VAL C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 207 through 229 removed outlier: 4.131A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 283 through 303 Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.696A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS E 11 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE E 12 " --> pdb=" O TYR E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 117 through 128 Processing helix chain 'E' and resid 146 through 152 Processing helix chain 'F' and resid 63 through 75 removed outlier: 4.024A pdb=" N ARG F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 95 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 112 through 124 removed outlier: 3.570A pdb=" N VAL F 116 " --> pdb=" O ASN F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 161 removed outlier: 3.669A pdb=" N TYR F 153 " --> pdb=" O PHE F 149 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN F 161 " --> pdb=" O ILE F 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 36 removed outlier: 3.614A pdb=" N LEU G 36 " --> pdb=" O TYR G 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 23 Processing helix chain 'J' and resid 27 through 32 Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'L' and resid 2 through 10 Processing helix chain 'L' and resid 36 through 40 Processing helix chain 'L' and resid 42 through 47 Processing helix chain 'L' and resid 47 through 56 removed outlier: 3.841A pdb=" N MET L 56 " --> pdb=" O ASP L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 65 Processing helix chain 'L' and resid 73 through 82 Processing helix chain 'L' and resid 132 through 136 removed outlier: 3.698A pdb=" N LEU L 136 " --> pdb=" O TYR L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 142 removed outlier: 3.770A pdb=" N VAL L 140 " --> pdb=" O THR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 175 removed outlier: 3.617A pdb=" N SER L 174 " --> pdb=" O ARG L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 218 Processing helix chain 'L' and resid 238 through 268 removed outlier: 4.165A pdb=" N PHE L 248 " --> pdb=" O LYS L 244 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG L 251 " --> pdb=" O GLU L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 287 removed outlier: 3.938A pdb=" N ARG L 280 " --> pdb=" O ASN L 276 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG L 281 " --> pdb=" O LYS L 277 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 25 removed outlier: 3.638A pdb=" N TYR O 14 " --> pdb=" O THR O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 55 removed outlier: 3.997A pdb=" N LEU O 50 " --> pdb=" O PRO O 46 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR O 51 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 85 No H-bonds generated for 'chain 'O' and resid 83 through 85' Processing helix chain 'O' and resid 91 through 97 Processing helix chain 'O' and resid 137 through 140 Processing helix chain 'O' and resid 174 through 182 Processing helix chain 'O' and resid 204 through 220 Processing helix chain 'O' and resid 243 through 248 removed outlier: 3.949A pdb=" N ILE O 247 " --> pdb=" O LYS O 244 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL O 248 " --> pdb=" O GLN O 245 " (cutoff:3.500A) Processing helix chain 'O' and resid 327 through 337 Processing helix chain 'O' and resid 359 through 370 removed outlier: 3.626A pdb=" N VAL O 363 " --> pdb=" O THR O 359 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR O 368 " --> pdb=" O ASP O 364 " (cutoff:3.500A) Processing helix chain 'O' and resid 493 through 503 Processing helix chain 'O' and resid 510 through 523 removed outlier: 3.516A pdb=" N ILE O 514 " --> pdb=" O GLN O 510 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLU O 516 " --> pdb=" O ASN O 512 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE O 523 " --> pdb=" O ARG O 519 " (cutoff:3.500A) Processing helix chain 'O' and resid 562 through 581 removed outlier: 3.529A pdb=" N GLY O 566 " --> pdb=" O ARG O 562 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR O 580 " --> pdb=" O LEU O 576 " (cutoff:3.500A) Processing helix chain 'O' and resid 604 through 611 Processing helix chain 'O' and resid 623 through 638 Processing helix chain 'O' and resid 658 through 668 removed outlier: 3.828A pdb=" N SER O 662 " --> pdb=" O THR O 658 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL O 666 " --> pdb=" O SER O 662 " (cutoff:3.500A) Processing helix chain 'O' and resid 680 through 684 removed outlier: 3.633A pdb=" N TYR O 683 " --> pdb=" O ALA O 680 " (cutoff:3.500A) Processing helix chain 'O' and resid 686 through 688 No H-bonds generated for 'chain 'O' and resid 686 through 688' Processing helix chain 'O' and resid 689 through 697 Processing helix chain 'O' and resid 713 through 718 Processing helix chain 'O' and resid 733 through 736 Processing helix chain 'O' and resid 767 through 778 removed outlier: 3.677A pdb=" N TYR O 778 " --> pdb=" O VAL O 774 " (cutoff:3.500A) Processing helix chain 'O' and resid 788 through 801 removed outlier: 4.734A pdb=" N LYS O 797 " --> pdb=" O GLU O 793 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N PHE O 798 " --> pdb=" O ARG O 794 " (cutoff:3.500A) Processing helix chain 'O' and resid 802 through 806 removed outlier: 3.933A pdb=" N MET O 805 " --> pdb=" O ALA O 802 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU O 806 " --> pdb=" O SER O 803 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 802 through 806' Processing helix chain 'O' and resid 808 through 823 removed outlier: 3.751A pdb=" N LYS O 823 " --> pdb=" O ARG O 819 " (cutoff:3.500A) Processing helix chain 'O' and resid 828 through 833 Processing helix chain 'S' and resid 37 through 51 removed outlier: 3.806A pdb=" N SER S 49 " --> pdb=" O MET S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 79 removed outlier: 4.702A pdb=" N GLY S 75 " --> pdb=" O LYS S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 105 Processing helix chain 'S' and resid 113 through 131 removed outlier: 3.864A pdb=" N PHE S 117 " --> pdb=" O THR S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 147 removed outlier: 3.757A pdb=" N ASP S 146 " --> pdb=" O SER S 143 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR S 147 " --> pdb=" O TYR S 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 143 through 147' Processing sheet with id=AA1, first strand: chain 'A' and resid 1228 through 1231 removed outlier: 6.021A pdb=" N ILE A 4 " --> pdb=" O GLU B1143 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLU B1143 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 6 " --> pdb=" O ASP B1141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 3.699A pdb=" N GLY A 64 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 removed outlier: 4.054A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 206 through 210 removed outlier: 3.797A pdb=" N PHE A 208 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 282 removed outlier: 3.982A pdb=" N ILE B1051 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 7.618A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLY A 291 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 316 removed outlier: 7.295A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 472 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AB2, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AB3, first strand: chain 'A' and resid 766 through 768 removed outlier: 6.458A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AB5, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AB6, first strand: chain 'A' and resid 1106 through 1111 Processing sheet with id=AB7, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 3.674A pdb=" N LYS A1015 " --> pdb=" O GLU A1012 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 135 through 137 removed outlier: 3.827A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 135 through 137 removed outlier: 3.827A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE G 50 " --> pdb=" O PRO G 71 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL G 73 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE G 48 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR G 75 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.603A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LYS B 104 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS B 116 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL B 106 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE B 114 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.603A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AC4, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.759A pdb=" N ASN B 169 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.518A pdb=" N ARG B 181 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 231 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC7, first strand: chain 'B' and resid 598 through 599 removed outlier: 3.881A pdb=" N GLU B 598 " --> pdb=" O ASP B 595 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 535 through 540 removed outlier: 5.503A pdb=" N LEU B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE B 532 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 538 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 removed outlier: 6.660A pdb=" N LYS B 864 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU B 861 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 870 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 852 " --> pdb=" O LEU B 813 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 715 removed outlier: 6.660A pdb=" N LYS B 864 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU B 861 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 870 " --> pdb=" O GLU B 855 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AD3, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.838A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1084 through 1086 removed outlier: 4.224A pdb=" N VAL B1084 " --> pdb=" O ILE B1118 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AD6, first strand: chain 'C' and resid 5 through 13 removed outlier: 3.700A pdb=" N ILE C 188 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AD8, first strand: chain 'C' and resid 37 through 43 removed outlier: 6.434A pdb=" N GLU C 140 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ASN C 43 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR C 138 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.521A pdb=" N HIS C 126 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 233 through 234 removed outlier: 6.365A pdb=" N LYS C 233 " --> pdb=" O TYR C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 35 through 40 removed outlier: 8.541A pdb=" N VAL E 60 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE E 82 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLN E 62 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE E 84 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE E 64 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE E 95 " --> pdb=" O PRO E 81 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE E 83 " --> pdb=" O PHE E 95 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 113 through 115 removed outlier: 6.008A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 84 through 90 removed outlier: 6.522A pdb=" N ILE G 105 " --> pdb=" O PHE G 154 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA G 156 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS G 107 " --> pdb=" O ALA G 156 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE G 158 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 12 through 16 removed outlier: 4.424A pdb=" N VAL L 179 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE L 176 " --> pdb=" O VAL L 201 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL L 201 " --> pdb=" O PHE L 176 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL L 99 " --> pdb=" O ILE L 154 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS L 156 " --> pdb=" O VAL L 99 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA L 101 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS L 88 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ASP L 102 " --> pdb=" O LYS L 88 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 25 through 29 removed outlier: 4.071A pdb=" N ILE L 232 " --> pdb=" O ASN L 26 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER L 28 " --> pdb=" O PHE L 230 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE L 230 " --> pdb=" O SER L 28 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 34 through 42 removed outlier: 7.890A pdb=" N CYS O 119 " --> pdb=" O ARG O 114 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG O 114 " --> pdb=" O CYS O 119 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU O 121 " --> pdb=" O GLU O 112 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU O 112 " --> pdb=" O LEU O 121 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU O 123 " --> pdb=" O VAL O 110 " (cutoff:3.500A) removed outlier: 9.750A pdb=" N VAL O 103 " --> pdb=" O LYS O 79 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LYS O 79 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU O 143 " --> pdb=" O LEU O 166 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU O 38 " --> pdb=" O PHE O 195 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 227 through 228 removed outlier: 6.948A pdb=" N PHE O 301 " --> pdb=" O ILE O 315 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP O 310 " --> pdb=" O VAL O 346 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LYS O 348 " --> pdb=" O TRP O 310 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL O 312 " --> pdb=" O LYS O 348 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 238 through 241 removed outlier: 7.323A pdb=" N ILE O 389 " --> pdb=" O TYR O 381 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N TYR O 381 " --> pdb=" O ILE O 389 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 436 through 441 removed outlier: 6.722A pdb=" N LYS O 428 " --> pdb=" O TYR O 439 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER O 441 " --> pdb=" O TYR O 426 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR O 426 " --> pdb=" O SER O 441 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASN O 431 " --> pdb=" O ASP O 400 " (cutoff:3.500A) removed outlier: 10.891A pdb=" N ASP O 400 " --> pdb=" O ASN O 431 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE O 480 " --> pdb=" O PRO O 492 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU O 482 " --> pdb=" O LEU O 490 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 415 through 417 Processing sheet with id=AF3, first strand: chain 'O' and resid 450 through 453 removed outlier: 8.458A pdb=" N LYS O 471 " --> pdb=" O ASN O 463 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 646 through 651 removed outlier: 6.405A pdb=" N VAL O 594 " --> pdb=" O VAL O 617 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR O 619 " --> pdb=" O VAL O 594 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA O 596 " --> pdb=" O THR O 619 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS O 593 " --> pdb=" O ILE O 674 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ASP O 676 " --> pdb=" O LYS O 593 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU O 595 " --> pdb=" O ASP O 676 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLN O 678 " --> pdb=" O LEU O 595 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE O 597 " --> pdb=" O GLN O 678 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN O 673 " --> pdb=" O LYS O 706 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU O 708 " --> pdb=" O ASN O 673 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE O 675 " --> pdb=" O LEU O 708 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N THR O 710 " --> pdb=" O ILE O 675 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TRP O 677 " --> pdb=" O THR O 710 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N MET O 712 " --> pdb=" O TRP O 677 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS O 843 " --> pdb=" O GLY O 704 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS O 706 " --> pdb=" O PHE O 841 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE O 841 " --> pdb=" O LYS O 706 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU O 708 " --> pdb=" O TYR O 839 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR O 839 " --> pdb=" O LEU O 708 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR O 710 " --> pdb=" O VAL O 837 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL O 837 " --> pdb=" O THR O 710 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER O 842 " --> pdb=" O LEU O 782 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU O 782 " --> pdb=" O SER O 842 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 724 through 727 1507 hydrogen bonds defined for protein. 4200 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: 18.73 Time building geometry restraints manager: 14.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11003 1.34 - 1.46: 7582 1.46 - 1.58: 18462 1.58 - 1.70: 79 1.70 - 1.82: 260 Bond restraints: 37386 Sorted by residual: bond pdb=" C2 SAM O 901 " pdb=" N3 SAM O 901 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.16e+00 bond pdb=" C8 SAM O 901 " pdb=" N7 SAM O 901 " ideal model delta sigma weight residual 1.298 1.345 -0.047 2.00e-02 2.50e+03 5.41e+00 bond pdb=" C2 SAM O 901 " pdb=" N1 SAM O 901 " ideal model delta sigma weight residual 1.329 1.375 -0.046 2.00e-02 2.50e+03 5.36e+00 bond pdb=" C MET L 56 " pdb=" N PRO L 57 " ideal model delta sigma weight residual 1.330 1.359 -0.029 1.25e-02 6.40e+03 5.28e+00 bond pdb=" N LYS O 433 " pdb=" CA LYS O 433 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.23e+00 ... (remaining 37381 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.96: 882 105.96 - 113.51: 20965 113.51 - 121.07: 18497 121.07 - 128.62: 10167 128.62 - 136.18: 191 Bond angle restraints: 50702 Sorted by residual: angle pdb=" C ASP O 307 " pdb=" N LYS O 308 " pdb=" CA LYS O 308 " ideal model delta sigma weight residual 121.54 134.43 -12.89 1.91e+00 2.74e-01 4.56e+01 angle pdb=" C VAL G 62 " pdb=" N ASN G 63 " pdb=" CA ASN G 63 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 angle pdb=" C PHE O 667 " pdb=" N TYR O 668 " pdb=" CA TYR O 668 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 angle pdb=" C TYR B 467 " pdb=" N LEU B 468 " pdb=" CA LEU B 468 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.88e+01 angle pdb=" CA LEU A 155 " pdb=" CB LEU A 155 " pdb=" CG LEU A 155 " ideal model delta sigma weight residual 116.30 131.03 -14.73 3.50e+00 8.16e-02 1.77e+01 ... (remaining 50697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.36: 21730 29.36 - 58.73: 885 58.73 - 88.09: 74 88.09 - 117.45: 5 117.45 - 146.81: 1 Dihedral angle restraints: 22695 sinusoidal: 9635 harmonic: 13060 Sorted by residual: dihedral pdb=" CA ASN O 512 " pdb=" C ASN O 512 " pdb=" N ILE O 513 " pdb=" CA ILE O 513 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" O2B GDP P 1 " pdb=" O3A GDP P 1 " pdb=" PB GDP P 1 " pdb=" PA GDP P 1 " ideal model delta sinusoidal sigma weight residual -180.00 -64.78 -115.22 1 2.00e+01 2.50e-03 3.42e+01 dihedral pdb=" CA ILE A 458 " pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta harmonic sigma weight residual -180.00 -152.28 -27.72 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 22692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 5016 0.076 - 0.152: 706 0.152 - 0.228: 50 0.228 - 0.303: 5 0.303 - 0.379: 3 Chirality restraints: 5780 Sorted by residual: chirality pdb=" CB VAL O 475 " pdb=" CA VAL O 475 " pdb=" CG1 VAL O 475 " pdb=" CG2 VAL O 475 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CB VAL B 677 " pdb=" CA VAL B 677 " pdb=" CG1 VAL B 677 " pdb=" CG2 VAL B 677 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" C3' A P 19 " pdb=" C4' A P 19 " pdb=" O3' A P 19 " pdb=" C2' A P 19 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 5777 not shown) Planarity restraints: 6261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS O 686 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO O 687 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO O 687 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO O 687 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL O 475 " 0.046 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO O 476 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO O 476 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO O 476 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 100 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO A 101 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.039 5.00e-02 4.00e+02 ... (remaining 6258 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 443 2.63 - 3.20: 29828 3.20 - 3.77: 56571 3.77 - 4.33: 82884 4.33 - 4.90: 134928 Nonbonded interactions: 304654 Sorted by model distance: nonbonded pdb=" OD1 ASP A 417 " pdb="MG MG A1301 " model vdw 2.067 2.170 nonbonded pdb=" OD1 ASP A 419 " pdb="MG MG A1301 " model vdw 2.088 2.170 nonbonded pdb=" O3' G P 30 " pdb="MG MG A1301 " model vdw 2.128 2.170 nonbonded pdb=" OH TYR B 38 " pdb=" O PRO B 131 " model vdw 2.266 2.440 nonbonded pdb=" O TYR A 486 " pdb=" OH TYR A 506 " model vdw 2.273 2.440 ... (remaining 304649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.030 Extract box with map and model: 10.390 Check model and map are aligned: 0.570 Set scattering table: 0.350 Process input model: 104.980 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 37386 Z= 0.355 Angle : 0.764 14.728 50702 Z= 0.422 Chirality : 0.053 0.379 5780 Planarity : 0.006 0.076 6261 Dihedral : 15.315 146.813 14255 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.07 % Allowed : 7.78 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -3.21 (0.10), residues: 4382 helix: -2.42 (0.09), residues: 1503 sheet: -1.18 (0.18), residues: 717 loop : -2.19 (0.11), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP O 677 HIS 0.011 0.001 HIS A 385 PHE 0.046 0.002 PHE A 938 TYR 0.040 0.002 TYR O 649 ARG 0.009 0.000 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 505 time to evaluate : 4.267 Fit side-chains revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8216 (tt0) cc_final: 0.7761 (tp40) REVERT: A 413 ASN cc_start: 0.8568 (t0) cc_final: 0.8096 (t0) REVERT: A 520 ASP cc_start: 0.7861 (m-30) cc_final: 0.7617 (t0) REVERT: A 677 MET cc_start: 0.8370 (ttp) cc_final: 0.8103 (ttt) REVERT: A 1047 PHE cc_start: 0.8926 (m-80) cc_final: 0.8719 (m-80) REVERT: A 1057 GLU cc_start: 0.7897 (tt0) cc_final: 0.7693 (mt-10) REVERT: A 1084 LYS cc_start: 0.8235 (tttt) cc_final: 0.7651 (mttp) REVERT: A 1152 ASP cc_start: 0.8156 (t70) cc_final: 0.7528 (t0) REVERT: B 205 TYR cc_start: 0.8018 (m-80) cc_final: 0.7585 (m-80) REVERT: B 216 GLN cc_start: 0.7423 (pm20) cc_final: 0.7219 (pm20) REVERT: B 256 MET cc_start: 0.8984 (mmt) cc_final: 0.8521 (mmt) REVERT: B 313 HIS cc_start: 0.7057 (t-90) cc_final: 0.6671 (t70) REVERT: B 994 ILE cc_start: 0.9022 (mt) cc_final: 0.8624 (mp) REVERT: C 195 LYS cc_start: 0.7917 (tttt) cc_final: 0.7650 (tttt) REVERT: J 26 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8675 (mmtm) REVERT: O 32 TYR cc_start: 0.8306 (m-10) cc_final: 0.8039 (m-10) REVERT: O 308 LYS cc_start: 0.7618 (pttm) cc_final: 0.7087 (ttpp) REVERT: O 348 LYS cc_start: 0.7389 (mmtt) cc_final: 0.6837 (tttt) REVERT: O 490 LEU cc_start: 0.8468 (mm) cc_final: 0.8260 (mt) REVERT: O 814 PHE cc_start: 0.8178 (t80) cc_final: 0.7931 (t80) outliers start: 3 outliers final: 1 residues processed: 507 average time/residue: 0.5293 time to fit residues: 424.5144 Evaluate side-chains 394 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 4.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 74 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 1.9990 chunk 333 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 344 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 399 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 114 HIS A 162 ASN A 167 GLN A 218 ASN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN A 435 GLN A 459 GLN A 548 HIS A 720 ASN A 822 GLN A 894 ASN A 941 GLN A 994 ASN A1081 ASN A1239 HIS B 61 ASN B 101 ASN B 169 ASN B 305 ASN B 318 HIS B 371 HIS B 376 ASN B 391 ASN B 408 ASN B 481 GLN B 487 GLN B 576 ASN B 682 ASN B 693 GLN B 740 GLN B 778 HIS B 779 GLN B 789 ASN B 858 GLN B 971 GLN B1040 GLN C 8 ASN C 109 ASN C 129 GLN C 137 GLN C 230 HIS E 129 GLN E 168 ASN F 119 GLN G 7 ASN G 29 ASN G 37 HIS G 100 GLN G 157 ASN J 16 HIS J 53 ASN L 42 ASN L 51 ASN L 122 HIS L 234 ASN ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 182 HIS O 218 HIS O 254 ASN O 466 ASN O 486 ASN O 509 ASN ** O 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 673 ASN O 818 ASN ** S 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37386 Z= 0.235 Angle : 0.530 9.965 50702 Z= 0.283 Chirality : 0.043 0.181 5780 Planarity : 0.004 0.059 6261 Dihedral : 10.358 149.192 5356 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.19 % Allowed : 11.73 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -1.77 (0.12), residues: 4382 helix: -0.61 (0.12), residues: 1537 sheet: -0.82 (0.19), residues: 714 loop : -1.70 (0.12), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP O 677 HIS 0.007 0.001 HIS A 385 PHE 0.034 0.001 PHE A 938 TYR 0.015 0.001 TYR A 466 ARG 0.006 0.000 ARG O 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 412 time to evaluate : 4.653 Fit side-chains revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8223 (tt0) cc_final: 0.7753 (tp40) REVERT: A 413 ASN cc_start: 0.8607 (t0) cc_final: 0.8119 (t0) REVERT: A 520 ASP cc_start: 0.7937 (m-30) cc_final: 0.7705 (t0) REVERT: A 619 VAL cc_start: 0.7680 (OUTLIER) cc_final: 0.7384 (p) REVERT: A 677 MET cc_start: 0.8526 (ttp) cc_final: 0.8282 (ttt) REVERT: A 1047 PHE cc_start: 0.8936 (m-80) cc_final: 0.8684 (m-80) REVERT: A 1084 LYS cc_start: 0.8233 (tttt) cc_final: 0.7858 (ttmm) REVERT: A 1086 MET cc_start: 0.8441 (mmm) cc_final: 0.8230 (mmp) REVERT: A 1152 ASP cc_start: 0.8234 (t70) cc_final: 0.7648 (t0) REVERT: B 205 TYR cc_start: 0.8048 (m-80) cc_final: 0.7642 (m-80) REVERT: B 256 MET cc_start: 0.9037 (mmt) cc_final: 0.8491 (mmt) REVERT: B 313 HIS cc_start: 0.7096 (t-90) cc_final: 0.6697 (t70) REVERT: B 354 MET cc_start: 0.8907 (mmm) cc_final: 0.8590 (mmm) REVERT: B 409 HIS cc_start: 0.6940 (t-90) cc_final: 0.6688 (t-90) REVERT: B 923 ARG cc_start: 0.7958 (mtt180) cc_final: 0.7733 (mtt90) REVERT: B 945 ASN cc_start: 0.7695 (p0) cc_final: 0.7482 (p0) REVERT: C 105 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7562 (m-30) REVERT: C 276 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7794 (mtm-85) REVERT: G 84 ILE cc_start: 0.5550 (OUTLIER) cc_final: 0.4868 (mp) REVERT: J 26 LYS cc_start: 0.9045 (mmmm) cc_final: 0.8754 (mmtm) REVERT: L 267 MET cc_start: 0.7764 (mtt) cc_final: 0.7291 (mtt) REVERT: L 279 GLN cc_start: 0.8387 (tp-100) cc_final: 0.8184 (tp-100) REVERT: O 348 LYS cc_start: 0.7425 (mmtt) cc_final: 0.6897 (tttt) REVERT: S 149 ASN cc_start: 0.7197 (m-40) cc_final: 0.6900 (m-40) outliers start: 48 outliers final: 26 residues processed: 444 average time/residue: 0.4708 time to fit residues: 340.9154 Evaluate side-chains 409 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 380 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 750 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 0.0770 chunk 124 optimal weight: 0.8980 chunk 332 optimal weight: 0.8980 chunk 272 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 400 optimal weight: 3.9990 chunk 432 optimal weight: 7.9990 chunk 356 optimal weight: 6.9990 chunk 396 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 321 optimal weight: 7.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN B 429 HIS L 7 ASN L 42 ASN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 486 ASN O 521 GLN S 84 ASN ** S 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37386 Z= 0.269 Angle : 0.529 9.595 50702 Z= 0.282 Chirality : 0.044 0.191 5780 Planarity : 0.004 0.052 6261 Dihedral : 10.173 148.486 5356 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.90 % Allowed : 13.43 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -1.09 (0.12), residues: 4382 helix: 0.22 (0.13), residues: 1538 sheet: -0.62 (0.19), residues: 714 loop : -1.45 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP O 677 HIS 0.007 0.001 HIS A 26 PHE 0.032 0.002 PHE A 938 TYR 0.016 0.001 TYR A 387 ARG 0.007 0.000 ARG G 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 391 time to evaluate : 4.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8173 (tt0) cc_final: 0.7717 (tp40) REVERT: A 413 ASN cc_start: 0.8618 (t0) cc_final: 0.8074 (t0) REVERT: A 677 MET cc_start: 0.8534 (ttp) cc_final: 0.8283 (ttt) REVERT: A 1084 LYS cc_start: 0.8251 (tttt) cc_final: 0.7878 (ttmm) REVERT: A 1152 ASP cc_start: 0.8259 (t70) cc_final: 0.7691 (t0) REVERT: B 205 TYR cc_start: 0.8020 (m-80) cc_final: 0.7776 (m-80) REVERT: B 226 LYS cc_start: 0.8136 (ptpt) cc_final: 0.7656 (tttp) REVERT: B 256 MET cc_start: 0.9058 (mmt) cc_final: 0.8526 (mmt) REVERT: B 286 TYR cc_start: 0.7397 (t80) cc_final: 0.7111 (t80) REVERT: B 313 HIS cc_start: 0.7127 (t-90) cc_final: 0.6757 (t70) REVERT: B 354 MET cc_start: 0.8944 (mmm) cc_final: 0.8573 (mmm) REVERT: B 409 HIS cc_start: 0.7026 (t-90) cc_final: 0.6749 (t-90) REVERT: B 945 ASN cc_start: 0.7734 (p0) cc_final: 0.7529 (p0) REVERT: C 105 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: E 177 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7872 (p0) REVERT: G 84 ILE cc_start: 0.5576 (OUTLIER) cc_final: 0.4892 (mp) REVERT: J 26 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8764 (mmtm) REVERT: S 149 ASN cc_start: 0.7208 (m-40) cc_final: 0.6890 (m-40) outliers start: 77 outliers final: 55 residues processed: 445 average time/residue: 0.4754 time to fit residues: 346.7906 Evaluate side-chains 426 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 368 time to evaluate : 4.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1207 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain O residue 466 ASN Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 631 GLU Chi-restraints excluded: chain O residue 701 THR Chi-restraints excluded: chain O residue 750 VAL Chi-restraints excluded: chain O residue 751 VAL Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 139 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 5.9990 chunk 300 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 191 optimal weight: 0.0980 chunk 268 optimal weight: 0.8980 chunk 401 optimal weight: 5.9990 chunk 425 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 380 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN B 967 GLN L 42 ASN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 37386 Z= 0.153 Angle : 0.473 10.266 50702 Z= 0.252 Chirality : 0.042 0.169 5780 Planarity : 0.003 0.050 6261 Dihedral : 9.896 146.660 5356 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.70 % Allowed : 14.69 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.12), residues: 4382 helix: 0.76 (0.13), residues: 1534 sheet: -0.44 (0.19), residues: 721 loop : -1.25 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 677 HIS 0.012 0.001 HIS L 212 PHE 0.030 0.001 PHE A 938 TYR 0.014 0.001 TYR B 340 ARG 0.006 0.000 ARG G 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 390 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8112 (tt0) cc_final: 0.7662 (tp40) REVERT: A 413 ASN cc_start: 0.8592 (t0) cc_final: 0.8110 (t0) REVERT: A 520 ASP cc_start: 0.7045 (t0) cc_final: 0.6839 (t0) REVERT: A 631 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7357 (mm-30) REVERT: A 677 MET cc_start: 0.8509 (ttp) cc_final: 0.8285 (ttt) REVERT: A 783 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7867 (m-10) REVERT: A 1084 LYS cc_start: 0.8213 (tttt) cc_final: 0.7492 (mmtp) REVERT: A 1152 ASP cc_start: 0.8214 (t70) cc_final: 0.7709 (t0) REVERT: B 205 TYR cc_start: 0.8050 (m-80) cc_final: 0.7721 (m-80) REVERT: B 226 LYS cc_start: 0.8117 (ptpt) cc_final: 0.7612 (tttp) REVERT: B 256 MET cc_start: 0.8974 (mmt) cc_final: 0.8621 (mmt) REVERT: B 286 TYR cc_start: 0.7320 (t80) cc_final: 0.7014 (t80) REVERT: B 354 MET cc_start: 0.8875 (mmm) cc_final: 0.8422 (mmm) REVERT: B 409 HIS cc_start: 0.7075 (t-90) cc_final: 0.6747 (t70) REVERT: B 478 ARG cc_start: 0.8030 (mtp180) cc_final: 0.7705 (mtp180) REVERT: B 945 ASN cc_start: 0.7671 (p0) cc_final: 0.7467 (p0) REVERT: B 1033 LYS cc_start: 0.8626 (mmtt) cc_final: 0.7942 (mmtm) REVERT: C 105 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7572 (m-30) REVERT: F 109 MET cc_start: 0.8717 (mpp) cc_final: 0.8432 (mmt) REVERT: G 84 ILE cc_start: 0.5429 (OUTLIER) cc_final: 0.4775 (mp) REVERT: J 26 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8731 (mmtm) REVERT: L 196 MET cc_start: 0.7669 (tmm) cc_final: 0.7371 (tmm) REVERT: O 814 PHE cc_start: 0.8147 (t80) cc_final: 0.7929 (t80) outliers start: 69 outliers final: 43 residues processed: 437 average time/residue: 0.4739 time to fit residues: 340.7699 Evaluate side-chains 411 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 365 time to evaluate : 4.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1237 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain O residue 466 ASN Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 574 THR Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 701 THR Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 139 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 5.9990 chunk 241 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 316 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 362 optimal weight: 0.8980 chunk 293 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 381 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN B 967 GLN L 42 ASN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 397 ASN O 486 ASN O 678 GLN S 145 ASN S 149 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37386 Z= 0.207 Angle : 0.487 9.104 50702 Z= 0.259 Chirality : 0.043 0.173 5780 Planarity : 0.003 0.051 6261 Dihedral : 9.854 146.712 5356 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.27 % Allowed : 15.19 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.12), residues: 4382 helix: 0.90 (0.13), residues: 1551 sheet: -0.37 (0.19), residues: 717 loop : -1.11 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 677 HIS 0.007 0.001 HIS L 212 PHE 0.031 0.001 PHE A 938 TYR 0.016 0.001 TYR O 333 ARG 0.005 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 380 time to evaluate : 3.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8128 (tt0) cc_final: 0.7682 (tp40) REVERT: A 413 ASN cc_start: 0.8613 (t0) cc_final: 0.8112 (t0) REVERT: A 631 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7381 (mm-30) REVERT: A 1084 LYS cc_start: 0.8196 (tttt) cc_final: 0.7825 (ttmm) REVERT: A 1152 ASP cc_start: 0.8237 (t70) cc_final: 0.7736 (t0) REVERT: B 205 TYR cc_start: 0.8037 (m-80) cc_final: 0.7805 (m-80) REVERT: B 226 LYS cc_start: 0.8060 (ptpt) cc_final: 0.7349 (pttm) REVERT: B 256 MET cc_start: 0.9000 (mmt) cc_final: 0.8538 (mmt) REVERT: B 286 TYR cc_start: 0.7337 (t80) cc_final: 0.7025 (t80) REVERT: B 409 HIS cc_start: 0.7112 (t-90) cc_final: 0.6790 (t70) REVERT: B 478 ARG cc_start: 0.7979 (mtp180) cc_final: 0.7664 (mtp180) REVERT: B 716 MET cc_start: 0.8261 (mtp) cc_final: 0.8001 (ttt) REVERT: B 1016 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8794 (mt) REVERT: B 1033 LYS cc_start: 0.8633 (mmtt) cc_final: 0.7937 (mmtm) REVERT: C 105 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: C 187 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.7999 (p90) REVERT: F 109 MET cc_start: 0.8700 (mpp) cc_final: 0.8415 (mmt) REVERT: G 84 ILE cc_start: 0.5440 (OUTLIER) cc_final: 0.4790 (mp) REVERT: J 26 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8745 (mmtm) REVERT: L 196 MET cc_start: 0.7690 (tmm) cc_final: 0.7325 (tmm) REVERT: O 757 MET cc_start: 0.8379 (mtt) cc_final: 0.8117 (mtp) REVERT: S 149 ASN cc_start: 0.6892 (m-40) cc_final: 0.6631 (m-40) outliers start: 92 outliers final: 72 residues processed: 447 average time/residue: 0.4770 time to fit residues: 351.5185 Evaluate side-chains 441 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 365 time to evaluate : 4.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1207 SER Chi-restraints excluded: chain A residue 1237 SER Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 135 MET Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain O residue 466 ASN Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 574 THR Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 701 THR Chi-restraints excluded: chain O residue 711 THR Chi-restraints excluded: chain O residue 750 VAL Chi-restraints excluded: chain O residue 751 VAL Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 139 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 2.9990 chunk 383 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 249 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 425 optimal weight: 9.9990 chunk 353 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN B 967 GLN F 111 GLN J 37 ASN L 42 ASN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37386 Z= 0.264 Angle : 0.517 11.624 50702 Z= 0.273 Chirality : 0.044 0.187 5780 Planarity : 0.004 0.050 6261 Dihedral : 9.898 146.362 5356 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.91 % Allowed : 15.09 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.13), residues: 4382 helix: 0.96 (0.13), residues: 1551 sheet: -0.32 (0.19), residues: 714 loop : -1.06 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP O 677 HIS 0.007 0.001 HIS L 212 PHE 0.033 0.002 PHE O 814 TYR 0.017 0.001 TYR A 466 ARG 0.007 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 373 time to evaluate : 4.650 Fit side-chains revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8125 (tt0) cc_final: 0.7709 (tp40) REVERT: A 413 ASN cc_start: 0.8639 (t0) cc_final: 0.7998 (t0) REVERT: A 520 ASP cc_start: 0.7914 (m-30) cc_final: 0.7692 (t0) REVERT: A 783 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.8018 (m-10) REVERT: A 1084 LYS cc_start: 0.8217 (tttt) cc_final: 0.7855 (ttmm) REVERT: A 1152 ASP cc_start: 0.8259 (t70) cc_final: 0.7756 (t0) REVERT: B 205 TYR cc_start: 0.8045 (m-80) cc_final: 0.7804 (m-80) REVERT: B 226 LYS cc_start: 0.8081 (ptpt) cc_final: 0.7369 (pttm) REVERT: B 256 MET cc_start: 0.9020 (mmt) cc_final: 0.8529 (mmt) REVERT: B 286 TYR cc_start: 0.7384 (t80) cc_final: 0.7058 (t80) REVERT: B 289 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7369 (m-30) REVERT: B 354 MET cc_start: 0.8976 (mmm) cc_final: 0.8631 (mmm) REVERT: B 409 HIS cc_start: 0.7102 (t-90) cc_final: 0.6778 (t70) REVERT: B 478 ARG cc_start: 0.7962 (mtp180) cc_final: 0.7652 (mtp180) REVERT: B 1016 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8877 (mt) REVERT: B 1033 LYS cc_start: 0.8634 (mmtt) cc_final: 0.7933 (mmtm) REVERT: C 105 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7576 (m-30) REVERT: C 187 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.7963 (p90) REVERT: E 115 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7061 (ttm170) REVERT: F 109 MET cc_start: 0.8747 (mpp) cc_final: 0.8269 (mmt) REVERT: G 44 MET cc_start: 0.7671 (ttm) cc_final: 0.7458 (ttm) REVERT: G 51 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7866 (mtp-110) REVERT: G 84 ILE cc_start: 0.5632 (OUTLIER) cc_final: 0.4959 (mp) REVERT: J 26 LYS cc_start: 0.9063 (mmmm) cc_final: 0.8768 (mmtm) REVERT: L 196 MET cc_start: 0.7632 (tmm) cc_final: 0.7355 (tmm) REVERT: O 114 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7050 (ttt-90) REVERT: O 757 MET cc_start: 0.8411 (mtt) cc_final: 0.8151 (mtp) REVERT: S 149 ASN cc_start: 0.6801 (m-40) cc_final: 0.6505 (m-40) outliers start: 118 outliers final: 91 residues processed: 461 average time/residue: 0.4854 time to fit residues: 368.8367 Evaluate side-chains 460 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 362 time to evaluate : 4.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1207 SER Chi-restraints excluded: chain A residue 1237 SER Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 135 MET Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain O residue 466 ASN Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 574 THR Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 631 GLU Chi-restraints excluded: chain O residue 701 THR Chi-restraints excluded: chain O residue 711 THR Chi-restraints excluded: chain O residue 750 VAL Chi-restraints excluded: chain O residue 751 VAL Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 139 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 chunk 310 optimal weight: 0.9990 chunk 240 optimal weight: 0.8980 chunk 358 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 424 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 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 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN B 967 GLN L 42 ASN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37386 Z= 0.212 Angle : 0.498 11.401 50702 Z= 0.264 Chirality : 0.043 0.175 5780 Planarity : 0.003 0.049 6261 Dihedral : 9.838 145.694 5356 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.49 % Allowed : 15.80 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.13), residues: 4382 helix: 1.08 (0.13), residues: 1550 sheet: -0.27 (0.19), residues: 714 loop : -1.00 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP O 677 HIS 0.008 0.001 HIS L 212 PHE 0.031 0.001 PHE A 938 TYR 0.016 0.001 TYR A 466 ARG 0.006 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 372 time to evaluate : 4.629 Fit side-chains revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8109 (tt0) cc_final: 0.7699 (tp40) REVERT: A 413 ASN cc_start: 0.8651 (t0) cc_final: 0.8147 (t0) REVERT: A 631 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7348 (mm-30) REVERT: A 783 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.8024 (m-10) REVERT: A 1084 LYS cc_start: 0.8209 (tttt) cc_final: 0.7843 (ttmm) REVERT: A 1152 ASP cc_start: 0.8244 (t70) cc_final: 0.7741 (t0) REVERT: B 205 TYR cc_start: 0.8037 (m-80) cc_final: 0.7793 (m-80) REVERT: B 226 LYS cc_start: 0.8063 (ptpt) cc_final: 0.7351 (pttm) REVERT: B 256 MET cc_start: 0.8998 (mmt) cc_final: 0.8526 (mmt) REVERT: B 286 TYR cc_start: 0.7360 (t80) cc_final: 0.6989 (t80) REVERT: B 289 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7362 (m-30) REVERT: B 354 MET cc_start: 0.8955 (mmm) cc_final: 0.8611 (mmm) REVERT: B 409 HIS cc_start: 0.7090 (t-90) cc_final: 0.6773 (t70) REVERT: B 478 ARG cc_start: 0.7945 (mtp180) cc_final: 0.7634 (mtp180) REVERT: B 1016 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8841 (mt) REVERT: B 1033 LYS cc_start: 0.8629 (mmtt) cc_final: 0.7930 (mmtm) REVERT: C 105 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: C 187 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.7962 (p90) REVERT: G 84 ILE cc_start: 0.5731 (OUTLIER) cc_final: 0.5081 (mp) REVERT: J 26 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8761 (mmtm) REVERT: L 196 MET cc_start: 0.7619 (tmm) cc_final: 0.7355 (tmm) REVERT: O 114 ARG cc_start: 0.7657 (ttm-80) cc_final: 0.7072 (ttm-80) REVERT: O 757 MET cc_start: 0.8431 (mtt) cc_final: 0.8173 (mtp) REVERT: S 149 ASN cc_start: 0.6713 (m-40) cc_final: 0.6370 (m-40) outliers start: 101 outliers final: 79 residues processed: 447 average time/residue: 0.4798 time to fit residues: 355.8916 Evaluate side-chains 450 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 365 time to evaluate : 4.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1207 SER Chi-restraints excluded: chain A residue 1237 SER Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 135 MET Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 574 THR Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 631 GLU Chi-restraints excluded: chain O residue 701 THR Chi-restraints excluded: chain O residue 711 THR Chi-restraints excluded: chain O residue 750 VAL Chi-restraints excluded: chain O residue 751 VAL Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 139 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 262 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 269 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 333 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN B 967 GLN F 111 GLN L 42 ASN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 37386 Z= 0.268 Angle : 0.525 11.063 50702 Z= 0.277 Chirality : 0.044 0.186 5780 Planarity : 0.004 0.049 6261 Dihedral : 9.869 145.776 5356 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.74 % Allowed : 15.98 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.13), residues: 4382 helix: 1.04 (0.13), residues: 1556 sheet: -0.27 (0.19), residues: 714 loop : -1.00 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP O 677 HIS 0.009 0.001 HIS L 212 PHE 0.032 0.001 PHE A 938 TYR 0.018 0.001 TYR A 466 ARG 0.006 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 371 time to evaluate : 4.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8644 (tp40) cc_final: 0.8298 (tp-100) REVERT: A 344 GLN cc_start: 0.8101 (tt0) cc_final: 0.7698 (tp40) REVERT: A 413 ASN cc_start: 0.8662 (t0) cc_final: 0.8142 (t0) REVERT: A 631 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7370 (mm-30) REVERT: A 783 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: A 1084 LYS cc_start: 0.8185 (tttt) cc_final: 0.7468 (mmtp) REVERT: A 1152 ASP cc_start: 0.8256 (t70) cc_final: 0.7754 (t0) REVERT: B 205 TYR cc_start: 0.8044 (m-80) cc_final: 0.7786 (m-80) REVERT: B 226 LYS cc_start: 0.8082 (ptpt) cc_final: 0.7363 (pttm) REVERT: B 256 MET cc_start: 0.9008 (mmt) cc_final: 0.8500 (mmt) REVERT: B 286 TYR cc_start: 0.7385 (t80) cc_final: 0.7019 (t80) REVERT: B 289 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7360 (m-30) REVERT: B 409 HIS cc_start: 0.7116 (t-90) cc_final: 0.6799 (t70) REVERT: B 478 ARG cc_start: 0.7958 (mtp180) cc_final: 0.7640 (mtp180) REVERT: B 1016 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8868 (mt) REVERT: B 1033 LYS cc_start: 0.8634 (mmtt) cc_final: 0.7930 (mmtm) REVERT: C 105 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: C 187 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.7990 (p90) REVERT: E 115 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7127 (ttm170) REVERT: E 177 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8010 (p0) REVERT: G 84 ILE cc_start: 0.5737 (OUTLIER) cc_final: 0.5085 (mp) REVERT: J 26 LYS cc_start: 0.9069 (mmmm) cc_final: 0.8778 (mmtm) REVERT: L 196 MET cc_start: 0.7588 (tmm) cc_final: 0.7387 (tmm) REVERT: O 114 ARG cc_start: 0.7694 (ttm-80) cc_final: 0.7077 (ttt-90) REVERT: O 757 MET cc_start: 0.8456 (mtt) cc_final: 0.8183 (mtp) REVERT: S 149 ASN cc_start: 0.6795 (m-40) cc_final: 0.6504 (m-40) outliers start: 111 outliers final: 90 residues processed: 453 average time/residue: 0.4845 time to fit residues: 361.2727 Evaluate side-chains 461 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 363 time to evaluate : 4.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1207 SER Chi-restraints excluded: chain A residue 1237 SER Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1087 CYS Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 135 MET Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 317 LEU Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 574 THR Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 631 GLU Chi-restraints excluded: chain O residue 701 THR Chi-restraints excluded: chain O residue 711 THR Chi-restraints excluded: chain O residue 750 VAL Chi-restraints excluded: chain O residue 751 VAL Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 139 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 385 optimal weight: 2.9990 chunk 406 optimal weight: 5.9990 chunk 370 optimal weight: 7.9990 chunk 395 optimal weight: 10.0000 chunk 237 optimal weight: 2.9990 chunk 172 optimal weight: 0.3980 chunk 310 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 357 optimal weight: 10.0000 chunk 373 optimal weight: 7.9990 chunk 393 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN B 967 GLN F 111 GLN L 42 ASN ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 37386 Z= 0.341 Angle : 0.555 11.144 50702 Z= 0.293 Chirality : 0.045 0.214 5780 Planarity : 0.004 0.049 6261 Dihedral : 9.952 145.806 5356 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.74 % Allowed : 16.35 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.13), residues: 4382 helix: 0.92 (0.13), residues: 1562 sheet: -0.29 (0.19), residues: 714 loop : -1.03 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP O 677 HIS 0.009 0.001 HIS L 212 PHE 0.034 0.002 PHE A 938 TYR 0.018 0.002 TYR A 466 ARG 0.008 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 368 time to evaluate : 4.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8663 (tp40) cc_final: 0.8366 (tp-100) REVERT: A 413 ASN cc_start: 0.8657 (t0) cc_final: 0.8034 (t0) REVERT: A 631 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7394 (mm-30) REVERT: A 783 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8296 (m-10) REVERT: A 1084 LYS cc_start: 0.8198 (tttt) cc_final: 0.7531 (mmtp) REVERT: A 1152 ASP cc_start: 0.8271 (t70) cc_final: 0.7769 (t0) REVERT: B 205 TYR cc_start: 0.8057 (m-80) cc_final: 0.7818 (m-80) REVERT: B 226 LYS cc_start: 0.8094 (ptpt) cc_final: 0.7596 (tttp) REVERT: B 256 MET cc_start: 0.9036 (mmt) cc_final: 0.8449 (mmt) REVERT: B 286 TYR cc_start: 0.7370 (t80) cc_final: 0.7013 (t80) REVERT: B 289 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: B 354 MET cc_start: 0.8970 (mmm) cc_final: 0.8609 (mmm) REVERT: B 382 ARG cc_start: 0.7543 (ttm110) cc_final: 0.7336 (ttm110) REVERT: B 409 HIS cc_start: 0.7114 (t-90) cc_final: 0.6794 (t70) REVERT: B 478 ARG cc_start: 0.7981 (mtp180) cc_final: 0.7657 (mtp180) REVERT: B 794 ARG cc_start: 0.7008 (mtt180) cc_final: 0.6433 (mtp-110) REVERT: B 1016 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8861 (mt) REVERT: B 1033 LYS cc_start: 0.8676 (mmtt) cc_final: 0.7988 (mmtm) REVERT: C 105 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: C 187 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.7934 (p90) REVERT: E 115 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7033 (ttm170) REVERT: E 177 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7460 (p0) REVERT: G 84 ILE cc_start: 0.5719 (OUTLIER) cc_final: 0.5061 (mp) REVERT: J 26 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8796 (mmtm) REVERT: O 114 ARG cc_start: 0.7741 (ttm-80) cc_final: 0.7126 (ttt-90) REVERT: O 757 MET cc_start: 0.8433 (mtt) cc_final: 0.8169 (mtp) REVERT: S 149 ASN cc_start: 0.6839 (m-40) cc_final: 0.6528 (m-40) outliers start: 111 outliers final: 95 residues processed: 452 average time/residue: 0.4933 time to fit residues: 364.8869 Evaluate side-chains 465 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 362 time to evaluate : 4.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1207 SER Chi-restraints excluded: chain A residue 1237 SER Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1087 CYS Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 135 MET Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 317 LEU Chi-restraints excluded: chain O residue 349 SER Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain O residue 466 ASN Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 574 THR Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 631 GLU Chi-restraints excluded: chain O residue 701 THR Chi-restraints excluded: chain O residue 711 THR Chi-restraints excluded: chain O residue 750 VAL Chi-restraints excluded: chain O residue 751 VAL Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 259 optimal weight: 2.9990 chunk 417 optimal weight: 0.6980 chunk 255 optimal weight: 0.5980 chunk 198 optimal weight: 0.5980 chunk 290 optimal weight: 0.9980 chunk 438 optimal weight: 0.9980 chunk 403 optimal weight: 0.0970 chunk 349 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN B 967 GLN L 42 ASN L 121 ASN ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 37386 Z= 0.143 Angle : 0.497 15.793 50702 Z= 0.261 Chirality : 0.042 0.183 5780 Planarity : 0.003 0.049 6261 Dihedral : 9.729 143.989 5356 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.24 % Favored : 96.74 % Rotamer: Outliers : 2.12 % Allowed : 17.06 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.13), residues: 4382 helix: 1.27 (0.14), residues: 1550 sheet: -0.21 (0.20), residues: 722 loop : -0.89 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 365 HIS 0.010 0.001 HIS L 212 PHE 0.029 0.001 PHE A 938 TYR 0.015 0.001 TYR A 466 ARG 0.008 0.000 ARG C 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 377 time to evaluate : 4.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8096 (tt0) cc_final: 0.7668 (tp40) REVERT: A 413 ASN cc_start: 0.8656 (t0) cc_final: 0.8208 (t0) REVERT: A 631 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7397 (mm-30) REVERT: A 783 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8215 (m-10) REVERT: A 1084 LYS cc_start: 0.8161 (tttt) cc_final: 0.7447 (mmtp) REVERT: A 1152 ASP cc_start: 0.8214 (t70) cc_final: 0.7723 (t0) REVERT: B 205 TYR cc_start: 0.8010 (m-80) cc_final: 0.7783 (m-80) REVERT: B 226 LYS cc_start: 0.8026 (ptpt) cc_final: 0.7184 (pttm) REVERT: B 256 MET cc_start: 0.8925 (mmt) cc_final: 0.8581 (mmt) REVERT: B 286 TYR cc_start: 0.7336 (t80) cc_final: 0.6986 (t80) REVERT: B 354 MET cc_start: 0.8920 (mmm) cc_final: 0.8568 (mmm) REVERT: B 382 ARG cc_start: 0.7534 (ttm110) cc_final: 0.7329 (ttm110) REVERT: B 409 HIS cc_start: 0.7085 (t-90) cc_final: 0.6769 (t70) REVERT: B 478 ARG cc_start: 0.7944 (mtp180) cc_final: 0.7621 (mtp180) REVERT: B 1033 LYS cc_start: 0.8620 (mmtt) cc_final: 0.7922 (mmtm) REVERT: C 105 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: E 115 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7153 (ttm170) REVERT: G 44 MET cc_start: 0.7611 (ttm) cc_final: 0.7400 (ttm) REVERT: G 84 ILE cc_start: 0.5558 (OUTLIER) cc_final: 0.4929 (mp) REVERT: J 26 LYS cc_start: 0.9006 (mmmm) cc_final: 0.8704 (mmtm) REVERT: O 114 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.7144 (ttt-90) REVERT: S 45 MET cc_start: 0.6809 (tpt) cc_final: 0.6227 (ptp) REVERT: S 149 ASN cc_start: 0.6735 (m-40) cc_final: 0.6334 (m-40) outliers start: 86 outliers final: 67 residues processed: 443 average time/residue: 0.4960 time to fit residues: 360.1658 Evaluate side-chains 433 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 362 time to evaluate : 4.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1207 SER Chi-restraints excluded: chain A residue 1237 SER Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 1087 CYS Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 270 ASP Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 262 ASP Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 317 LEU Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 574 THR Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 751 VAL Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 277 optimal weight: 0.8980 chunk 371 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 321 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 349 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 359 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN B 967 GLN L 42 ASN ** L 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 678 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.102793 restraints weight = 49927.909| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.63 r_work: 0.2979 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37386 Z= 0.269 Angle : 0.531 11.242 50702 Z= 0.280 Chirality : 0.044 0.186 5780 Planarity : 0.004 0.050 6261 Dihedral : 9.802 144.990 5356 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.05 % Allowed : 17.23 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.13), residues: 4382 helix: 1.18 (0.13), residues: 1553 sheet: -0.21 (0.20), residues: 714 loop : -0.89 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP O 677 HIS 0.011 0.001 HIS L 212 PHE 0.039 0.002 PHE O 814 TYR 0.018 0.001 TYR A 466 ARG 0.007 0.000 ARG C 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8183.06 seconds wall clock time: 149 minutes 41.85 seconds (8981.85 seconds total)