Starting phenix.real_space_refine on Wed Feb 21 04:38:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ric_4888/02_2024/6ric_4888.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ric_4888/02_2024/6ric_4888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ric_4888/02_2024/6ric_4888.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ric_4888/02_2024/6ric_4888.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ric_4888/02_2024/6ric_4888.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ric_4888/02_2024/6ric_4888.pdb" } resolution = 2.8 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 Mg 1 5.21 5 S 136 5.16 5 C 19079 2.51 5 N 4926 2.21 5 O 5531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A ASP 473": "OD1" <-> "OD2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ASP 547": "OD1" <-> "OD2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A GLU 626": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A ASP 655": "OD1" <-> "OD2" Residue "A ASP 656": "OD1" <-> "OD2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "A ARG 751": "NH1" <-> "NH2" Residue "A GLU 851": "OE1" <-> "OE2" Residue "A ASP 862": "OD1" <-> "OD2" Residue "A ASP 870": "OD1" <-> "OD2" Residue "A ARG 872": "NH1" <-> "NH2" Residue "A ASP 883": "OD1" <-> "OD2" Residue "A ARG 897": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A GLU 910": "OE1" <-> "OE2" Residue "A PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 984": "OD1" <-> "OD2" Residue "A ARG 1010": "NH1" <-> "NH2" Residue "A ARG 1024": "NH1" <-> "NH2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A ARG 1043": "NH1" <-> "NH2" Residue "A ASP 1062": "OD1" <-> "OD2" Residue "A GLU 1076": "OE1" <-> "OE2" Residue "A ASP 1112": "OD1" <-> "OD2" Residue "A TYR 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 64": "OE1" <-> "OE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" 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 GLU 306": "OE1" <-> "OE2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 504": "OD1" <-> "OD2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B ASP 547": "OD1" <-> "OD2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 572": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ASP 613": "OD1" <-> "OD2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B ARG 648": "NH1" <-> "NH2" Residue "B ASP 659": "OD1" <-> "OD2" Residue "B ASP 662": "OD1" <-> "OD2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 856": "NH1" <-> "NH2" Residue "B ARG 876": "NH1" <-> "NH2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 906": "OE1" <-> "OE2" Residue "B ARG 923": "NH1" <-> "NH2" Residue "B GLU 931": "OE1" <-> "OE2" Residue "B ARG 950": "NH1" <-> "NH2" Residue "B GLU 959": "OE1" <-> "OE2" Residue "B ASP 1024": "OD1" <-> "OD2" Residue "B PHE 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1055": "OE1" <-> "OE2" Residue "B ASP 1083": "OD1" <-> "OD2" Residue "B ARG 1105": "NH1" <-> "NH2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "B ARG 1145": "NH1" <-> "NH2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 107": "OD1" <-> "OD2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 217": "OD1" <-> "OD2" Residue "C ASP 238": "OD1" <-> "OD2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C ASP 278": "OD1" <-> "OD2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E ARG 138": "NH1" <-> "NH2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ASP 83": "OD1" <-> "OD2" Residue "I TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "I ASP 310": "OD1" <-> "OD2" Residue "I GLU 311": "OE1" <-> "OE2" Residue "I ASP 591": "OD1" <-> "OD2" Residue "I GLU 636": "OE1" <-> "OE2" Residue "I ARG 659": "NH1" <-> "NH2" Residue "I ARG 710": "NH1" <-> "NH2" Residue "I GLU 718": "OE1" <-> "OE2" Residue "I GLU 725": "OE1" <-> "OE2" Residue "I ARG 784": "NH1" <-> "NH2" Residue "I GLU 787": "OE1" <-> "OE2" Residue "J GLU 17": "OE1" <-> "OE2" Residue "J TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 30": "OD1" <-> "OD2" Residue "S ASP 33": "OD1" <-> "OD2" Residue "S ASP 34": "OD1" <-> "OD2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 77": "OE1" <-> "OE2" Residue "S TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 81": "OD1" <-> "OD2" Residue "S ARG 89": "NH1" <-> "NH2" Residue "S ARG 119": "NH1" <-> "NH2" Residue "S TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29677 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 10071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1254, 10071 Classifications: {'peptide': 1254} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1210} Chain breaks: 2 Chain: "B" Number of atoms: 8991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8991 Classifications: {'peptide': 1118} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1065} Chain breaks: 5 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: "I" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3241 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain breaks: 4 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: "S" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1036 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 360 SG CYS A 49 42.342 96.300 104.792 1.00 76.90 S ATOM 382 SG CYS A 52 42.158 100.011 104.469 1.00 76.24 S ATOM 434 SG CYS A 59 44.247 98.550 102.025 1.00 70.98 S ATOM 694 SG CYS A 90 85.908 80.211 118.549 1.00 58.96 S ATOM 718 SG CYS A 93 86.199 82.282 121.392 1.00 54.54 S ATOM 1016 SG CYS A 130 88.806 82.154 120.170 1.00 75.08 S ATOM 1059 SG CYS A 135 86.760 79.053 122.200 1.00 66.32 S ATOM 18471 SG CYS B1087 56.731 106.118 109.825 1.00 65.04 S ATOM 18494 SG CYS B1090 56.778 102.999 109.806 1.00 64.98 S ATOM 18583 SG CYS B1103 53.832 103.280 110.439 1.00 64.18 S ATOM 18608 SG CYS B1106 56.957 103.678 112.694 1.00 59.66 S ATOM 28194 SG CYS J 7 41.982 98.820 31.606 1.00 36.99 S ATOM 28213 SG CYS J 10 41.164 101.876 29.227 1.00 39.06 S ATOM 28450 SG CYS J 39 44.645 100.542 29.558 1.00 39.65 S ATOM 28456 SG CYS J 40 41.588 99.348 27.951 1.00 40.29 S Time building chain proxies: 15.62, per 1000 atoms: 0.53 Number of scatterers: 29677 At special positions: 0 Unit cell: (152.28, 160.38, 154.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 136 16.00 Mg 1 11.99 O 5531 8.00 N 4926 7.00 C 19079 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=0, symmetry=0 Time building additional restraints: 11.32 Conformation dependent library (CDL) restraints added in 5.7 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 49 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " 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 135 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 39 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 40 " Number of angles added : 21 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7002 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 47 sheets defined 39.7% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 38 through 42 removed outlier: 3.743A pdb=" N GLY A 42 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.713A pdb=" N GLU A 58 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS A 59 " --> pdb=" O GLU A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 59' Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.518A pdb=" N ILE A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 124 removed outlier: 4.317A pdb=" N LEU A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 removed outlier: 3.658A pdb=" N GLN A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.515A pdb=" N TRP A 177 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.502A pdb=" N LEU A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.704A pdb=" N VAL A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.558A pdb=" N ILE A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.535A pdb=" N TYR A 264 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 265' Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.549A 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 331 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 458 through 470 removed outlier: 4.005A pdb=" N VAL A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 470 " --> pdb=" O TYR A 466 " (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 removed outlier: 3.503A pdb=" N TYR A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.774A pdb=" N PHE A 532 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 572 removed outlier: 3.501A pdb=" N PHE A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.603A pdb=" N LEU A 581 " --> pdb=" O THR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 615 removed outlier: 3.537A pdb=" N ASN A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 609 " --> pdb=" O ALA A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 656 removed outlier: 3.632A pdb=" N ILE A 654 " --> pdb=" O ARG A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 667 removed outlier: 3.516A pdb=" N ALA A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 681 removed outlier: 3.981A pdb=" N TYR A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 700 removed outlier: 3.534A pdb=" N ARG A 700 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 727 through 764 removed outlier: 3.762A pdb=" N PHE A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 746 " --> pdb=" O SER A 742 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 809 through 821 removed outlier: 3.669A pdb=" N LYS A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 846 removed outlier: 4.094A pdb=" N VAL A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 875 removed outlier: 3.560A pdb=" N ASP A 862 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A 867 " --> pdb=" O MET A 863 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 873 " --> pdb=" O ASP A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.537A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 removed outlier: 3.717A pdb=" N THR A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 943 Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 984 through 996 removed outlier: 4.057A pdb=" N LEU A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 994 " --> pdb=" O SER A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1004 removed outlier: 3.707A pdb=" N ASN A1004 " --> pdb=" O GLY A1001 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1001 through 1004' Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1033 through 1046 removed outlier: 3.609A pdb=" N PHE A1044 " --> pdb=" O MET A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1093 removed outlier: 3.686A pdb=" N VAL A1088 " --> pdb=" O LYS A1084 " (cutoff:3.500A) Proline residue: A1090 - end of helix removed outlier: 3.616A pdb=" N ALA A1093 " --> pdb=" O LEU A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1136 removed outlier: 3.572A pdb=" N LEU A1133 " --> pdb=" O LEU A1130 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A1136 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1152 Processing helix chain 'A' and resid 1155 through 1170 removed outlier: 3.515A pdb=" N THR A1170 " --> pdb=" O ALA A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1207 through 1216 removed outlier: 4.026A pdb=" N ASP A1216 " --> pdb=" O ALA A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1234 through 1239 Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.607A pdb=" N LEU B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 31 through 44 removed outlier: 3.520A pdb=" N HIS B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.518A pdb=" N GLY B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 260 through 278 Processing helix chain 'B' and resid 282 through 298 removed outlier: 3.796A pdb=" N ALA B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 313 removed outlier: 4.058A pdb=" N GLU B 310 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.539A pdb=" N ASN B 320 " --> pdb=" O PRO B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.908A pdb=" N PHE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.604A pdb=" N HIS B 357 " --> pdb=" O MET B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 384 removed outlier: 3.578A pdb=" N TYR B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 407 through 416 removed outlier: 3.762A pdb=" N SER B 413 " --> pdb=" O HIS B 409 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 498 through 514 removed outlier: 3.520A pdb=" N LEU B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 522 removed outlier: 3.557A pdb=" N ILE B 521 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.949A pdb=" N THR B 550 " --> pdb=" O CYS B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 638 removed outlier: 3.568A 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: 3.671A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 683 through 695 removed outlier: 3.995A pdb=" N ALA B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE B 688 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 731 removed outlier: 4.117A pdb=" N GLU B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 730 " --> pdb=" O LYS B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 767 removed outlier: 3.507A pdb=" N ARG B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.534A pdb=" N ASN B 788 " --> pdb=" O LEU B 784 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 784 through 788' Processing helix chain 'B' and resid 898 through 902 removed outlier: 3.572A pdb=" N LEU B 902 " --> pdb=" O GLU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 923 removed outlier: 3.509A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 923 " --> pdb=" O SER B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 941 Processing helix chain 'B' and resid 961 through 977 Processing helix chain 'B' and resid 981 through 990 Processing helix chain 'B' and resid 1054 through 1064 removed outlier: 3.545A pdb=" N LEU B1061 " --> pdb=" O GLU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1075 Processing helix chain 'B' and resid 1103 through 1109 removed outlier: 3.792A pdb=" N LYS B1108 " --> pdb=" O LEU B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1133 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 48 through 58 removed outlier: 3.566A pdb=" N TRP C 52 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 5.353A pdb=" N MET C 62 " --> pdb=" O ILE C 59 " (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 121 Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 162 through 174 removed outlier: 3.582A pdb=" N ASN C 172 " --> pdb=" O ARG C 168 " (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 230 removed outlier: 3.852A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.657A pdb=" N PHE C 265 " --> pdb=" O ILE C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 302 Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.665A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS E 11 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE E 12 " --> pdb=" O TYR E 8 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 Processing helix chain 'E' and resid 117 through 128 removed outlier: 3.925A pdb=" N ILE E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 152 Processing helix chain 'F' and resid 63 through 74 Processing helix chain 'F' and resid 78 through 95 Processing helix chain 'F' and resid 112 through 123 removed outlier: 3.680A pdb=" N VAL F 116 " --> pdb=" O ASN F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 161 removed outlier: 3.584A pdb=" N LEU F 160 " --> pdb=" O LYS F 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'I' and resid 107 through 119 removed outlier: 3.589A pdb=" N LEU I 114 " --> pdb=" O ASN I 110 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 169 No H-bonds generated for 'chain 'I' and resid 167 through 169' Processing helix chain 'I' and resid 170 through 178 Processing helix chain 'I' and resid 178 through 186 Processing helix chain 'I' and resid 255 through 261 removed outlier: 3.781A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 267 removed outlier: 4.352A pdb=" N LEU I 266 " --> pdb=" O VAL I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 272 Processing helix chain 'I' and resid 273 through 279 Processing helix chain 'I' and resid 283 through 285 No H-bonds generated for 'chain 'I' and resid 283 through 285' Processing helix chain 'I' and resid 286 through 291 removed outlier: 3.681A pdb=" N ILE I 291 " --> pdb=" O TYR I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 650 removed outlier: 3.611A pdb=" N LEU I 642 " --> pdb=" O THR I 638 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS I 643 " --> pdb=" O ASP I 639 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU I 647 " --> pdb=" O LYS I 643 " (cutoff:3.500A) Processing helix chain 'I' and resid 689 through 691 No H-bonds generated for 'chain 'I' and resid 689 through 691' Processing helix chain 'I' and resid 705 through 710 Processing helix chain 'I' and resid 723 through 742 removed outlier: 3.517A pdb=" N ILE I 736 " --> pdb=" O ASN I 732 " (cutoff:3.500A) Processing helix chain 'I' and resid 756 through 769 removed outlier: 3.575A pdb=" N LEU I 760 " --> pdb=" O ASN I 756 " (cutoff:3.500A) Processing helix chain 'I' and resid 773 through 792 removed outlier: 5.983A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU I 787 " --> pdb=" O THR I 783 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 23 removed outlier: 3.527A pdb=" N TYR J 19 " --> pdb=" O SER J 15 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS J 20 " --> pdb=" O HIS J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 32 Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'S' and resid 24 through 29 Processing helix chain 'S' and resid 37 through 48 removed outlier: 3.750A pdb=" N GLU S 42 " --> pdb=" O GLU S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 81 removed outlier: 3.668A pdb=" N ILE S 74 " --> pdb=" O SER S 70 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLY S 75 " --> pdb=" O LYS S 71 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP S 81 " --> pdb=" O GLU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 85 removed outlier: 3.563A pdb=" N LYS S 85 " --> pdb=" O SER S 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 82 through 85' Processing helix chain 'S' and resid 114 through 131 removed outlier: 3.585A pdb=" N LYS S 126 " --> pdb=" O LEU S 122 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE S 128 " --> pdb=" O GLY S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 139 Processing sheet with id=AA1, first strand: chain 'A' and resid 1229 through 1231 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 4.316A pdb=" N SER A 67 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 removed outlier: 3.979A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 158 " --> pdb=" O ASN A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 282 removed outlier: 3.812A pdb=" N ILE B1051 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 7.401A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLY A 291 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 316 removed outlier: 7.129A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 472 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AB1, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 768 removed outlier: 6.393A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AB4, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AB5, first strand: chain 'A' and resid 1106 through 1111 Processing sheet with id=AB6, first strand: chain 'A' and resid 998 through 999 Processing sheet with id=AB7, first strand: chain 'A' and resid 1006 through 1011 removed outlier: 3.628A pdb=" N ILE A1021 " --> pdb=" O ASN A1006 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 135 through 138 removed outlier: 3.612A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1264 through 1265 Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 59 removed outlier: 6.611A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 52 through 59 removed outlier: 6.611A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.304A 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 Processing sheet with id=AC5, first strand: chain 'B' and resid 179 through 182 removed outlier: 3.646A pdb=" N VAL B 231 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC7, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC8, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC9, first strand: chain 'B' and resid 535 through 540 removed outlier: 5.514A pdb=" N LEU B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE B 532 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 538 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 715 removed outlier: 6.270A pdb=" N MET B 872 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL B 854 " --> pdb=" O MET B 872 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLU B 874 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N SER B 852 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 715 removed outlier: 6.270A pdb=" N MET B 872 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL B 854 " --> pdb=" O MET B 872 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLU B 874 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N SER B 852 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AD4, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.773A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N VAL B 913 " --> pdb=" O HIS B 741 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR B 743 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE B 915 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA B 745 " --> pdb=" O ILE B 915 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1084 through 1087 removed outlier: 4.347A pdb=" N VAL B1084 " --> pdb=" O ILE B1118 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AD7, first strand: chain 'C' and resid 5 through 13 Processing sheet with id=AD8, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AD9, first strand: chain 'C' and resid 37 through 43 removed outlier: 3.558A pdb=" N ILE C 37 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU C 140 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN C 43 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR C 138 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AE2, first strand: chain 'C' and resid 233 through 234 removed outlier: 6.155A pdb=" N LYS C 233 " --> pdb=" O TYR C 244 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AE4, first strand: chain 'E' and resid 112 through 115 removed outlier: 4.308A pdb=" N SER E 112 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'G' and resid 3 through 6 removed outlier: 4.215A pdb=" N LYS G 47 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA G 77 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA G 45 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS G 43 " --> pdb=" O ILE G 40 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 84 through 91 removed outlier: 6.050A pdb=" N ILE G 105 " --> pdb=" O PHE G 154 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA G 156 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LYS G 107 " --> pdb=" O ALA G 156 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE G 158 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 220 through 228 removed outlier: 3.520A pdb=" N ILE I 217 " --> pdb=" O LEU I 220 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP I 228 " --> pdb=" O VAL I 209 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL I 209 " --> pdb=" O ASP I 228 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N MET I 121 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU I 214 " --> pdb=" O MET I 121 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N LEU I 123 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 10.919A pdb=" N LYS I 216 " --> pdb=" O LEU I 123 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR I 234 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 162 through 166 removed outlier: 6.023A pdb=" N ILE I 130 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE I 166 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL I 132 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 664 through 665 removed outlier: 4.664A pdb=" N ILE I 658 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 669 through 670 1193 hydrogen bonds defined for protein. 3303 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: 12.42 Time building geometry restraints manager: 12.31 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: 9251 1.34 - 1.46: 5168 1.46 - 1.57: 15634 1.57 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 30269 Sorted by residual: bond pdb=" C ILE I 264 " pdb=" N PRO I 265 " ideal model delta sigma weight residual 1.335 1.373 -0.037 1.30e-02 5.92e+03 8.31e+00 bond pdb=" CG1 ILE B 722 " pdb=" CD1 ILE B 722 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.19e+00 bond pdb=" CA PRO I 716 " pdb=" CB PRO I 716 " ideal model delta sigma weight residual 1.531 1.520 0.011 6.20e-03 2.60e+04 3.42e+00 bond pdb=" CB VAL A 534 " pdb=" CG1 VAL A 534 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 bond pdb=" CG1 ILE A1247 " pdb=" CD1 ILE A1247 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.00e+00 ... (remaining 30264 not shown) Histogram of bond angle deviations from ideal: 96.39 - 103.92: 370 103.92 - 111.44: 12492 111.44 - 118.97: 11901 118.97 - 126.50: 15855 126.50 - 134.03: 288 Bond angle restraints: 40906 Sorted by residual: angle pdb=" N GLN A 459 " pdb=" CA GLN A 459 " pdb=" C GLN A 459 " ideal model delta sigma weight residual 111.37 118.60 -7.23 1.65e+00 3.67e-01 1.92e+01 angle pdb=" C GLU B 533 " pdb=" N ASN B 534 " pdb=" CA ASN B 534 " ideal model delta sigma weight residual 121.54 129.47 -7.93 1.91e+00 2.74e-01 1.72e+01 angle pdb=" N GLY B1044 " pdb=" CA GLY B1044 " pdb=" C GLY B1044 " ideal model delta sigma weight residual 112.18 117.68 -5.50 1.34e+00 5.57e-01 1.69e+01 angle pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta sigma weight residual 120.82 126.86 -6.04 1.50e+00 4.44e-01 1.62e+01 angle pdb=" N ASN G 63 " pdb=" CA ASN G 63 " pdb=" C ASN G 63 " ideal model delta sigma weight residual 110.80 118.53 -7.73 2.13e+00 2.20e-01 1.32e+01 ... (remaining 40901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 16425 17.23 - 34.47: 1616 34.47 - 51.70: 298 51.70 - 68.94: 40 68.94 - 86.17: 23 Dihedral angle restraints: 18402 sinusoidal: 7565 harmonic: 10837 Sorted by residual: dihedral pdb=" CA VAL G 62 " pdb=" C VAL G 62 " pdb=" N ASN G 63 " pdb=" CA ASN G 63 " ideal model delta harmonic sigma weight residual 180.00 -140.16 -39.84 0 5.00e+00 4.00e-02 6.35e+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 -146.93 -33.07 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA ASN B 736 " pdb=" C ASN B 736 " pdb=" N CYS B 737 " pdb=" CA CYS B 737 " ideal model delta harmonic sigma weight residual -180.00 -151.90 -28.10 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 18399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3980 0.075 - 0.149: 612 0.149 - 0.224: 44 0.224 - 0.298: 6 0.298 - 0.373: 1 Chirality restraints: 4643 Sorted by residual: chirality pdb=" CB ILE F 77 " pdb=" CA ILE F 77 " pdb=" CG1 ILE F 77 " pdb=" CG2 ILE F 77 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB ILE I 161 " pdb=" CA ILE I 161 " pdb=" CG1 ILE I 161 " pdb=" CG2 ILE I 161 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE A 106 " pdb=" CA ILE A 106 " pdb=" CG1 ILE A 106 " pdb=" CG2 ILE A 106 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 4640 not shown) Planarity restraints: 5165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 100 " -0.045 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO A 101 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 172 " -0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO I 173 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO I 173 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO I 173 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 140 " -0.041 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO B 141 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " -0.034 5.00e-02 4.00e+02 ... (remaining 5162 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 383 2.63 - 3.20: 24663 3.20 - 3.77: 47270 3.77 - 4.33: 71106 4.33 - 4.90: 112917 Nonbonded interactions: 256339 Sorted by model distance: nonbonded pdb=" OD1 ASP A 417 " pdb="MG MG A1301 " model vdw 2.068 2.170 nonbonded pdb=" OG SER A 145 " pdb=" O LYS A 148 " model vdw 2.243 2.440 nonbonded pdb=" O ALA B 673 " pdb=" OG SER B 956 " model vdw 2.258 2.440 nonbonded pdb=" O ARG B 249 " pdb=" OG SER B 253 " model vdw 2.265 2.440 nonbonded pdb=" OH TYR B 309 " pdb=" OE2 GLU I 725 " model vdw 2.266 2.440 ... (remaining 256334 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.290 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 84.020 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 0.080 30269 Z= 0.361 Angle : 0.754 10.840 40906 Z= 0.417 Chirality : 0.053 0.373 4643 Planarity : 0.006 0.067 5165 Dihedral : 14.009 86.175 11400 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.16 (0.11), residues: 3619 helix: -4.19 (0.06), residues: 1314 sheet: -1.83 (0.20), residues: 512 loop : -1.77 (0.12), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 809 HIS 0.011 0.001 HIS A 385 PHE 0.042 0.002 PHE A 938 TYR 0.025 0.002 TYR E 8 ARG 0.010 0.001 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 710 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8409 (ttpp) REVERT: A 705 TYR cc_start: 0.8465 (m-80) cc_final: 0.8260 (m-80) REVERT: A 853 ASN cc_start: 0.8048 (t0) cc_final: 0.7827 (t0) REVERT: A 974 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8280 (ttmm) REVERT: A 1043 ARG cc_start: 0.8010 (ttp-170) cc_final: 0.7631 (ttm110) REVERT: A 1218 LYS cc_start: 0.8269 (mptt) cc_final: 0.7415 (mppt) REVERT: A 1222 ASN cc_start: 0.8350 (m110) cc_final: 0.7849 (m110) REVERT: B 23 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8450 (mmtm) REVERT: B 501 GLU cc_start: 0.7687 (pt0) cc_final: 0.7485 (pt0) REVERT: B 555 ARG cc_start: 0.8568 (mtt-85) cc_final: 0.8251 (mtp85) REVERT: B 804 ASN cc_start: 0.7983 (m110) cc_final: 0.7699 (m-40) REVERT: B 987 ASP cc_start: 0.8058 (m-30) cc_final: 0.7717 (m-30) REVERT: B 1025 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8424 (mtpt) REVERT: B 1034 LYS cc_start: 0.8052 (mttm) cc_final: 0.7842 (mttm) REVERT: B 1096 GLN cc_start: 0.7532 (mt0) cc_final: 0.7028 (mt0) REVERT: C 164 GLU cc_start: 0.7376 (mp0) cc_final: 0.7042 (mp0) REVERT: C 283 ASP cc_start: 0.7695 (t70) cc_final: 0.7110 (t70) REVERT: E 21 ARG cc_start: 0.8101 (ptm-80) cc_final: 0.7583 (ptp-170) REVERT: E 22 ASP cc_start: 0.7932 (t70) cc_final: 0.7662 (t0) REVERT: G 69 ASN cc_start: 0.8157 (m-40) cc_final: 0.7868 (m-40) REVERT: G 84 ILE cc_start: 0.8067 (mp) cc_final: 0.7621 (mm) REVERT: I 605 LYS cc_start: 0.8303 (tttt) cc_final: 0.6399 (ttmt) REVERT: I 660 VAL cc_start: 0.7772 (t) cc_final: 0.7442 (p) REVERT: I 703 ASN cc_start: 0.5904 (t0) cc_final: 0.5446 (t0) REVERT: J 62 ILE cc_start: 0.7433 (mt) cc_final: 0.7197 (mt) outliers start: 1 outliers final: 1 residues processed: 711 average time/residue: 1.5199 time to fit residues: 1252.9030 Evaluate side-chains 479 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 478 time to evaluate : 3.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 686 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 0.9990 chunk 275 optimal weight: 0.7980 chunk 152 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 146 optimal weight: 0.4980 chunk 284 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 173 optimal weight: 0.8980 chunk 211 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN A 513 ASN A 526 ASN A 548 HIS A 611 ASN A 660 ASN A 773 GLN ** A 894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 941 GLN A 947 HIS ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 ASN ** A1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN B 298 GLN B 318 HIS B 391 ASN B 481 GLN B 620 GLN B 682 ASN B 693 GLN B 740 GLN B 741 HIS ** B 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN B 971 GLN B 977 ASN B1040 GLN B1089 ASN C 8 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 168 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN G 29 ASN ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 271 HIS ** I 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 695 ASN ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN S 90 ASN S 145 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30269 Z= 0.176 Angle : 0.543 8.301 40906 Z= 0.290 Chirality : 0.044 0.173 4643 Planarity : 0.004 0.041 5165 Dihedral : 5.135 30.211 3996 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.26 % Allowed : 13.48 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.12), residues: 3619 helix: -1.83 (0.12), residues: 1329 sheet: -1.39 (0.21), residues: 512 loop : -1.13 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 365 HIS 0.007 0.001 HIS A 385 PHE 0.034 0.001 PHE A 938 TYR 0.018 0.001 TYR A 732 ARG 0.008 0.000 ARG I 659 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 522 time to evaluate : 3.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8409 (mt) cc_final: 0.8177 (mp) REVERT: A 68 ILE cc_start: 0.6639 (OUTLIER) cc_final: 0.6271 (pt) REVERT: A 179 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8387 (mp) REVERT: A 182 ILE cc_start: 0.8057 (mt) cc_final: 0.7839 (mm) REVERT: A 497 LYS cc_start: 0.8895 (ttpt) cc_final: 0.8536 (ttpp) REVERT: A 617 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7731 (mptp) REVERT: A 974 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8199 (ttmm) REVERT: A 1067 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7584 (ttp80) REVERT: B 205 TYR cc_start: 0.7286 (m-80) cc_final: 0.7025 (m-80) REVERT: B 223 SER cc_start: 0.8203 (OUTLIER) cc_final: 0.7954 (p) REVERT: B 649 MET cc_start: 0.8177 (mmp) cc_final: 0.7953 (mmt) REVERT: B 720 ARG cc_start: 0.7813 (mtp-110) cc_final: 0.7548 (mtp-110) REVERT: B 804 ASN cc_start: 0.7973 (m110) cc_final: 0.7710 (m-40) REVERT: B 1034 LYS cc_start: 0.8134 (mttm) cc_final: 0.7889 (mttm) REVERT: B 1082 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7925 (pt0) REVERT: B 1131 MET cc_start: 0.8604 (mmm) cc_final: 0.8166 (mmm) REVERT: C 119 GLU cc_start: 0.8320 (mp0) cc_final: 0.8106 (mp0) REVERT: C 154 ILE cc_start: 0.7665 (tp) cc_final: 0.7356 (mt) REVERT: E 21 ARG cc_start: 0.8112 (ptm-80) cc_final: 0.7672 (ptp-170) REVERT: E 22 ASP cc_start: 0.7892 (t70) cc_final: 0.7631 (t0) REVERT: E 62 GLN cc_start: 0.8311 (mt0) cc_final: 0.8072 (mt0) REVERT: G 15 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7708 (mm-30) REVERT: G 47 LYS cc_start: 0.7844 (pptt) cc_final: 0.7271 (ptpp) REVERT: G 55 GLU cc_start: 0.7656 (tp30) cc_final: 0.7278 (mm-30) REVERT: G 84 ILE cc_start: 0.7922 (mp) cc_final: 0.7495 (mm) REVERT: I 599 LEU cc_start: 0.6949 (tt) cc_final: 0.6545 (pp) REVERT: I 660 VAL cc_start: 0.7576 (t) cc_final: 0.7257 (p) REVERT: I 703 ASN cc_start: 0.6274 (t0) cc_final: 0.5910 (t0) REVERT: S 50 LYS cc_start: 0.8367 (ttmm) cc_final: 0.8111 (ttmm) REVERT: S 70 SER cc_start: 0.8544 (t) cc_final: 0.8220 (m) outliers start: 76 outliers final: 24 residues processed: 559 average time/residue: 1.4783 time to fit residues: 966.4872 Evaluate side-chains 491 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 461 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1067 ARG Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 1082 GLN Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain S residue 121 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 183 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 274 optimal weight: 0.4980 chunk 224 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 330 optimal weight: 8.9990 chunk 356 optimal weight: 7.9990 chunk 294 optimal weight: 0.4980 chunk 327 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 264 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 GLN A 526 ASN A 611 ASN A 651 GLN A 773 GLN A 830 GLN A 894 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 481 GLN B 778 HIS ** B 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN B 971 GLN B 977 ASN ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN E 98 ASN F 140 ASN G 7 ASN G 29 ASN G 64 ASN ** I 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 740 HIS ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN S 90 ASN ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 30269 Z= 0.379 Angle : 0.619 9.639 40906 Z= 0.327 Chirality : 0.048 0.192 4643 Planarity : 0.004 0.043 5165 Dihedral : 5.204 34.612 3994 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.51 % Allowed : 15.00 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.13), residues: 3619 helix: -0.78 (0.13), residues: 1325 sheet: -1.22 (0.20), residues: 528 loop : -0.85 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 315 HIS 0.015 0.001 HIS A 385 PHE 0.035 0.002 PHE A 938 TYR 0.022 0.002 TYR A 732 ARG 0.009 0.001 ARG I 784 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 506 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6567 (pt) REVERT: A 182 ILE cc_start: 0.8176 (mt) cc_final: 0.7947 (mm) REVERT: A 193 ASP cc_start: 0.7065 (m-30) cc_final: 0.6773 (m-30) REVERT: A 555 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8867 (mm) REVERT: A 617 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7828 (mptp) REVERT: A 650 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7281 (mtp180) REVERT: A 834 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8154 (mttp) REVERT: A 974 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8371 (ttmm) REVERT: B 54 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6671 (mtm110) REVERT: B 297 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8223 (tppt) REVERT: B 804 ASN cc_start: 0.8125 (m110) cc_final: 0.7892 (m-40) REVERT: B 987 ASP cc_start: 0.8050 (m-30) cc_final: 0.7722 (m-30) REVERT: B 1034 LYS cc_start: 0.8284 (mttm) cc_final: 0.8034 (mttm) REVERT: B 1056 MET cc_start: 0.8713 (mtm) cc_final: 0.8375 (mtp) REVERT: B 1096 GLN cc_start: 0.7585 (mt0) cc_final: 0.7149 (mt0) REVERT: B 1119 ASP cc_start: 0.7832 (t0) cc_final: 0.7372 (t0) REVERT: B 1131 MET cc_start: 0.8658 (mmm) cc_final: 0.8183 (mmm) REVERT: C 129 GLN cc_start: 0.7504 (mm110) cc_final: 0.7294 (mm-40) REVERT: E 21 ARG cc_start: 0.8148 (ptm-80) cc_final: 0.7682 (ptp-170) REVERT: E 22 ASP cc_start: 0.8009 (t70) cc_final: 0.7754 (t0) REVERT: E 66 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: E 179 SER cc_start: 0.8602 (t) cc_final: 0.8336 (p) REVERT: G 29 ASN cc_start: 0.8185 (m110) cc_final: 0.7881 (m-40) REVERT: G 33 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7820 (ttmm) REVERT: G 52 GLU cc_start: 0.7463 (tp30) cc_final: 0.7216 (tm-30) REVERT: G 60 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6957 (mt-10) REVERT: G 69 ASN cc_start: 0.8141 (m-40) cc_final: 0.7884 (m-40) REVERT: G 84 ILE cc_start: 0.7922 (mp) cc_final: 0.7489 (mm) REVERT: G 104 LEU cc_start: 0.7680 (mt) cc_final: 0.7381 (mt) REVERT: I 599 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6552 (pp) REVERT: S 70 SER cc_start: 0.8567 (t) cc_final: 0.8231 (m) REVERT: S 149 ASN cc_start: 0.6445 (p0) cc_final: 0.6097 (m-40) outliers start: 118 outliers final: 45 residues processed: 567 average time/residue: 1.4587 time to fit residues: 969.8316 Evaluate side-chains 507 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 453 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 976 SER Chi-restraints excluded: chain B residue 1114 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 599 LEU Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 686 ILE Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 115 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 326 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 221 optimal weight: 0.6980 chunk 331 optimal weight: 10.0000 chunk 350 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 314 optimal weight: 0.0470 chunk 94 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN A 611 ASN A 894 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS B 481 GLN ** B 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN B 977 ASN ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN F 140 ASN G 7 ASN G 63 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 HIS ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30269 Z= 0.152 Angle : 0.506 9.033 40906 Z= 0.268 Chirality : 0.043 0.179 4643 Planarity : 0.003 0.040 5165 Dihedral : 4.707 26.250 3994 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.44 % Allowed : 17.89 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: -0.80 (0.13), residues: 3619 helix: -0.03 (0.14), residues: 1325 sheet: -0.89 (0.22), residues: 502 loop : -0.69 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 365 HIS 0.008 0.001 HIS A 385 PHE 0.031 0.001 PHE A 938 TYR 0.023 0.001 TYR I 109 ARG 0.009 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 491 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6714 (pt) REVERT: A 70 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7718 (mppt) REVERT: A 140 GLN cc_start: 0.7369 (pm20) cc_final: 0.7092 (pm20) REVERT: A 182 ILE cc_start: 0.8114 (mt) cc_final: 0.7876 (mm) REVERT: A 974 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8350 (ttmm) REVERT: B 205 TYR cc_start: 0.7333 (m-80) cc_final: 0.7024 (m-80) REVERT: B 216 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: B 297 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8294 (tppt) REVERT: B 565 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: B 645 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7344 (mm-40) REVERT: B 652 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8013 (mttp) REVERT: B 720 ARG cc_start: 0.7771 (mtp-110) cc_final: 0.7450 (mtp-110) REVERT: B 905 ASP cc_start: 0.8384 (p0) cc_final: 0.7997 (p0) REVERT: B 987 ASP cc_start: 0.7929 (m-30) cc_final: 0.7619 (m-30) REVERT: B 1034 LYS cc_start: 0.8223 (mttm) cc_final: 0.7987 (mttm) REVERT: B 1056 MET cc_start: 0.8659 (mtm) cc_final: 0.8345 (mtp) REVERT: B 1082 GLN cc_start: 0.8099 (pm20) cc_final: 0.7873 (pt0) REVERT: B 1096 GLN cc_start: 0.7483 (mt0) cc_final: 0.7053 (mt0) REVERT: B 1131 MET cc_start: 0.8646 (mmm) cc_final: 0.8239 (mmm) REVERT: E 21 ARG cc_start: 0.8098 (ptm-80) cc_final: 0.7720 (ptp-170) REVERT: E 22 ASP cc_start: 0.7910 (t70) cc_final: 0.7672 (t0) REVERT: E 144 GLU cc_start: 0.7828 (pt0) cc_final: 0.7618 (pt0) REVERT: E 179 SER cc_start: 0.8536 (t) cc_final: 0.8277 (p) REVERT: G 33 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7983 (tttm) REVERT: G 55 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7066 (tp30) REVERT: I 294 ASP cc_start: 0.6907 (m-30) cc_final: 0.6686 (m-30) REVERT: I 599 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6479 (pp) REVERT: I 703 ASN cc_start: 0.6573 (t0) cc_final: 0.6258 (t0) REVERT: S 50 LYS cc_start: 0.8420 (ttmm) cc_final: 0.8197 (ttmm) REVERT: S 70 SER cc_start: 0.8560 (t) cc_final: 0.8248 (m) REVERT: S 84 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.7370 (m110) outliers start: 82 outliers final: 20 residues processed: 537 average time/residue: 1.4678 time to fit residues: 924.2901 Evaluate side-chains 487 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 459 time to evaluate : 3.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 599 LEU Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 686 ILE Chi-restraints excluded: chain S residue 84 ASN Chi-restraints excluded: chain S residue 138 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 292 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 299 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 314 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 385 HIS A 526 ASN A 611 ASN A 894 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS B 481 GLN ** B 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN B 971 GLN B 977 ASN ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 98 ASN ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN G 7 ASN G 29 ASN G 63 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 HIS J 37 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30269 Z= 0.273 Angle : 0.554 8.032 40906 Z= 0.291 Chirality : 0.045 0.190 4643 Planarity : 0.004 0.040 5165 Dihedral : 4.759 27.473 3994 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.36 % Allowed : 17.68 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: -0.59 (0.14), residues: 3619 helix: 0.19 (0.14), residues: 1341 sheet: -0.85 (0.22), residues: 512 loop : -0.60 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 315 HIS 0.012 0.001 HIS A 385 PHE 0.034 0.002 PHE A 938 TYR 0.020 0.001 TYR A 732 ARG 0.011 0.001 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 478 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6543 (pt) REVERT: A 77 GLU cc_start: 0.7734 (mp0) cc_final: 0.7480 (mp0) REVERT: A 182 ILE cc_start: 0.8173 (mt) cc_final: 0.7931 (mm) REVERT: A 193 ASP cc_start: 0.7039 (m-30) cc_final: 0.6727 (m-30) REVERT: A 555 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8874 (mm) REVERT: A 650 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7400 (mtp180) REVERT: A 862 ASP cc_start: 0.7479 (m-30) cc_final: 0.7222 (m-30) REVERT: A 974 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8362 (ttmm) REVERT: B 54 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6559 (mtm110) REVERT: B 205 TYR cc_start: 0.7359 (m-80) cc_final: 0.7038 (m-80) REVERT: B 297 LYS cc_start: 0.8526 (ttmm) cc_final: 0.8324 (tppt) REVERT: B 565 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7974 (mt-10) REVERT: B 645 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7359 (mm-40) REVERT: B 652 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8028 (mttp) REVERT: B 967 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7044 (tm130) REVERT: B 1033 LYS cc_start: 0.8180 (mttp) cc_final: 0.7609 (mtmt) REVERT: B 1034 LYS cc_start: 0.8227 (mttm) cc_final: 0.7978 (mttm) REVERT: B 1056 MET cc_start: 0.8697 (mtm) cc_final: 0.8358 (mtp) REVERT: B 1096 GLN cc_start: 0.7483 (mt0) cc_final: 0.7026 (mt0) REVERT: B 1131 MET cc_start: 0.8676 (mmm) cc_final: 0.8220 (mmm) REVERT: C 251 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8366 (tp) REVERT: E 21 ARG cc_start: 0.8107 (ptm-80) cc_final: 0.7706 (ptp-170) REVERT: E 22 ASP cc_start: 0.7942 (t70) cc_final: 0.7709 (t0) REVERT: E 179 SER cc_start: 0.8566 (t) cc_final: 0.8302 (p) REVERT: F 77 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8661 (tp) REVERT: F 162 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8080 (mttp) REVERT: G 33 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7801 (ttmm) REVERT: G 55 GLU cc_start: 0.7251 (mm-30) cc_final: 0.7042 (tp30) REVERT: G 104 LEU cc_start: 0.7611 (mt) cc_final: 0.7317 (mt) REVERT: I 294 ASP cc_start: 0.6908 (m-30) cc_final: 0.6707 (m-30) REVERT: S 70 SER cc_start: 0.8572 (t) cc_final: 0.8242 (m) REVERT: S 149 ASN cc_start: 0.6202 (p0) cc_final: 0.5760 (m-40) outliers start: 113 outliers final: 42 residues processed: 543 average time/residue: 1.4993 time to fit residues: 951.0299 Evaluate side-chains 495 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 441 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1010 ARG Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 967 GLN Chi-restraints excluded: chain B residue 1114 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 686 ILE Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain S residue 91 LYS Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 121 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 0.9980 chunk 315 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 351 optimal weight: 6.9990 chunk 291 optimal weight: 0.5980 chunk 162 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN A 611 ASN A 894 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** B 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN E 98 ASN ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN G 7 ASN G 29 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30269 Z= 0.198 Angle : 0.527 10.418 40906 Z= 0.275 Chirality : 0.044 0.179 4643 Planarity : 0.003 0.053 5165 Dihedral : 4.586 24.441 3994 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.89 % Allowed : 18.63 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: -0.40 (0.14), residues: 3619 helix: 0.43 (0.14), residues: 1345 sheet: -0.84 (0.22), residues: 512 loop : -0.54 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 315 HIS 0.008 0.001 HIS I 284 PHE 0.031 0.001 PHE A 938 TYR 0.020 0.001 TYR I 109 ARG 0.012 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 476 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6588 (pt) REVERT: A 182 ILE cc_start: 0.8150 (mt) cc_final: 0.7905 (mm) REVERT: A 193 ASP cc_start: 0.7037 (m-30) cc_final: 0.6705 (m-30) REVERT: A 347 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.6498 (tmt170) REVERT: A 372 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7712 (tp30) REVERT: A 555 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8880 (mm) REVERT: A 650 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7397 (ttp-170) REVERT: A 834 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8193 (mttp) REVERT: A 862 ASP cc_start: 0.7438 (m-30) cc_final: 0.7170 (m-30) REVERT: A 974 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8313 (ttmm) REVERT: A 1200 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8056 (mmtm) REVERT: B 60 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6333 (mtmp) REVERT: B 205 TYR cc_start: 0.7346 (m-80) cc_final: 0.7035 (m-80) REVERT: B 565 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: B 645 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7353 (mm-40) REVERT: B 652 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8065 (mttp) REVERT: B 720 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.7406 (mtp-110) REVERT: B 1033 LYS cc_start: 0.8127 (mttp) cc_final: 0.7559 (mtmt) REVERT: B 1034 LYS cc_start: 0.8210 (mttm) cc_final: 0.7952 (mttm) REVERT: B 1056 MET cc_start: 0.8685 (mtm) cc_final: 0.8381 (mtp) REVERT: B 1082 GLN cc_start: 0.8108 (pm20) cc_final: 0.7878 (pt0) REVERT: B 1096 GLN cc_start: 0.7426 (mt0) cc_final: 0.7016 (mt0) REVERT: B 1131 MET cc_start: 0.8662 (mmm) cc_final: 0.8168 (mmm) REVERT: B 1145 ARG cc_start: 0.6935 (mtm110) cc_final: 0.6269 (mtm180) REVERT: C 251 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8340 (tp) REVERT: E 21 ARG cc_start: 0.8101 (ptm-80) cc_final: 0.7712 (ptp-170) REVERT: E 22 ASP cc_start: 0.7894 (t70) cc_final: 0.7670 (t0) REVERT: E 179 SER cc_start: 0.8548 (t) cc_final: 0.8295 (p) REVERT: F 77 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8646 (tp) REVERT: G 33 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7810 (ttmm) REVERT: G 55 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7090 (tp30) REVERT: G 60 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6895 (mt-10) REVERT: I 164 ILE cc_start: 0.6128 (OUTLIER) cc_final: 0.5883 (tt) REVERT: S 50 LYS cc_start: 0.8446 (ttmm) cc_final: 0.8203 (ttmm) REVERT: S 70 SER cc_start: 0.8561 (t) cc_final: 0.8239 (m) REVERT: S 149 ASN cc_start: 0.6131 (p0) cc_final: 0.5742 (m-40) outliers start: 97 outliers final: 37 residues processed: 530 average time/residue: 1.5165 time to fit residues: 940.4640 Evaluate side-chains 506 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 454 time to evaluate : 4.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1200 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 845 LYS Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 976 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 686 ILE Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain S residue 115 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 338 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 198 optimal weight: 0.0170 chunk 295 optimal weight: 0.0970 chunk 196 optimal weight: 4.9990 chunk 349 optimal weight: 0.3980 chunk 218 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.3020 ------------------------------------------------------------------------------- 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 526 ASN A 611 ASN A 894 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** B 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN B 977 ASN ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN E 98 ASN F 140 ASN G 7 ASN G 63 ASN I 110 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 HIS S 145 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30269 Z= 0.207 Angle : 0.534 8.927 40906 Z= 0.278 Chirality : 0.044 0.204 4643 Planarity : 0.003 0.048 5165 Dihedral : 4.524 28.193 3994 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.83 % Allowed : 19.38 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: -0.27 (0.14), residues: 3619 helix: 0.60 (0.14), residues: 1344 sheet: -0.74 (0.22), residues: 511 loop : -0.51 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 315 HIS 0.009 0.001 HIS I 284 PHE 0.031 0.001 PHE A 938 TYR 0.018 0.001 TYR A 732 ARG 0.012 0.000 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 469 time to evaluate : 3.730 Fit side-chains revert: symmetry clash REVERT: A 68 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6696 (pt) REVERT: A 77 GLU cc_start: 0.7591 (mp0) cc_final: 0.7145 (mp0) REVERT: A 182 ILE cc_start: 0.8137 (mt) cc_final: 0.7888 (mm) REVERT: A 193 ASP cc_start: 0.7047 (m-30) cc_final: 0.6728 (m-30) REVERT: A 372 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7743 (tp30) REVERT: A 555 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8880 (mm) REVERT: A 650 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7488 (ttp-170) REVERT: A 834 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8149 (mttp) REVERT: A 862 ASP cc_start: 0.7414 (m-30) cc_final: 0.7206 (m-30) REVERT: A 974 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8322 (ttmm) REVERT: A 1200 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8044 (mmtm) REVERT: B 54 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6552 (mtm110) REVERT: B 60 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6308 (mtmp) REVERT: B 205 TYR cc_start: 0.7327 (m-80) cc_final: 0.7006 (m-80) REVERT: B 273 ARG cc_start: 0.7040 (ttp80) cc_final: 0.6763 (ttp80) REVERT: B 565 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: B 645 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7358 (mm-40) REVERT: B 652 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8035 (mttp) REVERT: B 720 ARG cc_start: 0.7729 (mtp-110) cc_final: 0.7308 (mtm110) REVERT: B 1034 LYS cc_start: 0.8207 (mttm) cc_final: 0.7935 (mttm) REVERT: B 1056 MET cc_start: 0.8685 (mtm) cc_final: 0.8374 (mtp) REVERT: B 1082 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7882 (pm20) REVERT: B 1096 GLN cc_start: 0.7426 (mt0) cc_final: 0.7019 (mt0) REVERT: B 1131 MET cc_start: 0.8663 (mmm) cc_final: 0.8269 (mmm) REVERT: B 1145 ARG cc_start: 0.6909 (mtm110) cc_final: 0.6205 (mtm180) REVERT: C 109 ASN cc_start: 0.7766 (m-40) cc_final: 0.7547 (t0) REVERT: C 251 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8296 (tp) REVERT: E 21 ARG cc_start: 0.8099 (ptm-80) cc_final: 0.7717 (ptp-170) REVERT: E 22 ASP cc_start: 0.7910 (t70) cc_final: 0.7680 (t0) REVERT: E 179 SER cc_start: 0.8536 (t) cc_final: 0.8320 (p) REVERT: F 77 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8642 (tp) REVERT: F 162 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8072 (mttp) REVERT: G 33 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7817 (ttmm) REVERT: G 55 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7066 (tp30) REVERT: G 60 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6840 (mt-10) REVERT: I 164 ILE cc_start: 0.6119 (OUTLIER) cc_final: 0.5866 (tt) REVERT: S 41 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7679 (tp) REVERT: S 50 LYS cc_start: 0.8398 (ttmm) cc_final: 0.8162 (ttmm) REVERT: S 70 SER cc_start: 0.8557 (t) cc_final: 0.8236 (m) REVERT: S 149 ASN cc_start: 0.6126 (p0) cc_final: 0.5765 (m-40) outliers start: 95 outliers final: 44 residues processed: 525 average time/residue: 1.5614 time to fit residues: 966.3315 Evaluate side-chains 510 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 448 time to evaluate : 3.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1200 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 845 LYS Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 976 SER Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1082 GLN Chi-restraints excluded: chain B residue 1114 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 686 ILE Chi-restraints excluded: chain I residue 741 LEU Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain S residue 115 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 238 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 526 ASN A 611 ASN A 894 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** B 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN B 971 GLN ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN F 140 ASN G 29 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 HIS S 145 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30269 Z= 0.287 Angle : 0.571 9.540 40906 Z= 0.296 Chirality : 0.046 0.191 4643 Planarity : 0.004 0.046 5165 Dihedral : 4.651 27.881 3994 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.86 % Allowed : 19.58 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: -0.30 (0.14), residues: 3619 helix: 0.54 (0.14), residues: 1346 sheet: -0.74 (0.22), residues: 511 loop : -0.51 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 315 HIS 0.008 0.001 HIS I 284 PHE 0.034 0.002 PHE A 938 TYR 0.021 0.001 TYR I 109 ARG 0.012 0.001 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 459 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6784 (pt) REVERT: A 182 ILE cc_start: 0.8166 (mt) cc_final: 0.7916 (mm) REVERT: A 193 ASP cc_start: 0.7107 (m-30) cc_final: 0.6786 (m-30) REVERT: A 555 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8881 (mm) REVERT: A 650 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7397 (mtp180) REVERT: A 834 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8193 (mttp) REVERT: A 862 ASP cc_start: 0.7417 (m-30) cc_final: 0.7157 (m-30) REVERT: A 974 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8369 (ttmm) REVERT: B 54 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6575 (mtm110) REVERT: B 60 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6338 (mtmp) REVERT: B 205 TYR cc_start: 0.7368 (m-80) cc_final: 0.6972 (m-80) REVERT: B 288 ASN cc_start: 0.7254 (m-40) cc_final: 0.6817 (m-40) REVERT: B 427 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7834 (pmm-80) REVERT: B 565 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: B 645 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7362 (mm-40) REVERT: B 652 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8024 (mttp) REVERT: B 967 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7274 (tm130) REVERT: B 1034 LYS cc_start: 0.8255 (mttm) cc_final: 0.7970 (mttm) REVERT: B 1056 MET cc_start: 0.8689 (mtm) cc_final: 0.8346 (mtp) REVERT: B 1096 GLN cc_start: 0.7525 (mt0) cc_final: 0.7072 (mt0) REVERT: B 1131 MET cc_start: 0.8685 (mmm) cc_final: 0.8148 (mmm) REVERT: C 251 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8324 (tp) REVERT: E 21 ARG cc_start: 0.8110 (ptm-80) cc_final: 0.7733 (ptp-170) REVERT: E 22 ASP cc_start: 0.7971 (t70) cc_final: 0.7746 (t0) REVERT: E 98 ASN cc_start: 0.8074 (m110) cc_final: 0.7780 (OUTLIER) REVERT: E 179 SER cc_start: 0.8568 (t) cc_final: 0.8312 (p) REVERT: F 77 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8654 (tp) REVERT: F 162 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8095 (mttp) REVERT: G 33 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7845 (ttmm) REVERT: G 55 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7096 (tp30) REVERT: G 60 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6895 (mt-10) REVERT: I 164 ILE cc_start: 0.6289 (OUTLIER) cc_final: 0.6029 (tt) REVERT: S 70 SER cc_start: 0.8566 (t) cc_final: 0.8243 (m) REVERT: S 149 ASN cc_start: 0.6130 (p0) cc_final: 0.5813 (m-40) outliers start: 96 outliers final: 48 residues processed: 516 average time/residue: 1.5460 time to fit residues: 936.7970 Evaluate side-chains 512 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 449 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 845 LYS Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 967 GLN Chi-restraints excluded: chain B residue 976 SER Chi-restraints excluded: chain B residue 1114 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 686 ILE Chi-restraints excluded: chain I residue 741 LEU Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain S residue 115 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 318 optimal weight: 4.9990 chunk 335 optimal weight: 10.0000 chunk 305 optimal weight: 4.9990 chunk 326 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 256 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 294 optimal weight: 0.2980 chunk 308 optimal weight: 5.9990 chunk 324 optimal weight: 9.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 526 ASN A 611 ASN A 894 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** B 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 GLN B 977 ASN C 24 GLN C 109 ASN E 52 HIS F 140 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 795 ASN S 145 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30269 Z= 0.319 Angle : 0.591 11.286 40906 Z= 0.306 Chirality : 0.046 0.197 4643 Planarity : 0.004 0.064 5165 Dihedral : 4.735 29.618 3994 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.62 % Allowed : 20.27 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: -0.34 (0.14), residues: 3619 helix: 0.49 (0.14), residues: 1346 sheet: -0.73 (0.22), residues: 511 loop : -0.52 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 315 HIS 0.004 0.001 HIS A 385 PHE 0.035 0.002 PHE A 938 TYR 0.021 0.002 TYR A 732 ARG 0.015 0.001 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 455 time to evaluate : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.7169 (OUTLIER) cc_final: 0.6793 (pp) REVERT: A 182 ILE cc_start: 0.8174 (mt) cc_final: 0.7930 (mm) REVERT: A 193 ASP cc_start: 0.7136 (m-30) cc_final: 0.6857 (m-30) REVERT: A 555 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8883 (mm) REVERT: A 650 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7434 (mtp180) REVERT: A 834 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8184 (mttp) REVERT: A 862 ASP cc_start: 0.7441 (m-30) cc_final: 0.7177 (m-30) REVERT: A 974 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8371 (ttmm) REVERT: A 1161 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: A 1200 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8108 (mmtm) REVERT: B 60 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6334 (mtmp) REVERT: B 205 TYR cc_start: 0.7357 (m-80) cc_final: 0.6951 (m-80) REVERT: B 288 ASN cc_start: 0.7255 (m-40) cc_final: 0.6819 (m-40) REVERT: B 297 LYS cc_start: 0.8504 (ttmm) cc_final: 0.8285 (tppt) REVERT: B 310 GLU cc_start: 0.6881 (tm-30) cc_final: 0.6510 (tm-30) REVERT: B 427 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7833 (pmm-80) REVERT: B 565 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: B 645 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7368 (mm-40) REVERT: B 652 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7981 (mttp) REVERT: B 720 ARG cc_start: 0.7829 (mtp-110) cc_final: 0.7412 (mtp-110) REVERT: B 987 ASP cc_start: 0.7973 (m-30) cc_final: 0.7663 (m-30) REVERT: B 1015 TYR cc_start: 0.9354 (OUTLIER) cc_final: 0.8789 (t80) REVERT: B 1034 LYS cc_start: 0.8279 (mttm) cc_final: 0.7729 (mtmm) REVERT: B 1056 MET cc_start: 0.8671 (mtm) cc_final: 0.8310 (mtp) REVERT: B 1096 GLN cc_start: 0.7549 (mt0) cc_final: 0.7101 (mt0) REVERT: B 1131 MET cc_start: 0.8695 (mmm) cc_final: 0.8156 (mmm) REVERT: C 251 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8330 (tp) REVERT: E 21 ARG cc_start: 0.8107 (ptm-80) cc_final: 0.7739 (ptp-170) REVERT: E 22 ASP cc_start: 0.7980 (t70) cc_final: 0.7759 (t0) REVERT: E 98 ASN cc_start: 0.8111 (m110) cc_final: 0.7880 (OUTLIER) REVERT: E 179 SER cc_start: 0.8586 (t) cc_final: 0.8326 (p) REVERT: F 77 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8654 (tp) REVERT: F 162 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8106 (mttp) REVERT: G 33 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7856 (ttmm) REVERT: G 55 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7224 (tp30) REVERT: G 60 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6955 (mt-10) REVERT: G 104 LEU cc_start: 0.7781 (mt) cc_final: 0.7486 (mt) REVERT: I 164 ILE cc_start: 0.6375 (OUTLIER) cc_final: 0.6160 (tt) REVERT: I 217 ILE cc_start: 0.5462 (OUTLIER) cc_final: 0.5132 (tt) REVERT: S 70 SER cc_start: 0.8576 (t) cc_final: 0.8246 (m) REVERT: S 149 ASN cc_start: 0.6111 (p0) cc_final: 0.5897 (m-40) outliers start: 88 outliers final: 51 residues processed: 503 average time/residue: 1.5247 time to fit residues: 899.2683 Evaluate side-chains 512 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 444 time to evaluate : 3.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1200 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 845 LYS Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 976 SER Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1080 ASP Chi-restraints excluded: chain B residue 1114 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 686 ILE Chi-restraints excluded: chain I residue 741 LEU Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain S residue 115 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 214 optimal weight: 2.9990 chunk 344 optimal weight: 9.9990 chunk 210 optimal weight: 0.9980 chunk 163 optimal weight: 0.0870 chunk 239 optimal weight: 0.8980 chunk 361 optimal weight: 1.9990 chunk 332 optimal weight: 10.0000 chunk 287 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN A 894 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** B 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN B 971 GLN ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN F 140 ASN G 7 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 HIS S 145 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30269 Z= 0.171 Angle : 0.541 12.221 40906 Z= 0.279 Chirality : 0.044 0.197 4643 Planarity : 0.004 0.062 5165 Dihedral : 4.469 26.572 3994 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.88 % Allowed : 21.04 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3619 helix: 0.78 (0.14), residues: 1341 sheet: -0.62 (0.22), residues: 510 loop : -0.49 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 315 HIS 0.004 0.001 HIS I 674 PHE 0.029 0.001 PHE A 938 TYR 0.023 0.001 TYR A 222 ARG 0.018 0.000 ARG B 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 464 time to evaluate : 3.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6732 (pp) REVERT: A 182 ILE cc_start: 0.8106 (mt) cc_final: 0.7850 (mm) REVERT: A 555 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8889 (mm) REVERT: A 834 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8140 (mttp) REVERT: A 974 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8272 (ttmm) REVERT: A 1161 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7201 (tp30) REVERT: B 60 LYS cc_start: 0.6802 (OUTLIER) cc_final: 0.6150 (mtmp) REVERT: B 205 TYR cc_start: 0.7332 (m-80) cc_final: 0.6957 (m-80) REVERT: B 288 ASN cc_start: 0.7223 (m-40) cc_final: 0.6788 (m-40) REVERT: B 297 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8242 (tppt) REVERT: B 310 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6442 (tm-30) REVERT: B 427 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7828 (pmm-80) REVERT: B 645 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7354 (mm-40) REVERT: B 720 ARG cc_start: 0.7693 (mtp-110) cc_final: 0.7266 (mtp-110) REVERT: B 987 ASP cc_start: 0.7960 (m-30) cc_final: 0.7640 (m-30) REVERT: B 1034 LYS cc_start: 0.8195 (mttm) cc_final: 0.7677 (mtmm) REVERT: B 1056 MET cc_start: 0.8649 (mtm) cc_final: 0.8357 (mtp) REVERT: B 1082 GLN cc_start: 0.8051 (pm20) cc_final: 0.7834 (pt0) REVERT: B 1096 GLN cc_start: 0.7412 (mt0) cc_final: 0.6957 (mt0) REVERT: B 1131 MET cc_start: 0.8655 (mmm) cc_final: 0.8122 (mmm) REVERT: B 1145 ARG cc_start: 0.6889 (mtm110) cc_final: 0.6576 (mtm-85) REVERT: C 132 ARG cc_start: 0.7413 (mtt180) cc_final: 0.7200 (mtt180) REVERT: C 251 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8319 (tp) REVERT: E 21 ARG cc_start: 0.8087 (ptm-80) cc_final: 0.7723 (ptp-170) REVERT: E 22 ASP cc_start: 0.7876 (t70) cc_final: 0.7656 (t0) REVERT: E 51 ARG cc_start: 0.8236 (tpp-160) cc_final: 0.7905 (tpp80) REVERT: E 179 SER cc_start: 0.8563 (t) cc_final: 0.8357 (p) REVERT: F 77 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8623 (tp) REVERT: G 33 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7902 (ttmm) REVERT: I 164 ILE cc_start: 0.6201 (OUTLIER) cc_final: 0.5967 (tt) REVERT: I 675 LEU cc_start: 0.7406 (pt) cc_final: 0.7205 (mp) REVERT: S 50 LYS cc_start: 0.8397 (ttmm) cc_final: 0.8151 (ttmm) REVERT: S 70 SER cc_start: 0.8654 (t) cc_final: 0.8338 (m) outliers start: 63 outliers final: 36 residues processed: 501 average time/residue: 1.4798 time to fit residues: 868.0311 Evaluate side-chains 495 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 448 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 845 LYS Chi-restraints excluded: chain B residue 976 SER Chi-restraints excluded: chain B residue 1080 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 228 optimal weight: 0.3980 chunk 306 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 265 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 288 optimal weight: 0.3980 chunk 120 optimal weight: 0.9980 chunk 296 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 HIS B 481 GLN ** B 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN ** B 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 145 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.147078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114042 restraints weight = 37354.893| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.83 r_work: 0.3083 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.527 30269 Z= 0.325 Angle : 0.715 59.198 40906 Z= 0.405 Chirality : 0.046 0.757 4643 Planarity : 0.004 0.132 5165 Dihedral : 4.471 26.735 3994 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.52 % Allowed : 21.52 % Favored : 76.96 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.92 % 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: -0.10 (0.14), residues: 3619 helix: 0.81 (0.14), residues: 1341 sheet: -0.63 (0.22), residues: 510 loop : -0.49 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 315 HIS 0.004 0.001 HIS I 674 PHE 0.029 0.001 PHE A 938 TYR 0.016 0.001 TYR A 705 ARG 0.015 0.000 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13987.22 seconds wall clock time: 248 minutes 37.13 seconds (14917.13 seconds total)