Starting phenix.real_space_refine on Sat Mar 23 13:05:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld0_23278/03_2024/7ld0_23278.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld0_23278/03_2024/7ld0_23278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld0_23278/03_2024/7ld0_23278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld0_23278/03_2024/7ld0_23278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld0_23278/03_2024/7ld0_23278.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld0_23278/03_2024/7ld0_23278.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 152 5.16 5 C 23416 2.51 5 N 6664 2.21 5 O 6744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 71": "OE1" <-> "OE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 569": "NH1" <-> "NH2" Residue "A PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B ARG 537": "NH1" <-> "NH2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B ARG 569": "NH1" <-> "NH2" Residue "B PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 449": "OE1" <-> "OE2" Residue "C GLU 469": "OE1" <-> "OE2" Residue "C ARG 484": "NH1" <-> "NH2" Residue "C GLU 525": "OE1" <-> "OE2" Residue "C ARG 537": "NH1" <-> "NH2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 686": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D GLU 449": "OE1" <-> "OE2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "D ARG 484": "NH1" <-> "NH2" Residue "D GLU 525": "OE1" <-> "OE2" Residue "D ARG 537": "NH1" <-> "NH2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "D ARG 569": "NH1" <-> "NH2" Residue "D PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 686": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E ARG 310": "NH1" <-> "NH2" Residue "E GLU 340": "OE1" <-> "OE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E GLU 414": "OE1" <-> "OE2" Residue "E GLU 449": "OE1" <-> "OE2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "E ARG 484": "NH1" <-> "NH2" Residue "E GLU 525": "OE1" <-> "OE2" Residue "E ARG 537": "NH1" <-> "NH2" Residue "E ARG 543": "NH1" <-> "NH2" Residue "E ARG 569": "NH1" <-> "NH2" Residue "E PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 686": "OE1" <-> "OE2" Residue "F GLU 71": "OE1" <-> "OE2" Residue "F ARG 307": "NH1" <-> "NH2" Residue "F ARG 310": "NH1" <-> "NH2" Residue "F GLU 340": "OE1" <-> "OE2" Residue "F GLU 399": "OE1" <-> "OE2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F GLU 414": "OE1" <-> "OE2" Residue "F GLU 449": "OE1" <-> "OE2" Residue "F GLU 469": "OE1" <-> "OE2" Residue "F ARG 484": "NH1" <-> "NH2" Residue "F GLU 525": "OE1" <-> "OE2" Residue "F ARG 537": "NH1" <-> "NH2" Residue "F ARG 543": "NH1" <-> "NH2" Residue "F ARG 569": "NH1" <-> "NH2" Residue "F PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 686": "OE1" <-> "OE2" Residue "G GLU 71": "OE1" <-> "OE2" Residue "G ARG 307": "NH1" <-> "NH2" Residue "G ARG 310": "NH1" <-> "NH2" Residue "G GLU 340": "OE1" <-> "OE2" Residue "G GLU 399": "OE1" <-> "OE2" Residue "G ARG 403": "NH1" <-> "NH2" Residue "G GLU 414": "OE1" <-> "OE2" Residue "G GLU 449": "OE1" <-> "OE2" Residue "G GLU 469": "OE1" <-> "OE2" Residue "G ARG 484": "NH1" <-> "NH2" Residue "G GLU 525": "OE1" <-> "OE2" Residue "G ARG 537": "NH1" <-> "NH2" Residue "G ARG 543": "NH1" <-> "NH2" Residue "G ARG 569": "NH1" <-> "NH2" Residue "G PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 686": "OE1" <-> "OE2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H ARG 307": "NH1" <-> "NH2" Residue "H ARG 310": "NH1" <-> "NH2" Residue "H GLU 340": "OE1" <-> "OE2" Residue "H GLU 399": "OE1" <-> "OE2" Residue "H ARG 403": "NH1" <-> "NH2" Residue "H GLU 414": "OE1" <-> "OE2" Residue "H GLU 449": "OE1" <-> "OE2" Residue "H GLU 469": "OE1" <-> "OE2" Residue "H ARG 484": "NH1" <-> "NH2" Residue "H GLU 525": "OE1" <-> "OE2" Residue "H ARG 537": "NH1" <-> "NH2" Residue "H ARG 543": "NH1" <-> "NH2" Residue "H ARG 569": "NH1" <-> "NH2" Residue "H PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 686": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36976 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "B" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "C" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "D" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "E" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "F" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "G" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Chain: "H" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4622 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 19, 'TRANS': 570} Chain breaks: 5 Time building chain proxies: 18.37, per 1000 atoms: 0.50 Number of scatterers: 36976 At special positions: 0 Unit cell: (206.01, 206.01, 82.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 152 16.00 O 6744 8.00 N 6664 7.00 C 23416 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: 14.75 Conformation dependent library (CDL) restraints added in 7.3 seconds 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8800 Finding SS restraints... Secondary structure from input PDB file: 336 helices and 8 sheets defined 72.6% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.527A pdb=" N LEU A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 141 through 151 removed outlier: 4.170A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 164 removed outlier: 3.965A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.680A pdb=" N LEU A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 removed outlier: 4.139A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.812A pdb=" N ALA A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 219 through 237 Processing helix chain 'A' and resid 238 through 248 Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 283 through 289 Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.634A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.632A pdb=" N PHE A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 309' Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.766A pdb=" N LEU A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 359 Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.834A pdb=" N ASP A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.799A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 430 through 437 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 461 through 477 Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 521 through 526 Processing helix chain 'A' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER A 578 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.506A pdb=" N LYS A 628 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 650 removed outlier: 3.683A pdb=" N CYS A 649 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG A 697 " --> pdb=" O GLU A 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 68 removed outlier: 3.782A pdb=" N GLU B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 101 " --> pdb=" O GLN B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 141 through 151 removed outlier: 4.170A pdb=" N GLN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 163 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 removed outlier: 3.679A pdb=" N LEU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 193 removed outlier: 4.139A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.812A pdb=" N ALA B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 219 through 237 Processing helix chain 'B' and resid 238 through 248 Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 283 through 289 Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.633A pdb=" N PHE B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 309' Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.765A pdb=" N LEU B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 359 Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP B 367 " --> pdb=" O LYS B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.800A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 430 through 437 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 461 through 477 Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 494 " --> pdb=" O TRP B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 500 No H-bonds generated for 'chain 'B' and resid 498 through 500' Processing helix chain 'B' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 Processing helix chain 'B' and resid 521 through 526 Processing helix chain 'B' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 587 removed outlier: 3.527A pdb=" N SER B 578 " --> pdb=" O SER B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 614 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.506A pdb=" N LYS B 628 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.681A pdb=" N CYS B 649 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 699 removed outlier: 3.657A pdb=" N ARG B 697 " --> pdb=" O GLU B 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.782A pdb=" N GLU C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 104 removed outlier: 3.520A pdb=" N ALA C 93 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 101 " --> pdb=" O GLN C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 133 Processing helix chain 'C' and resid 141 through 151 removed outlier: 4.171A pdb=" N GLN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.679A pdb=" N LEU C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 193 removed outlier: 4.139A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.811A pdb=" N ALA C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 219 through 237 Processing helix chain 'C' and resid 238 through 248 removed outlier: 3.534A pdb=" N GLN C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.633A pdb=" N PHE C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA C 309 " --> pdb=" O PRO C 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 304 through 309' Processing helix chain 'C' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.765A pdb=" N LEU C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 359 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.836A pdb=" N ASP C 367 " --> pdb=" O LYS C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.800A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 430 through 437 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 461 through 477 Processing helix chain 'C' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 500 No H-bonds generated for 'chain 'C' and resid 498 through 500' Processing helix chain 'C' and resid 501 through 508 removed outlier: 3.658A pdb=" N CYS C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 518 Processing helix chain 'C' and resid 521 through 526 Processing helix chain 'C' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG C 535 " --> pdb=" O LEU C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER C 578 " --> pdb=" O SER C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 614 Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.505A pdb=" N LYS C 628 " --> pdb=" O ALA C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 650 removed outlier: 3.681A pdb=" N CYS C 649 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 68 removed outlier: 3.782A pdb=" N GLU D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA D 93 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU D 101 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN D 114 " --> pdb=" O ARG D 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 141 through 151 removed outlier: 4.171A pdb=" N GLN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.680A pdb=" N LEU D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 193 removed outlier: 4.138A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.812A pdb=" N ALA D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 217 No H-bonds generated for 'chain 'D' and resid 215 through 217' Processing helix chain 'D' and resid 219 through 237 Processing helix chain 'D' and resid 238 through 248 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 254 through 259 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 283 through 289 Processing helix chain 'D' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.631A pdb=" N PHE D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA D 309 " --> pdb=" O PRO D 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 304 through 309' Processing helix chain 'D' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG D 329 " --> pdb=" O ASP D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.767A pdb=" N LEU D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 359 Processing helix chain 'D' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP D 367 " --> pdb=" O LYS D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.800A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 430 through 437 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'D' and resid 461 through 477 Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 494 " --> pdb=" O TRP D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 500 No H-bonds generated for 'chain 'D' and resid 498 through 500' Processing helix chain 'D' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 518 Processing helix chain 'D' and resid 521 through 526 Processing helix chain 'D' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG D 535 " --> pdb=" O LEU D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER D 578 " --> pdb=" O SER D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 614 removed outlier: 3.856A pdb=" N MET D 612 " --> pdb=" O ILE D 608 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY D 613 " --> pdb=" O GLN D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.506A pdb=" N LYS D 628 " --> pdb=" O ALA D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 650 removed outlier: 3.682A pdb=" N CYS D 649 " --> pdb=" O THR D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG D 697 " --> pdb=" O GLU D 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.782A pdb=" N GLU E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 79 removed outlier: 3.871A pdb=" N ALA E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL E 95 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU E 101 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN E 114 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 133 Processing helix chain 'E' and resid 141 through 151 removed outlier: 4.171A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE E 151 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE E 163 " --> pdb=" O ARG E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 172 removed outlier: 3.681A pdb=" N LEU E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 193 removed outlier: 4.138A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.813A pdb=" N ALA E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 214 removed outlier: 3.562A pdb=" N TRP E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 217 No H-bonds generated for 'chain 'E' and resid 215 through 217' Processing helix chain 'E' and resid 219 through 237 Processing helix chain 'E' and resid 238 through 248 Processing helix chain 'E' and resid 251 through 253 No H-bonds generated for 'chain 'E' and resid 251 through 253' Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 283 through 289 Processing helix chain 'E' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 309 removed outlier: 3.632A pdb=" N PHE E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA E 309 " --> pdb=" O PRO E 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 304 through 309' Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG E 329 " --> pdb=" O ASP E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.765A pdb=" N LEU E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 359 Processing helix chain 'E' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP E 367 " --> pdb=" O LYS E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.799A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 413 through 423 Processing helix chain 'E' and resid 430 through 437 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 447 through 454 Processing helix chain 'E' and resid 461 through 477 Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.730A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 494 " --> pdb=" O TRP E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 500 No H-bonds generated for 'chain 'E' and resid 498 through 500' Processing helix chain 'E' and resid 501 through 508 removed outlier: 3.656A pdb=" N CYS E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 518 Processing helix chain 'E' and resid 521 through 526 Processing helix chain 'E' and resid 531 through 543 removed outlier: 3.611A pdb=" N ARG E 535 " --> pdb=" O LEU E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER E 578 " --> pdb=" O SER E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 614 removed outlier: 3.636A pdb=" N MET E 612 " --> pdb=" O ILE E 608 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY E 613 " --> pdb=" O GLN E 609 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 614 " --> pdb=" O SER E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.505A pdb=" N LYS E 628 " --> pdb=" O ALA E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 650 removed outlier: 3.682A pdb=" N CYS E 649 " --> pdb=" O THR E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG E 697 " --> pdb=" O GLU E 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 68 removed outlier: 3.781A pdb=" N GLU F 66 " --> pdb=" O GLN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA F 93 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU F 101 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 3.665A pdb=" N GLN F 114 " --> pdb=" O ARG F 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 141 through 151 removed outlier: 4.170A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE F 151 " --> pdb=" O LEU F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE F 163 " --> pdb=" O ARG F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 172 removed outlier: 3.680A pdb=" N LEU F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 193 removed outlier: 4.138A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.812A pdb=" N ALA F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 219 through 237 Processing helix chain 'F' and resid 238 through 248 Processing helix chain 'F' and resid 251 through 253 No H-bonds generated for 'chain 'F' and resid 251 through 253' Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 264 through 278 Processing helix chain 'F' and resid 283 through 289 Processing helix chain 'F' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 309 removed outlier: 3.631A pdb=" N PHE F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA F 309 " --> pdb=" O PRO F 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 304 through 309' Processing helix chain 'F' and resid 323 through 329 removed outlier: 3.503A pdb=" N GLN F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG F 329 " --> pdb=" O ASP F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 335 removed outlier: 3.766A pdb=" N LEU F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 359 Processing helix chain 'F' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP F 367 " --> pdb=" O LYS F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.799A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 413 through 423 Processing helix chain 'F' and resid 430 through 437 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 447 through 454 Processing helix chain 'F' and resid 461 through 477 Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU F 494 " --> pdb=" O TRP F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 500 No H-bonds generated for 'chain 'F' and resid 498 through 500' Processing helix chain 'F' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 518 Processing helix chain 'F' and resid 521 through 526 Processing helix chain 'F' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG F 535 " --> pdb=" O LEU F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER F 578 " --> pdb=" O SER F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 614 Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.506A pdb=" N LYS F 628 " --> pdb=" O ALA F 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 650 removed outlier: 3.682A pdb=" N CYS F 649 " --> pdb=" O THR F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG F 697 " --> pdb=" O GLU F 693 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 68 removed outlier: 3.781A pdb=" N GLU G 66 " --> pdb=" O GLN G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 79 removed outlier: 3.873A pdb=" N ALA G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA G 93 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL G 95 " --> pdb=" O GLY G 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU G 101 " --> pdb=" O GLN G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 124 removed outlier: 3.666A pdb=" N GLN G 114 " --> pdb=" O ARG G 110 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 133 Processing helix chain 'G' and resid 141 through 151 removed outlier: 4.169A pdb=" N GLN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE G 163 " --> pdb=" O ARG G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 172 removed outlier: 3.680A pdb=" N LEU G 169 " --> pdb=" O LEU G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 193 removed outlier: 4.138A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS G 193 " --> pdb=" O GLU G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.813A pdb=" N ALA G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 214 removed outlier: 3.562A pdb=" N TRP G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 219 through 237 Processing helix chain 'G' and resid 238 through 248 Processing helix chain 'G' and resid 251 through 253 No H-bonds generated for 'chain 'G' and resid 251 through 253' Processing helix chain 'G' and resid 254 through 259 Processing helix chain 'G' and resid 264 through 278 Processing helix chain 'G' and resid 283 through 289 Processing helix chain 'G' and resid 295 through 303 removed outlier: 3.634A pdb=" N LEU G 299 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 309 removed outlier: 3.633A pdb=" N PHE G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA G 309 " --> pdb=" O PRO G 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 304 through 309' Processing helix chain 'G' and resid 323 through 329 removed outlier: 3.504A pdb=" N GLN G 328 " --> pdb=" O PRO G 324 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG G 329 " --> pdb=" O ASP G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 335 removed outlier: 3.765A pdb=" N LEU G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 359 Processing helix chain 'G' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP G 367 " --> pdb=" O LYS G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 removed outlier: 3.799A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 397 Processing helix chain 'G' and resid 413 through 423 Processing helix chain 'G' and resid 430 through 437 Processing helix chain 'G' and resid 439 through 444 Processing helix chain 'G' and resid 447 through 454 Processing helix chain 'G' and resid 461 through 477 Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU G 494 " --> pdb=" O TRP G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 500 No H-bonds generated for 'chain 'G' and resid 498 through 500' Processing helix chain 'G' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 518 Processing helix chain 'G' and resid 521 through 526 Processing helix chain 'G' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG G 535 " --> pdb=" O LEU G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER G 578 " --> pdb=" O SER G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 606 through 614 Processing helix chain 'G' and resid 625 through 629 removed outlier: 3.505A pdb=" N LYS G 628 " --> pdb=" O ALA G 625 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 650 removed outlier: 3.682A pdb=" N CYS G 649 " --> pdb=" O THR G 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 699 removed outlier: 3.656A pdb=" N ARG G 697 " --> pdb=" O GLU G 693 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 removed outlier: 3.781A pdb=" N GLU H 66 " --> pdb=" O GLN H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 79 removed outlier: 3.872A pdb=" N ALA H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 104 removed outlier: 3.521A pdb=" N ALA H 93 " --> pdb=" O GLY H 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL H 95 " --> pdb=" O GLY H 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU H 101 " --> pdb=" O GLN H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 124 removed outlier: 3.666A pdb=" N GLN H 114 " --> pdb=" O ARG H 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 141 through 151 removed outlier: 4.170A pdb=" N GLN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE H 151 " --> pdb=" O LEU H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 164 removed outlier: 3.964A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE H 163 " --> pdb=" O ARG H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 172 removed outlier: 3.680A pdb=" N LEU H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 193 removed outlier: 4.138A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS H 193 " --> pdb=" O GLU H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 206 removed outlier: 3.812A pdb=" N ALA H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 214 removed outlier: 3.561A pdb=" N TRP H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 217 No H-bonds generated for 'chain 'H' and resid 215 through 217' Processing helix chain 'H' and resid 219 through 237 Processing helix chain 'H' and resid 238 through 248 Processing helix chain 'H' and resid 251 through 253 No H-bonds generated for 'chain 'H' and resid 251 through 253' Processing helix chain 'H' and resid 254 through 259 Processing helix chain 'H' and resid 264 through 278 Processing helix chain 'H' and resid 283 through 289 Processing helix chain 'H' and resid 295 through 303 removed outlier: 3.635A pdb=" N LEU H 299 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 309 removed outlier: 3.632A pdb=" N PHE H 308 " --> pdb=" O ASP H 304 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA H 309 " --> pdb=" O PRO H 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 304 through 309' Processing helix chain 'H' and resid 323 through 329 removed outlier: 3.505A pdb=" N GLN H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG H 329 " --> pdb=" O ASP H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 335 removed outlier: 3.767A pdb=" N LEU H 334 " --> pdb=" O LEU H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 359 Processing helix chain 'H' and resid 363 through 369 removed outlier: 3.835A pdb=" N ASP H 367 " --> pdb=" O LYS H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 removed outlier: 3.800A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 397 Processing helix chain 'H' and resid 413 through 423 Processing helix chain 'H' and resid 430 through 437 Processing helix chain 'H' and resid 439 through 444 Processing helix chain 'H' and resid 447 through 454 Processing helix chain 'H' and resid 461 through 477 Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.731A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU H 494 " --> pdb=" O TRP H 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 500 No H-bonds generated for 'chain 'H' and resid 498 through 500' Processing helix chain 'H' and resid 501 through 508 removed outlier: 3.657A pdb=" N CYS H 508 " --> pdb=" O GLY H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 518 Processing helix chain 'H' and resid 521 through 526 Processing helix chain 'H' and resid 531 through 543 removed outlier: 3.610A pdb=" N ARG H 535 " --> pdb=" O LEU H 531 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 587 removed outlier: 3.528A pdb=" N SER H 578 " --> pdb=" O SER H 574 " (cutoff:3.500A) Processing helix chain 'H' and resid 606 through 614 Processing helix chain 'H' and resid 625 through 629 removed outlier: 3.506A pdb=" N LYS H 628 " --> pdb=" O ALA H 625 " (cutoff:3.500A) Processing helix chain 'H' and resid 638 through 650 removed outlier: 3.682A pdb=" N CYS H 649 " --> pdb=" O THR H 645 " (cutoff:3.500A) Processing helix chain 'H' and resid 690 through 699 removed outlier: 3.657A pdb=" N ARG H 697 " --> pdb=" O GLU H 693 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 566 through 567 removed outlier: 6.840A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 681 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 566 through 567 removed outlier: 6.840A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 681 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 566 through 567 removed outlier: 6.841A pdb=" N SER C 567 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 681 " --> pdb=" O PRO C 655 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 566 through 567 removed outlier: 6.841A pdb=" N SER D 567 " --> pdb=" O VAL D 620 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE D 681 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 566 through 567 removed outlier: 6.840A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE E 681 " --> pdb=" O PRO E 655 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 566 through 567 removed outlier: 6.841A pdb=" N SER F 567 " --> pdb=" O VAL F 620 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE F 681 " --> pdb=" O PRO F 655 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 566 through 567 removed outlier: 6.840A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE G 681 " --> pdb=" O PRO G 655 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 566 through 567 removed outlier: 6.840A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE H 681 " --> pdb=" O PRO H 655 " (cutoff:3.500A) 1882 hydrogen bonds defined for protein. 5574 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: 12.67 Time building geometry restraints manager: 15.98 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: 12508 1.34 - 1.46: 5545 1.46 - 1.58: 19307 1.58 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 37552 Sorted by residual: bond pdb=" N ILE D 608 " pdb=" CA ILE D 608 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.51e+00 bond pdb=" N VAL B 611 " pdb=" CA VAL B 611 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.46e+00 bond pdb=" N ILE E 608 " pdb=" CA ILE E 608 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.42e+00 bond pdb=" CA SER D 381 " pdb=" CB SER D 381 " ideal model delta sigma weight residual 1.530 1.489 0.040 1.48e-02 4.57e+03 7.41e+00 bond pdb=" N VAL C 611 " pdb=" CA VAL C 611 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.37e+00 ... (remaining 37547 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.32: 683 106.32 - 113.28: 20906 113.28 - 120.24: 13822 120.24 - 127.20: 14946 127.20 - 134.16: 371 Bond angle restraints: 50728 Sorted by residual: angle pdb=" CA SER F 77 " pdb=" C SER F 77 " pdb=" O SER F 77 " ideal model delta sigma weight residual 122.14 117.34 4.80 1.24e+00 6.50e-01 1.50e+01 angle pdb=" N ALA F 78 " pdb=" CA ALA F 78 " pdb=" C ALA F 78 " ideal model delta sigma weight residual 112.86 108.21 4.65 1.22e+00 6.72e-01 1.45e+01 angle pdb=" N VAL H 611 " pdb=" CA VAL H 611 " pdb=" C VAL H 611 " ideal model delta sigma weight residual 110.62 106.80 3.82 1.02e+00 9.61e-01 1.40e+01 angle pdb=" N LEU A 607 " pdb=" CA LEU A 607 " pdb=" C LEU A 607 " ideal model delta sigma weight residual 111.28 107.33 3.95 1.09e+00 8.42e-01 1.31e+01 angle pdb=" CA ALA B 78 " pdb=" C ALA B 78 " pdb=" O ALA B 78 " ideal model delta sigma weight residual 120.32 116.09 4.23 1.18e+00 7.18e-01 1.29e+01 ... (remaining 50723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 20467 17.03 - 34.06: 2026 34.06 - 51.09: 273 51.09 - 68.13: 42 68.13 - 85.16: 32 Dihedral angle restraints: 22840 sinusoidal: 9296 harmonic: 13544 Sorted by residual: dihedral pdb=" CA THR B 140 " pdb=" C THR B 140 " pdb=" N ARG B 141 " pdb=" CA ARG B 141 " ideal model delta harmonic sigma weight residual 180.00 156.36 23.64 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA THR C 140 " pdb=" C THR C 140 " pdb=" N ARG C 141 " pdb=" CA ARG C 141 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA THR E 140 " pdb=" C THR E 140 " pdb=" N ARG E 141 " pdb=" CA ARG E 141 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 22837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4832 0.051 - 0.102: 866 0.102 - 0.153: 122 0.153 - 0.203: 23 0.203 - 0.254: 5 Chirality restraints: 5848 Sorted by residual: chirality pdb=" CA LEU A 607 " pdb=" N LEU A 607 " pdb=" C LEU A 607 " pdb=" CB LEU A 607 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA LEU D 607 " pdb=" N LEU D 607 " pdb=" C LEU D 607 " pdb=" CB LEU D 607 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA LEU B 607 " pdb=" N LEU B 607 " pdb=" C LEU B 607 " pdb=" CB LEU B 607 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 5845 not shown) Planarity restraints: 6536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 79 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C LEU D 79 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU D 79 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS D 80 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 79 " 0.017 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C LEU C 79 " -0.062 2.00e-02 2.50e+03 pdb=" O LEU C 79 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS C 80 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 79 " -0.017 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C LEU E 79 " 0.062 2.00e-02 2.50e+03 pdb=" O LEU E 79 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS E 80 " -0.022 2.00e-02 2.50e+03 ... (remaining 6533 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 7152 2.76 - 3.30: 38646 3.30 - 3.83: 57420 3.83 - 4.37: 70395 4.37 - 4.90: 115408 Nonbonded interactions: 289021 Sorted by model distance: nonbonded pdb=" N VAL C 61 " pdb=" OD1 ASP C 63 " model vdw 2.229 2.520 nonbonded pdb=" N VAL H 61 " pdb=" OD1 ASP H 63 " model vdw 2.229 2.520 nonbonded pdb=" N VAL F 61 " pdb=" OD1 ASP F 63 " model vdw 2.229 2.520 nonbonded pdb=" N VAL A 61 " pdb=" OD1 ASP A 63 " model vdw 2.230 2.520 nonbonded pdb=" N VAL E 61 " pdb=" OD1 ASP E 63 " model vdw 2.230 2.520 ... (remaining 289016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 11.300 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 95.370 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 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 0.040 37552 Z= 0.377 Angle : 0.651 6.745 50728 Z= 0.405 Chirality : 0.040 0.254 5848 Planarity : 0.006 0.049 6536 Dihedral : 13.277 85.157 14040 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.12), residues: 4624 helix: -0.77 (0.09), residues: 3040 sheet: -3.47 (0.29), residues: 144 loop : -2.19 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 638 HIS 0.004 0.001 HIS H 583 PHE 0.010 0.001 PHE G 476 TYR 0.011 0.001 TYR A 380 ARG 0.024 0.002 ARG D 569 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1119 time to evaluate : 4.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.7832 (m110) cc_final: 0.7623 (m-40) REVERT: A 157 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.8143 (mtm110) REVERT: A 196 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6651 (tm-30) REVERT: A 197 GLU cc_start: 0.6824 (mp0) cc_final: 0.6576 (mp0) REVERT: A 264 GLU cc_start: 0.6619 (mp0) cc_final: 0.6401 (mp0) REVERT: A 380 TYR cc_start: 0.8093 (m-80) cc_final: 0.7810 (m-80) REVERT: A 495 ASP cc_start: 0.7405 (t0) cc_final: 0.7163 (t0) REVERT: A 520 GLU cc_start: 0.6716 (tp30) cc_final: 0.6400 (tp30) REVERT: A 589 PHE cc_start: 0.8304 (m-10) cc_final: 0.8092 (m-10) REVERT: A 609 GLN cc_start: 0.7973 (tp40) cc_final: 0.7484 (tp40) REVERT: A 682 LYS cc_start: 0.6846 (tptp) cc_final: 0.6489 (tptp) REVERT: A 694 LYS cc_start: 0.8372 (tmtt) cc_final: 0.8092 (tptp) REVERT: B 156 ASN cc_start: 0.7883 (m110) cc_final: 0.7529 (m-40) REVERT: B 197 GLU cc_start: 0.6913 (mp0) cc_final: 0.6692 (mp0) REVERT: B 201 ARG cc_start: 0.7791 (mtp180) cc_final: 0.7579 (ttp80) REVERT: B 212 LEU cc_start: 0.8381 (mt) cc_final: 0.7866 (mt) REVERT: B 215 CYS cc_start: 0.7152 (m) cc_final: 0.6845 (m) REVERT: B 246 VAL cc_start: 0.8417 (t) cc_final: 0.8210 (t) REVERT: B 340 GLU cc_start: 0.7718 (mp0) cc_final: 0.7397 (mp0) REVERT: B 352 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 378 VAL cc_start: 0.7007 (p) cc_final: 0.6731 (m) REVERT: B 458 LYS cc_start: 0.7293 (mmpt) cc_final: 0.7078 (mmpt) REVERT: B 459 SER cc_start: 0.8326 (t) cc_final: 0.8061 (p) REVERT: B 495 ASP cc_start: 0.7562 (t0) cc_final: 0.7357 (t0) REVERT: B 520 GLU cc_start: 0.6793 (tp30) cc_final: 0.6560 (tp30) REVERT: B 565 PHE cc_start: 0.7501 (t80) cc_final: 0.7182 (t80) REVERT: B 694 LYS cc_start: 0.8067 (tmtt) cc_final: 0.7726 (tptp) REVERT: C 100 GLU cc_start: 0.7794 (mp0) cc_final: 0.7541 (mp0) REVERT: C 197 GLU cc_start: 0.6895 (mp0) cc_final: 0.6629 (mp0) REVERT: C 286 GLU cc_start: 0.6783 (tp30) cc_final: 0.6521 (tp30) REVERT: C 520 GLU cc_start: 0.6843 (tp30) cc_final: 0.6473 (tp30) REVERT: C 526 ASP cc_start: 0.6948 (m-30) cc_final: 0.6740 (m-30) REVERT: C 589 PHE cc_start: 0.8064 (m-10) cc_final: 0.7765 (m-10) REVERT: C 682 LYS cc_start: 0.7159 (tptp) cc_final: 0.6848 (tptp) REVERT: C 686 GLU cc_start: 0.7375 (pp20) cc_final: 0.7060 (pp20) REVERT: C 694 LYS cc_start: 0.7980 (tmtt) cc_final: 0.7619 (tptt) REVERT: D 156 ASN cc_start: 0.7899 (m110) cc_final: 0.7606 (m-40) REVERT: D 197 GLU cc_start: 0.6872 (mp0) cc_final: 0.6605 (mp0) REVERT: D 201 ARG cc_start: 0.7669 (mtp180) cc_final: 0.7455 (ttp80) REVERT: D 261 LYS cc_start: 0.7773 (mmtp) cc_final: 0.7528 (mmtp) REVERT: D 271 CYS cc_start: 0.6014 (m) cc_final: 0.5728 (m) REVERT: D 340 GLU cc_start: 0.7751 (mp0) cc_final: 0.7463 (mp0) REVERT: D 352 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7293 (mm-30) REVERT: D 378 VAL cc_start: 0.6769 (p) cc_final: 0.6394 (m) REVERT: D 383 ASN cc_start: 0.7489 (t0) cc_final: 0.7196 (t0) REVERT: D 454 ASP cc_start: 0.7645 (m-30) cc_final: 0.7413 (m-30) REVERT: D 565 PHE cc_start: 0.7692 (t80) cc_final: 0.7449 (t80) REVERT: D 609 GLN cc_start: 0.8127 (tp40) cc_final: 0.7814 (tp40) REVERT: D 682 LYS cc_start: 0.6966 (tptp) cc_final: 0.6505 (tptp) REVERT: D 694 LYS cc_start: 0.8005 (tmtt) cc_final: 0.7644 (tptt) REVERT: D 695 ILE cc_start: 0.8223 (pt) cc_final: 0.7970 (pt) REVERT: E 71 GLU cc_start: 0.7281 (pm20) cc_final: 0.6908 (pm20) REVERT: E 143 GLN cc_start: 0.7454 (mp10) cc_final: 0.7127 (mp10) REVERT: E 157 ARG cc_start: 0.8335 (mtm-85) cc_final: 0.8105 (mtm110) REVERT: E 189 GLU cc_start: 0.7414 (tm-30) cc_final: 0.6685 (tm-30) REVERT: E 609 GLN cc_start: 0.8180 (tp40) cc_final: 0.7882 (tp40) REVERT: F 156 ASN cc_start: 0.7565 (m110) cc_final: 0.7172 (m110) REVERT: F 159 ARG cc_start: 0.8106 (tpt90) cc_final: 0.7899 (tpt90) REVERT: F 189 GLU cc_start: 0.7542 (tm-30) cc_final: 0.6975 (tm-30) REVERT: F 197 GLU cc_start: 0.6807 (mp0) cc_final: 0.6543 (mp0) REVERT: F 201 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7413 (mtm180) REVERT: F 215 CYS cc_start: 0.7067 (m) cc_final: 0.6793 (m) REVERT: F 219 ASP cc_start: 0.6928 (t70) cc_final: 0.6698 (t0) REVERT: F 340 GLU cc_start: 0.7768 (mp0) cc_final: 0.7563 (mp0) REVERT: F 352 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7198 (mm-30) REVERT: F 378 VAL cc_start: 0.6750 (p) cc_final: 0.6283 (m) REVERT: F 454 ASP cc_start: 0.7568 (m-30) cc_final: 0.7338 (m-30) REVERT: F 458 LYS cc_start: 0.7123 (mmpt) cc_final: 0.6915 (mmpt) REVERT: F 609 GLN cc_start: 0.8007 (tp40) cc_final: 0.7557 (tp40) REVERT: G 100 GLU cc_start: 0.7753 (mp0) cc_final: 0.7496 (mp0) REVERT: G 143 GLN cc_start: 0.7546 (mp10) cc_final: 0.7213 (mp10) REVERT: G 153 VAL cc_start: 0.7616 (t) cc_final: 0.7380 (t) REVERT: G 189 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7043 (tm-30) REVERT: G 197 GLU cc_start: 0.6720 (mp0) cc_final: 0.6502 (mp0) REVERT: G 391 LYS cc_start: 0.7738 (ttpt) cc_final: 0.7499 (ttmm) REVERT: G 452 GLN cc_start: 0.8052 (tt0) cc_final: 0.7590 (tt0) REVERT: G 516 HIS cc_start: 0.8146 (p90) cc_final: 0.7703 (p90) REVERT: G 520 GLU cc_start: 0.6772 (tp30) cc_final: 0.6475 (tp30) REVERT: G 609 GLN cc_start: 0.7971 (tp40) cc_final: 0.7561 (tp40) REVERT: G 694 LYS cc_start: 0.8409 (tmtt) cc_final: 0.8012 (tmtt) REVERT: H 100 GLU cc_start: 0.7888 (mp0) cc_final: 0.7622 (mp0) REVERT: H 156 ASN cc_start: 0.7776 (m110) cc_final: 0.7354 (m110) REVERT: H 189 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7066 (tm-30) REVERT: H 197 GLU cc_start: 0.6877 (mp0) cc_final: 0.6654 (mp0) REVERT: H 246 VAL cc_start: 0.8286 (t) cc_final: 0.8076 (t) REVERT: H 253 TRP cc_start: 0.7834 (m100) cc_final: 0.7320 (m100) REVERT: H 340 GLU cc_start: 0.7678 (mp0) cc_final: 0.7237 (mp0) REVERT: H 352 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7175 (mm-30) REVERT: H 378 VAL cc_start: 0.6941 (p) cc_final: 0.6634 (m) REVERT: H 450 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6430 (mt-10) REVERT: H 454 ASP cc_start: 0.7645 (m-30) cc_final: 0.7392 (m-30) REVERT: H 458 LYS cc_start: 0.7241 (mmpt) cc_final: 0.7037 (mmpt) REVERT: H 495 ASP cc_start: 0.7561 (t0) cc_final: 0.7318 (t0) REVERT: H 592 PHE cc_start: 0.7401 (t80) cc_final: 0.7082 (t80) REVERT: H 694 LYS cc_start: 0.8131 (tmtt) cc_final: 0.7900 (tptt) outliers start: 0 outliers final: 0 residues processed: 1119 average time/residue: 0.5448 time to fit residues: 934.1763 Evaluate side-chains 1041 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1041 time to evaluate : 4.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 398 optimal weight: 1.9990 chunk 357 optimal weight: 0.0010 chunk 198 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 241 optimal weight: 0.7980 chunk 191 optimal weight: 0.7980 chunk 369 optimal weight: 0.2980 chunk 143 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 428 optimal weight: 4.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 522 GLN B 156 ASN B 232 ASN B 522 GLN C 156 ASN C 437 GLN C 534 HIS C 571 ASN D 156 ASN D 232 ASN D 571 ASN E 156 ASN F 156 ASN ** F 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 685 HIS G 156 ASN G 522 GLN H 156 ASN H 232 ASN H 383 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37552 Z= 0.227 Angle : 0.696 11.993 50728 Z= 0.345 Chirality : 0.043 0.180 5848 Planarity : 0.005 0.044 6536 Dihedral : 4.613 23.152 5128 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.86 % Allowed : 11.81 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.12), residues: 4624 helix: 0.08 (0.09), residues: 3152 sheet: -3.27 (0.32), residues: 160 loop : -2.08 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 103 HIS 0.011 0.001 HIS B 587 PHE 0.020 0.002 PHE C 565 TYR 0.010 0.001 TYR C 503 ARG 0.006 0.001 ARG D 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1082 time to evaluate : 4.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.6843 (mp0) cc_final: 0.6600 (mp0) REVERT: A 189 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7133 (tm-30) REVERT: A 195 SER cc_start: 0.7774 (m) cc_final: 0.7340 (t) REVERT: A 197 GLU cc_start: 0.6861 (mp0) cc_final: 0.6470 (mp0) REVERT: A 392 ARG cc_start: 0.7820 (ttm170) cc_final: 0.7431 (ttp-110) REVERT: A 520 GLU cc_start: 0.6942 (tp30) cc_final: 0.6615 (tp30) REVERT: A 609 GLN cc_start: 0.7953 (tp40) cc_final: 0.7437 (tp40) REVERT: A 694 LYS cc_start: 0.8264 (tmtt) cc_final: 0.7817 (tptp) REVERT: A 695 ILE cc_start: 0.8763 (pt) cc_final: 0.8530 (pt) REVERT: B 156 ASN cc_start: 0.7583 (m-40) cc_final: 0.7269 (m-40) REVERT: B 159 ARG cc_start: 0.7993 (tpt90) cc_final: 0.7784 (tpt90) REVERT: B 212 LEU cc_start: 0.8347 (mt) cc_final: 0.8101 (mp) REVERT: B 450 GLU cc_start: 0.6432 (mt-10) cc_final: 0.6210 (mt-10) REVERT: B 454 ASP cc_start: 0.7509 (m-30) cc_final: 0.7190 (m-30) REVERT: B 511 ASP cc_start: 0.7610 (p0) cc_final: 0.7366 (p0) REVERT: B 520 GLU cc_start: 0.6904 (tp30) cc_final: 0.6601 (tp30) REVERT: B 540 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8164 (t) REVERT: B 694 LYS cc_start: 0.8031 (tmtt) cc_final: 0.7676 (tptt) REVERT: C 100 GLU cc_start: 0.7827 (mp0) cc_final: 0.7562 (mp0) REVERT: C 169 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8111 (mt) REVERT: C 189 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7190 (tm-30) REVERT: C 195 SER cc_start: 0.7790 (m) cc_final: 0.7423 (t) REVERT: C 286 GLU cc_start: 0.6881 (tp30) cc_final: 0.6672 (tp30) REVERT: C 380 TYR cc_start: 0.7937 (m-80) cc_final: 0.7682 (m-80) REVERT: C 413 LYS cc_start: 0.7719 (mmtp) cc_final: 0.7333 (mtpp) REVERT: C 483 ASP cc_start: 0.8029 (t0) cc_final: 0.7824 (t0) REVERT: C 686 GLU cc_start: 0.7515 (pp20) cc_final: 0.7243 (pp20) REVERT: C 694 LYS cc_start: 0.7840 (tmtt) cc_final: 0.7500 (tptt) REVERT: D 156 ASN cc_start: 0.7902 (m-40) cc_final: 0.7559 (m-40) REVERT: D 157 ARG cc_start: 0.7912 (mtt180) cc_final: 0.7427 (mtm180) REVERT: D 191 MET cc_start: 0.7643 (mmp) cc_final: 0.7362 (mmp) REVERT: D 195 SER cc_start: 0.7835 (m) cc_final: 0.7451 (t) REVERT: D 196 GLU cc_start: 0.6738 (tm-30) cc_final: 0.6414 (tm-30) REVERT: D 197 GLU cc_start: 0.6818 (mp0) cc_final: 0.6428 (mp0) REVERT: D 201 ARG cc_start: 0.7567 (mtp180) cc_final: 0.7367 (mtm110) REVERT: D 261 LYS cc_start: 0.7698 (mmtp) cc_final: 0.7477 (mmtp) REVERT: D 286 GLU cc_start: 0.6722 (tp30) cc_final: 0.6504 (tp30) REVERT: D 303 LEU cc_start: 0.8356 (mp) cc_final: 0.8144 (mt) REVERT: D 352 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7285 (mm-30) REVERT: D 395 ARG cc_start: 0.7595 (ptp-110) cc_final: 0.7333 (ttp-110) REVERT: D 454 ASP cc_start: 0.7584 (m-30) cc_final: 0.7341 (m-30) REVERT: D 540 THR cc_start: 0.8486 (p) cc_final: 0.8238 (t) REVERT: D 565 PHE cc_start: 0.7726 (t80) cc_final: 0.7446 (t80) REVERT: D 682 LYS cc_start: 0.7002 (tptp) cc_final: 0.6602 (tptp) REVERT: D 694 LYS cc_start: 0.7788 (tmtt) cc_final: 0.7511 (tptt) REVERT: D 695 ILE cc_start: 0.8506 (pt) cc_final: 0.8228 (pt) REVERT: E 189 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7008 (tm-30) REVERT: E 349 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7841 (mp) REVERT: E 444 LEU cc_start: 0.8535 (mp) cc_final: 0.8319 (mt) REVERT: E 511 ASP cc_start: 0.7960 (p0) cc_final: 0.7709 (p0) REVERT: E 609 GLN cc_start: 0.8183 (tp40) cc_final: 0.7909 (tp40) REVERT: F 156 ASN cc_start: 0.7363 (m-40) cc_final: 0.7010 (m-40) REVERT: F 189 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7234 (tm-30) REVERT: F 196 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6562 (tm-30) REVERT: F 197 GLU cc_start: 0.6871 (mp0) cc_final: 0.6589 (mp0) REVERT: F 201 ARG cc_start: 0.7479 (mtp180) cc_final: 0.7202 (mtp85) REVERT: F 212 LEU cc_start: 0.8438 (mt) cc_final: 0.7973 (mp) REVERT: F 215 CYS cc_start: 0.7124 (m) cc_final: 0.6814 (m) REVERT: F 282 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6171 (mm-30) REVERT: F 303 LEU cc_start: 0.8354 (mp) cc_final: 0.8135 (mt) REVERT: F 352 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7102 (mm-30) REVERT: F 450 GLU cc_start: 0.6501 (mt-10) cc_final: 0.6252 (mt-10) REVERT: F 454 ASP cc_start: 0.7588 (m-30) cc_final: 0.7296 (m-30) REVERT: F 540 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.8009 (t) REVERT: F 609 GLN cc_start: 0.7758 (tp40) cc_final: 0.7246 (tp40) REVERT: F 612 MET cc_start: 0.7357 (tpp) cc_final: 0.6782 (tpp) REVERT: F 681 ILE cc_start: 0.7019 (mp) cc_final: 0.6743 (mp) REVERT: F 694 LYS cc_start: 0.7961 (tmtt) cc_final: 0.7614 (tptt) REVERT: G 100 GLU cc_start: 0.7685 (mp0) cc_final: 0.7426 (mp0) REVERT: G 111 GLU cc_start: 0.7397 (tp30) cc_final: 0.7080 (tp30) REVERT: G 189 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7249 (tm-30) REVERT: G 196 GLU cc_start: 0.6530 (tm-30) cc_final: 0.6256 (tm-30) REVERT: G 391 LYS cc_start: 0.7667 (ttpt) cc_final: 0.7435 (mtpp) REVERT: G 483 ASP cc_start: 0.7810 (t0) cc_final: 0.7547 (t70) REVERT: G 520 GLU cc_start: 0.7007 (tp30) cc_final: 0.6704 (tp30) REVERT: G 526 ASP cc_start: 0.7119 (m-30) cc_final: 0.6900 (m-30) REVERT: G 609 GLN cc_start: 0.7716 (tp40) cc_final: 0.7185 (tp40) REVERT: G 694 LYS cc_start: 0.8185 (tmtt) cc_final: 0.7757 (tmtt) REVERT: H 156 ASN cc_start: 0.7512 (m-40) cc_final: 0.7243 (m110) REVERT: H 195 SER cc_start: 0.7583 (m) cc_final: 0.7348 (t) REVERT: H 197 GLU cc_start: 0.6996 (mp0) cc_final: 0.6748 (mp0) REVERT: H 201 ARG cc_start: 0.7525 (mtp180) cc_final: 0.7259 (mtp85) REVERT: H 212 LEU cc_start: 0.8329 (mt) cc_final: 0.8039 (mp) REVERT: H 352 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7124 (mm-30) REVERT: H 495 ASP cc_start: 0.7548 (t0) cc_final: 0.7191 (t0) REVERT: H 592 PHE cc_start: 0.7366 (t80) cc_final: 0.6999 (t80) REVERT: H 682 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6518 (tptp) outliers start: 73 outliers final: 37 residues processed: 1107 average time/residue: 0.5739 time to fit residues: 971.3166 Evaluate side-chains 1034 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 991 time to evaluate : 4.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 282 GLU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 540 THR Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 679 ASN Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 679 ASN Chi-restraints excluded: chain H residue 682 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 238 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 356 optimal weight: 1.9990 chunk 291 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 429 optimal weight: 0.7980 chunk 463 optimal weight: 3.9990 chunk 382 optimal weight: 3.9990 chunk 425 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 344 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 534 HIS A 652 ASN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 232 ASN B 685 HIS ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 652 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN D 232 ASN D 685 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN E 534 HIS ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 ASN F 383 ASN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 ASN G 522 GLN G 534 HIS G 585 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 ASN H 232 ASN H 383 ASN H 522 GLN H 652 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 37552 Z= 0.354 Angle : 0.693 10.087 50728 Z= 0.348 Chirality : 0.045 0.193 5848 Planarity : 0.005 0.048 6536 Dihedral : 4.824 25.451 5128 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.16 % Allowed : 15.66 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.12), residues: 4624 helix: 0.03 (0.09), residues: 3152 sheet: -2.97 (0.34), residues: 160 loop : -1.91 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 420 HIS 0.009 0.001 HIS F 587 PHE 0.022 0.002 PHE E 565 TYR 0.019 0.002 TYR B 568 ARG 0.006 0.001 ARG G 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1046 time to evaluate : 4.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 SER cc_start: 0.8008 (m) cc_final: 0.7634 (t) REVERT: A 196 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6523 (tm-30) REVERT: A 197 GLU cc_start: 0.6920 (mp0) cc_final: 0.6664 (mp0) REVERT: A 209 ASP cc_start: 0.7624 (t0) cc_final: 0.7295 (t0) REVERT: A 289 ARG cc_start: 0.7643 (ttm-80) cc_final: 0.7296 (mmt90) REVERT: A 489 ASP cc_start: 0.7617 (m-30) cc_final: 0.7417 (m-30) REVERT: A 520 GLU cc_start: 0.7114 (tp30) cc_final: 0.6815 (tp30) REVERT: A 592 PHE cc_start: 0.7258 (t80) cc_final: 0.7017 (t80) REVERT: A 694 LYS cc_start: 0.8326 (tmtt) cc_final: 0.7847 (tptp) REVERT: A 695 ILE cc_start: 0.8775 (pt) cc_final: 0.8540 (pt) REVERT: B 100 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: B 156 ASN cc_start: 0.7617 (m110) cc_final: 0.7318 (m110) REVERT: B 197 GLU cc_start: 0.7097 (mp0) cc_final: 0.6807 (mp0) REVERT: B 200 GLN cc_start: 0.8098 (tt0) cc_final: 0.7542 (mt0) REVERT: B 363 LYS cc_start: 0.7386 (mppt) cc_final: 0.6873 (mppt) REVERT: B 392 ARG cc_start: 0.7897 (ttp-170) cc_final: 0.7605 (ttp80) REVERT: B 485 SER cc_start: 0.7879 (t) cc_final: 0.7465 (t) REVERT: B 520 GLU cc_start: 0.7086 (tp30) cc_final: 0.6679 (tp30) REVERT: B 694 LYS cc_start: 0.8295 (tmtt) cc_final: 0.8049 (tptt) REVERT: C 100 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7008 (mt-10) REVERT: C 169 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8161 (mt) REVERT: C 173 LYS cc_start: 0.8308 (mtmm) cc_final: 0.8086 (mtmm) REVERT: C 195 SER cc_start: 0.8041 (m) cc_final: 0.7537 (t) REVERT: C 197 GLU cc_start: 0.6964 (mp0) cc_final: 0.6590 (mp0) REVERT: C 248 LYS cc_start: 0.8516 (mmtp) cc_final: 0.8174 (mttp) REVERT: C 286 GLU cc_start: 0.7058 (tp30) cc_final: 0.6840 (tp30) REVERT: C 544 GLU cc_start: 0.6669 (tm-30) cc_final: 0.6440 (tm-30) REVERT: C 686 GLU cc_start: 0.7517 (pp20) cc_final: 0.7219 (pp20) REVERT: C 694 LYS cc_start: 0.7985 (tmtt) cc_final: 0.7592 (tptt) REVERT: D 156 ASN cc_start: 0.7712 (m110) cc_final: 0.7392 (m-40) REVERT: D 157 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7544 (mtm180) REVERT: D 195 SER cc_start: 0.8051 (m) cc_final: 0.7722 (t) REVERT: D 196 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6441 (tm-30) REVERT: D 197 GLU cc_start: 0.7033 (mp0) cc_final: 0.6638 (mp0) REVERT: D 201 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7388 (ttp80) REVERT: D 213 TYR cc_start: 0.7843 (t80) cc_final: 0.7551 (t80) REVERT: D 248 LYS cc_start: 0.8383 (mmtp) cc_final: 0.8038 (mttp) REVERT: D 249 ARG cc_start: 0.7401 (mtt90) cc_final: 0.7118 (mtt90) REVERT: D 286 GLU cc_start: 0.6893 (tp30) cc_final: 0.6692 (tp30) REVERT: D 289 ARG cc_start: 0.7734 (ttm-80) cc_final: 0.7402 (mtm-85) REVERT: D 352 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7278 (mm-30) REVERT: D 395 ARG cc_start: 0.7603 (ptp-110) cc_final: 0.7351 (ttp-110) REVERT: D 448 GLU cc_start: 0.7141 (tt0) cc_final: 0.6902 (tt0) REVERT: D 497 ARG cc_start: 0.6878 (mtm180) cc_final: 0.6626 (ptp-170) REVERT: D 565 PHE cc_start: 0.7785 (t80) cc_final: 0.7569 (t80) REVERT: D 609 GLN cc_start: 0.8162 (tp40) cc_final: 0.7803 (tp40) REVERT: D 694 LYS cc_start: 0.8025 (tmtt) cc_final: 0.7630 (tptt) REVERT: D 695 ILE cc_start: 0.8513 (pt) cc_final: 0.8253 (pt) REVERT: E 100 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7609 (mm-30) REVERT: E 189 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7047 (tm-30) REVERT: E 196 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6124 (tm-30) REVERT: E 247 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6547 (tm-30) REVERT: E 340 GLU cc_start: 0.7749 (mp0) cc_final: 0.7395 (mp0) REVERT: E 349 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7909 (mp) REVERT: E 375 LYS cc_start: 0.7941 (mttt) cc_final: 0.7620 (mttm) REVERT: E 413 LYS cc_start: 0.8122 (mmmm) cc_final: 0.7843 (mmtm) REVERT: E 444 LEU cc_start: 0.8552 (mp) cc_final: 0.8342 (mm) REVERT: E 448 GLU cc_start: 0.7134 (tt0) cc_final: 0.6813 (tt0) REVERT: E 485 SER cc_start: 0.7531 (t) cc_final: 0.7004 (t) REVERT: E 522 GLN cc_start: 0.8316 (mt0) cc_final: 0.8112 (mt0) REVERT: E 544 GLU cc_start: 0.6787 (tm-30) cc_final: 0.6486 (tm-30) REVERT: E 609 GLN cc_start: 0.8053 (tp40) cc_final: 0.7828 (tp40) REVERT: E 694 LYS cc_start: 0.8387 (tmtt) cc_final: 0.7937 (tmtt) REVERT: F 71 GLU cc_start: 0.6400 (pm20) cc_final: 0.5993 (pm20) REVERT: F 100 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: F 156 ASN cc_start: 0.7437 (m110) cc_final: 0.7126 (m110) REVERT: F 197 GLU cc_start: 0.6984 (mp0) cc_final: 0.6740 (mp0) REVERT: F 201 ARG cc_start: 0.7545 (mtp180) cc_final: 0.7186 (mtp85) REVERT: F 212 LEU cc_start: 0.8440 (mt) cc_final: 0.8162 (mp) REVERT: F 232 ASN cc_start: 0.8215 (m-40) cc_final: 0.7973 (m-40) REVERT: F 247 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6594 (tm-30) REVERT: F 304 ASP cc_start: 0.7307 (t0) cc_final: 0.7036 (t0) REVERT: F 352 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7333 (mm-30) REVERT: F 383 ASN cc_start: 0.8190 (t0) cc_final: 0.7905 (t0) REVERT: F 450 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6439 (mt-10) REVERT: F 454 ASP cc_start: 0.7496 (m-30) cc_final: 0.7150 (m-30) REVERT: F 484 ARG cc_start: 0.6965 (ttp80) cc_final: 0.6657 (ttp80) REVERT: F 540 THR cc_start: 0.8398 (t) cc_final: 0.8067 (t) REVERT: F 592 PHE cc_start: 0.7484 (t80) cc_final: 0.7282 (t80) REVERT: F 609 GLN cc_start: 0.7833 (tp40) cc_final: 0.7303 (tp40) REVERT: F 612 MET cc_start: 0.7270 (tpp) cc_final: 0.6701 (tpp) REVERT: F 638 TRP cc_start: 0.6990 (m-90) cc_final: 0.6636 (m-90) REVERT: F 694 LYS cc_start: 0.8225 (tmtt) cc_final: 0.7845 (tptp) REVERT: G 100 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: G 157 ARG cc_start: 0.8287 (mtp180) cc_final: 0.7989 (ttm110) REVERT: G 189 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7700 (tm-30) REVERT: G 197 GLU cc_start: 0.6891 (mp0) cc_final: 0.6620 (mp0) REVERT: G 340 GLU cc_start: 0.7916 (mp0) cc_final: 0.7633 (mp0) REVERT: G 349 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7899 (mp) REVERT: G 376 ARG cc_start: 0.6235 (mtt-85) cc_final: 0.5797 (mtt-85) REVERT: G 694 LYS cc_start: 0.8336 (tmtt) cc_final: 0.7893 (tmtt) REVERT: H 100 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7755 (mm-30) REVERT: H 156 ASN cc_start: 0.7581 (m110) cc_final: 0.7294 (m110) REVERT: H 201 ARG cc_start: 0.7639 (mtp180) cc_final: 0.7337 (mtp85) REVERT: H 209 ASP cc_start: 0.7480 (t0) cc_final: 0.7226 (t0) REVERT: H 280 ASN cc_start: 0.8110 (t0) cc_final: 0.7875 (t0) REVERT: H 340 GLU cc_start: 0.7576 (mp0) cc_final: 0.7150 (mp0) REVERT: H 352 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7124 (mm-30) REVERT: H 363 LYS cc_start: 0.7467 (mppt) cc_final: 0.6966 (mppt) REVERT: H 383 ASN cc_start: 0.8300 (t0) cc_final: 0.8011 (t0) REVERT: H 454 ASP cc_start: 0.7575 (m-30) cc_final: 0.7294 (m-30) REVERT: H 540 THR cc_start: 0.8450 (m) cc_final: 0.8079 (t) REVERT: H 544 GLU cc_start: 0.7069 (tm-30) cc_final: 0.6800 (tm-30) REVERT: H 682 LYS cc_start: 0.6981 (tptp) cc_final: 0.6493 (tptp) outliers start: 124 outliers final: 66 residues processed: 1119 average time/residue: 0.5859 time to fit residues: 1002.4536 Evaluate side-chains 1072 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 997 time to evaluate : 4.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 484 ARG Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 654 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 424 optimal weight: 1.9990 chunk 322 optimal weight: 1.9990 chunk 222 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 chunk 288 optimal weight: 9.9990 chunk 430 optimal weight: 1.9990 chunk 456 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 408 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 522 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN D 522 GLN D 571 ASN D 585 GLN D 587 HIS D 685 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN E 200 GLN E 422 GLN E 571 ASN F 73 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 437 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37552 Z= 0.283 Angle : 0.653 12.006 50728 Z= 0.323 Chirality : 0.043 0.242 5848 Planarity : 0.005 0.048 6536 Dihedral : 4.692 24.066 5128 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.37 % Allowed : 17.86 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.12), residues: 4624 helix: 0.18 (0.09), residues: 3136 sheet: -2.78 (0.37), residues: 160 loop : -1.97 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 662 HIS 0.020 0.001 HIS B 685 PHE 0.022 0.002 PHE E 565 TYR 0.016 0.002 TYR G 380 ARG 0.007 0.000 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1016 time to evaluate : 4.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 SER cc_start: 0.7971 (m) cc_final: 0.7568 (t) REVERT: A 196 GLU cc_start: 0.6931 (tm-30) cc_final: 0.6207 (tm-30) REVERT: A 197 GLU cc_start: 0.6942 (mp0) cc_final: 0.6662 (mp0) REVERT: A 209 ASP cc_start: 0.7615 (t0) cc_final: 0.7256 (t0) REVERT: A 392 ARG cc_start: 0.7921 (ttm170) cc_final: 0.7442 (ttp-110) REVERT: A 395 ARG cc_start: 0.7652 (ptp-110) cc_final: 0.7435 (ttm110) REVERT: A 483 ASP cc_start: 0.7965 (t0) cc_final: 0.7567 (t0) REVERT: A 520 GLU cc_start: 0.7156 (tp30) cc_final: 0.6832 (tp30) REVERT: A 592 PHE cc_start: 0.7276 (t80) cc_final: 0.7007 (t80) REVERT: A 694 LYS cc_start: 0.8283 (tmtt) cc_final: 0.7790 (tptp) REVERT: A 695 ILE cc_start: 0.8785 (pt) cc_final: 0.8538 (pt) REVERT: B 100 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7153 (mt-10) REVERT: B 156 ASN cc_start: 0.7557 (m110) cc_final: 0.7268 (m110) REVERT: B 197 GLU cc_start: 0.7108 (mp0) cc_final: 0.6778 (mp0) REVERT: B 200 GLN cc_start: 0.8092 (tt0) cc_final: 0.7543 (mt0) REVERT: B 363 LYS cc_start: 0.7424 (mppt) cc_final: 0.6898 (mppt) REVERT: B 454 ASP cc_start: 0.7445 (m-30) cc_final: 0.7164 (m-30) REVERT: B 485 SER cc_start: 0.7849 (t) cc_final: 0.7356 (t) REVERT: B 520 GLU cc_start: 0.7116 (tp30) cc_final: 0.6679 (tp30) REVERT: B 540 THR cc_start: 0.8550 (t) cc_final: 0.8252 (t) REVERT: B 694 LYS cc_start: 0.8324 (tmtt) cc_final: 0.7951 (tptp) REVERT: C 100 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: C 169 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7861 (mt) REVERT: C 173 LYS cc_start: 0.8328 (mtmm) cc_final: 0.7890 (mtmm) REVERT: C 195 SER cc_start: 0.7950 (m) cc_final: 0.7472 (t) REVERT: C 196 GLU cc_start: 0.6915 (tm-30) cc_final: 0.6185 (tm-30) REVERT: C 197 GLU cc_start: 0.6986 (mp0) cc_final: 0.6674 (mp0) REVERT: C 248 LYS cc_start: 0.8496 (mmtp) cc_final: 0.8141 (mttp) REVERT: C 392 ARG cc_start: 0.8042 (ttm170) cc_final: 0.7648 (ttp-110) REVERT: C 413 LYS cc_start: 0.8112 (mmmm) cc_final: 0.7543 (mmtm) REVERT: C 431 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6363 (pm20) REVERT: C 544 GLU cc_start: 0.6747 (tm-30) cc_final: 0.6511 (tm-30) REVERT: C 586 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8497 (mm) REVERT: C 686 GLU cc_start: 0.7510 (pp20) cc_final: 0.7218 (pp20) REVERT: C 694 LYS cc_start: 0.8037 (tmtt) cc_final: 0.7609 (tptt) REVERT: D 156 ASN cc_start: 0.7683 (m110) cc_final: 0.7372 (m110) REVERT: D 157 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7736 (mtm-85) REVERT: D 195 SER cc_start: 0.8042 (m) cc_final: 0.7675 (t) REVERT: D 196 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6510 (tm-30) REVERT: D 197 GLU cc_start: 0.7074 (mp0) cc_final: 0.6626 (mp0) REVERT: D 201 ARG cc_start: 0.7647 (mtp180) cc_final: 0.7389 (ttp80) REVERT: D 213 TYR cc_start: 0.7930 (t80) cc_final: 0.7630 (t80) REVERT: D 247 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6612 (tm-30) REVERT: D 248 LYS cc_start: 0.8361 (mmtp) cc_final: 0.7864 (mttp) REVERT: D 352 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7259 (mm-30) REVERT: D 395 ARG cc_start: 0.7587 (ptp-110) cc_final: 0.7352 (ttp-110) REVERT: D 448 GLU cc_start: 0.7159 (tt0) cc_final: 0.6794 (tt0) REVERT: D 485 SER cc_start: 0.7806 (t) cc_final: 0.7229 (t) REVERT: D 609 GLN cc_start: 0.8151 (tp40) cc_final: 0.7799 (tp40) REVERT: D 694 LYS cc_start: 0.8010 (tmtt) cc_final: 0.7694 (tptt) REVERT: D 695 ILE cc_start: 0.8521 (pt) cc_final: 0.8297 (pt) REVERT: E 100 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7540 (mm-30) REVERT: E 157 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.8032 (ttm110) REVERT: E 196 GLU cc_start: 0.6858 (tm-30) cc_final: 0.5789 (tm-30) REVERT: E 197 GLU cc_start: 0.6655 (mp0) cc_final: 0.6396 (mp0) REVERT: E 200 GLN cc_start: 0.7982 (mt0) cc_final: 0.7449 (mt0) REVERT: E 349 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7939 (mp) REVERT: E 375 LYS cc_start: 0.7938 (mttt) cc_final: 0.7595 (mttm) REVERT: E 540 THR cc_start: 0.8394 (m) cc_final: 0.8010 (t) REVERT: E 544 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6623 (tm-30) REVERT: E 586 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8391 (mm) REVERT: E 694 LYS cc_start: 0.8386 (tmtt) cc_final: 0.7929 (tmtt) REVERT: F 71 GLU cc_start: 0.6288 (pm20) cc_final: 0.5881 (pm20) REVERT: F 156 ASN cc_start: 0.7427 (m110) cc_final: 0.7102 (m110) REVERT: F 196 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6813 (tm-30) REVERT: F 197 GLU cc_start: 0.7037 (mp0) cc_final: 0.6775 (mp0) REVERT: F 201 ARG cc_start: 0.7548 (mtp180) cc_final: 0.7208 (mtp85) REVERT: F 212 LEU cc_start: 0.8319 (mt) cc_final: 0.7961 (mp) REVERT: F 232 ASN cc_start: 0.8220 (m-40) cc_final: 0.7974 (m-40) REVERT: F 247 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6603 (tm-30) REVERT: F 304 ASP cc_start: 0.7295 (t0) cc_final: 0.7052 (t70) REVERT: F 352 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7328 (mm-30) REVERT: F 383 ASN cc_start: 0.8152 (t0) cc_final: 0.7907 (t0) REVERT: F 450 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6410 (mt-10) REVERT: F 454 ASP cc_start: 0.7459 (m-30) cc_final: 0.7125 (m-30) REVERT: F 484 ARG cc_start: 0.6945 (ttp80) cc_final: 0.6658 (ttp80) REVERT: F 520 GLU cc_start: 0.7032 (tp30) cc_final: 0.6663 (tp30) REVERT: F 540 THR cc_start: 0.8454 (t) cc_final: 0.8132 (t) REVERT: F 544 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6867 (tm-30) REVERT: F 592 PHE cc_start: 0.7472 (t80) cc_final: 0.7238 (t80) REVERT: F 609 GLN cc_start: 0.7825 (tp40) cc_final: 0.7287 (tp40) REVERT: F 612 MET cc_start: 0.7274 (tpp) cc_final: 0.6686 (tpp) REVERT: F 638 TRP cc_start: 0.6973 (m-90) cc_final: 0.6643 (m-90) REVERT: F 694 LYS cc_start: 0.8229 (tmtt) cc_final: 0.7857 (tptp) REVERT: G 100 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: G 157 ARG cc_start: 0.8282 (mtp180) cc_final: 0.8045 (ttm110) REVERT: G 197 GLU cc_start: 0.6933 (mp0) cc_final: 0.6648 (mp0) REVERT: G 247 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6559 (tm-30) REVERT: G 349 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7830 (mp) REVERT: G 376 ARG cc_start: 0.6197 (mtt-85) cc_final: 0.5815 (mtt-85) REVERT: G 694 LYS cc_start: 0.8296 (tmtt) cc_final: 0.7822 (tmtt) REVERT: H 100 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7613 (mm-30) REVERT: H 156 ASN cc_start: 0.7526 (m110) cc_final: 0.7231 (m110) REVERT: H 189 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7712 (tm-30) REVERT: H 197 GLU cc_start: 0.7026 (mp0) cc_final: 0.6728 (mp0) REVERT: H 201 ARG cc_start: 0.7634 (mtp180) cc_final: 0.7336 (mtp85) REVERT: H 209 ASP cc_start: 0.7515 (t0) cc_final: 0.7225 (t0) REVERT: H 352 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7124 (mm-30) REVERT: H 363 LYS cc_start: 0.7410 (mppt) cc_final: 0.6898 (mppt) REVERT: H 383 ASN cc_start: 0.8203 (t0) cc_final: 0.7914 (t0) REVERT: H 454 ASP cc_start: 0.7511 (m-30) cc_final: 0.7270 (m-30) REVERT: H 485 SER cc_start: 0.7916 (t) cc_final: 0.7476 (t) REVERT: H 540 THR cc_start: 0.8427 (m) cc_final: 0.8041 (t) REVERT: H 544 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6825 (tm-30) REVERT: H 592 PHE cc_start: 0.7556 (t80) cc_final: 0.7270 (t80) REVERT: H 612 MET cc_start: 0.6915 (tpp) cc_final: 0.6452 (tpp) REVERT: H 693 GLU cc_start: 0.7098 (tp30) cc_final: 0.6853 (tp30) REVERT: H 694 LYS cc_start: 0.8343 (tptt) cc_final: 0.8110 (tptp) outliers start: 132 outliers final: 67 residues processed: 1082 average time/residue: 0.5559 time to fit residues: 914.1062 Evaluate side-chains 1065 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 987 time to evaluate : 4.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 379 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 339 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 389 optimal weight: 0.0770 chunk 315 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 232 optimal weight: 5.9990 chunk 409 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN D 73 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 422 GLN D 522 GLN D 585 GLN D 587 HIS E 73 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 37552 Z= 0.424 Angle : 0.702 12.498 50728 Z= 0.355 Chirality : 0.046 0.234 5848 Planarity : 0.005 0.054 6536 Dihedral : 4.938 25.896 5128 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.01 % Allowed : 18.60 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.12), residues: 4624 helix: -0.03 (0.09), residues: 3088 sheet: -2.70 (0.38), residues: 160 loop : -1.94 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 420 HIS 0.034 0.001 HIS D 685 PHE 0.023 0.002 PHE E 565 TYR 0.019 0.002 TYR G 568 ARG 0.007 0.001 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1027 time to evaluate : 3.760 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 100 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7212 (mm-30) REVERT: A 155 GLU cc_start: 0.6965 (mp0) cc_final: 0.6745 (mp0) REVERT: A 157 ARG cc_start: 0.8317 (mtm-85) cc_final: 0.8057 (ttm110) REVERT: A 173 LYS cc_start: 0.8292 (mtmm) cc_final: 0.8020 (mtmm) REVERT: A 195 SER cc_start: 0.8077 (m) cc_final: 0.7812 (t) REVERT: A 196 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6343 (tm-30) REVERT: A 197 GLU cc_start: 0.6951 (mp0) cc_final: 0.6747 (mp0) REVERT: A 200 GLN cc_start: 0.8077 (tt0) cc_final: 0.7693 (tt0) REVERT: A 209 ASP cc_start: 0.7692 (t0) cc_final: 0.7283 (t0) REVERT: A 444 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8283 (mt) REVERT: A 483 ASP cc_start: 0.8001 (t0) cc_final: 0.7417 (t70) REVERT: A 489 ASP cc_start: 0.7685 (m-30) cc_final: 0.7485 (m-30) REVERT: A 520 GLU cc_start: 0.7182 (tp30) cc_final: 0.6866 (tp30) REVERT: A 592 PHE cc_start: 0.7370 (t80) cc_final: 0.7093 (t80) REVERT: A 694 LYS cc_start: 0.8345 (tmtt) cc_final: 0.7855 (tptp) REVERT: A 695 ILE cc_start: 0.8788 (pt) cc_final: 0.8550 (pt) REVERT: B 94 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6682 (pm20) REVERT: B 100 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7255 (mt-10) REVERT: B 156 ASN cc_start: 0.7533 (m110) cc_final: 0.7249 (m110) REVERT: B 197 GLU cc_start: 0.7132 (mp0) cc_final: 0.6832 (mp0) REVERT: B 200 GLN cc_start: 0.8185 (tt0) cc_final: 0.7620 (mt0) REVERT: B 363 LYS cc_start: 0.7534 (mppt) cc_final: 0.7028 (mppt) REVERT: B 392 ARG cc_start: 0.7988 (ttp-170) cc_final: 0.7784 (ttp-170) REVERT: B 416 GLU cc_start: 0.6295 (mp0) cc_final: 0.6026 (mp0) REVERT: B 454 ASP cc_start: 0.7449 (m-30) cc_final: 0.7164 (m-30) REVERT: B 520 GLU cc_start: 0.7148 (tp30) cc_final: 0.6696 (tp30) REVERT: B 587 HIS cc_start: 0.8416 (m90) cc_final: 0.8134 (m90) REVERT: B 694 LYS cc_start: 0.8477 (tmtt) cc_final: 0.8090 (tptp) REVERT: C 100 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: C 169 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7786 (mt) REVERT: C 173 LYS cc_start: 0.8375 (mtmm) cc_final: 0.7953 (mtmm) REVERT: C 189 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7719 (tm-30) REVERT: C 195 SER cc_start: 0.8138 (m) cc_final: 0.7666 (t) REVERT: C 196 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6351 (tm-30) REVERT: C 197 GLU cc_start: 0.6988 (mp0) cc_final: 0.6387 (mp0) REVERT: C 200 GLN cc_start: 0.8041 (tt0) cc_final: 0.7699 (tt0) REVERT: C 247 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6523 (tm-30) REVERT: C 248 LYS cc_start: 0.8501 (mmtp) cc_final: 0.7962 (mttp) REVERT: C 392 ARG cc_start: 0.8074 (ttm170) cc_final: 0.7665 (ttp-110) REVERT: C 413 LYS cc_start: 0.8208 (mmmm) cc_final: 0.7608 (mmtm) REVERT: C 444 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8271 (mt) REVERT: C 544 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6612 (tm-30) REVERT: C 694 LYS cc_start: 0.8134 (tmtt) cc_final: 0.7656 (tmtt) REVERT: D 100 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: D 156 ASN cc_start: 0.7693 (m110) cc_final: 0.7333 (m110) REVERT: D 157 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7827 (mtm-85) REVERT: D 189 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7711 (tm-30) REVERT: D 195 SER cc_start: 0.8101 (m) cc_final: 0.7726 (t) REVERT: D 196 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6422 (tm-30) REVERT: D 197 GLU cc_start: 0.7088 (mp0) cc_final: 0.6650 (mp0) REVERT: D 200 GLN cc_start: 0.7994 (tt0) cc_final: 0.7598 (tt0) REVERT: D 201 ARG cc_start: 0.7686 (mtp180) cc_final: 0.7415 (ttp80) REVERT: D 215 CYS cc_start: 0.7074 (m) cc_final: 0.6803 (m) REVERT: D 247 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6645 (tm-30) REVERT: D 248 LYS cc_start: 0.8395 (mmtp) cc_final: 0.7910 (mttp) REVERT: D 352 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7261 (mm-30) REVERT: D 363 LYS cc_start: 0.7570 (mppt) cc_final: 0.7160 (mppt) REVERT: D 395 ARG cc_start: 0.7661 (ptp-110) cc_final: 0.7348 (ttp-110) REVERT: D 448 GLU cc_start: 0.7229 (tt0) cc_final: 0.6797 (mt-10) REVERT: D 609 GLN cc_start: 0.8184 (tp40) cc_final: 0.7837 (tp40) REVERT: D 694 LYS cc_start: 0.8156 (tmtt) cc_final: 0.7744 (tptt) REVERT: D 695 ILE cc_start: 0.8585 (pt) cc_final: 0.8369 (pt) REVERT: E 100 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: E 196 GLU cc_start: 0.6938 (tm-30) cc_final: 0.5817 (tm-30) REVERT: E 200 GLN cc_start: 0.8053 (mt0) cc_final: 0.7403 (mt0) REVERT: E 247 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6628 (tm-30) REVERT: E 296 VAL cc_start: 0.7537 (m) cc_final: 0.7191 (t) REVERT: E 349 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7952 (mp) REVERT: E 448 GLU cc_start: 0.7049 (tt0) cc_final: 0.6807 (tt0) REVERT: E 540 THR cc_start: 0.8429 (m) cc_final: 0.8070 (t) REVERT: E 544 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6648 (tm-30) REVERT: E 694 LYS cc_start: 0.8478 (tmtt) cc_final: 0.7802 (tptt) REVERT: F 71 GLU cc_start: 0.6593 (pm20) cc_final: 0.6158 (pm20) REVERT: F 156 ASN cc_start: 0.7461 (m110) cc_final: 0.7127 (m110) REVERT: F 197 GLU cc_start: 0.7065 (mp0) cc_final: 0.6789 (mp0) REVERT: F 201 ARG cc_start: 0.7590 (mtp180) cc_final: 0.7252 (mtp85) REVERT: F 212 LEU cc_start: 0.8259 (mt) cc_final: 0.8030 (mp) REVERT: F 247 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6662 (tm-30) REVERT: F 352 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7394 (mm-30) REVERT: F 363 LYS cc_start: 0.7446 (mppt) cc_final: 0.6989 (mppt) REVERT: F 383 ASN cc_start: 0.8305 (t0) cc_final: 0.8022 (t0) REVERT: F 450 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6480 (mt-10) REVERT: F 454 ASP cc_start: 0.7446 (m-30) cc_final: 0.7128 (m-30) REVERT: F 484 ARG cc_start: 0.6987 (ttp80) cc_final: 0.6741 (ttp80) REVERT: F 520 GLU cc_start: 0.7082 (tp30) cc_final: 0.6698 (tp30) REVERT: F 540 THR cc_start: 0.8537 (t) cc_final: 0.8256 (t) REVERT: F 544 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6946 (tm-30) REVERT: F 592 PHE cc_start: 0.7561 (t80) cc_final: 0.7290 (t80) REVERT: F 609 GLN cc_start: 0.7815 (tp40) cc_final: 0.7269 (tp40) REVERT: F 612 MET cc_start: 0.7325 (tpp) cc_final: 0.6725 (tpp) REVERT: F 638 TRP cc_start: 0.6997 (m-90) cc_final: 0.6684 (m-90) REVERT: F 694 LYS cc_start: 0.8375 (tmtt) cc_final: 0.7974 (tptp) REVERT: G 100 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: G 155 GLU cc_start: 0.7069 (mp0) cc_final: 0.6799 (mp0) REVERT: G 157 ARG cc_start: 0.8305 (mtp180) cc_final: 0.8006 (ttm110) REVERT: G 196 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6268 (tm-30) REVERT: G 197 GLU cc_start: 0.6963 (mp0) cc_final: 0.6719 (mp0) REVERT: G 244 ARG cc_start: 0.7136 (mmm160) cc_final: 0.6823 (tpp-160) REVERT: G 247 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6607 (tm-30) REVERT: G 325 ASP cc_start: 0.6652 (t70) cc_final: 0.6448 (t70) REVERT: G 349 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7917 (mp) REVERT: G 376 ARG cc_start: 0.6242 (mtt-85) cc_final: 0.5929 (mtt-85) REVERT: G 444 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8431 (mt) REVERT: G 485 SER cc_start: 0.7761 (t) cc_final: 0.7257 (t) REVERT: G 592 PHE cc_start: 0.7452 (t80) cc_final: 0.7140 (t80) REVERT: G 694 LYS cc_start: 0.8344 (tmtt) cc_final: 0.7904 (tmtt) REVERT: H 100 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7616 (mm-30) REVERT: H 156 ASN cc_start: 0.7566 (m110) cc_final: 0.7251 (m110) REVERT: H 196 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6733 (tm-30) REVERT: H 197 GLU cc_start: 0.7105 (mp0) cc_final: 0.6795 (mp0) REVERT: H 201 ARG cc_start: 0.7653 (mtp180) cc_final: 0.7370 (mtp85) REVERT: H 209 ASP cc_start: 0.7617 (t0) cc_final: 0.7304 (t0) REVERT: H 247 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6619 (tm-30) REVERT: H 352 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7129 (mm-30) REVERT: H 363 LYS cc_start: 0.7550 (mppt) cc_final: 0.7085 (mppt) REVERT: H 454 ASP cc_start: 0.7521 (m-30) cc_final: 0.7259 (m-30) REVERT: H 485 SER cc_start: 0.7929 (t) cc_final: 0.7425 (t) REVERT: H 544 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6812 (tm-30) REVERT: H 592 PHE cc_start: 0.7681 (t80) cc_final: 0.7424 (t80) REVERT: H 612 MET cc_start: 0.6989 (tpp) cc_final: 0.6514 (tpp) REVERT: H 693 GLU cc_start: 0.7167 (tp30) cc_final: 0.6914 (tp30) REVERT: H 694 LYS cc_start: 0.8411 (tptt) cc_final: 0.8202 (tptt) outliers start: 157 outliers final: 96 residues processed: 1108 average time/residue: 0.5463 time to fit residues: 922.0863 Evaluate side-chains 1111 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1001 time to evaluate : 4.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 484 ARG Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 191 MET Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 654 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 153 optimal weight: 2.9990 chunk 410 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 456 optimal weight: 0.5980 chunk 379 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 239 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 422 GLN D 522 GLN D 585 GLN D 587 HIS D 685 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN F 522 GLN F 652 ASN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37552 Z= 0.219 Angle : 0.642 12.608 50728 Z= 0.314 Chirality : 0.041 0.198 5848 Planarity : 0.004 0.049 6536 Dihedral : 4.641 23.812 5128 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.65 % Allowed : 20.15 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4624 helix: 0.31 (0.10), residues: 3136 sheet: -2.59 (0.38), residues: 160 loop : -2.06 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 662 HIS 0.013 0.001 HIS B 685 PHE 0.023 0.001 PHE E 565 TYR 0.016 0.001 TYR G 568 ARG 0.008 0.000 ARG E 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1028 time to evaluate : 4.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.6864 (mp0) cc_final: 0.6650 (mp0) REVERT: A 157 ARG cc_start: 0.8259 (mtm-85) cc_final: 0.8010 (ttm110) REVERT: A 195 SER cc_start: 0.7997 (m) cc_final: 0.7737 (t) REVERT: A 196 GLU cc_start: 0.7054 (tm-30) cc_final: 0.5853 (tm-30) REVERT: A 197 GLU cc_start: 0.6953 (mp0) cc_final: 0.6735 (mp0) REVERT: A 200 GLN cc_start: 0.8047 (tt0) cc_final: 0.7136 (mt0) REVERT: A 376 ARG cc_start: 0.6533 (mtm-85) cc_final: 0.6290 (mtm-85) REVERT: A 392 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7459 (ttp-110) REVERT: A 444 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8296 (mt) REVERT: A 483 ASP cc_start: 0.7960 (t0) cc_final: 0.7660 (t0) REVERT: A 520 GLU cc_start: 0.7174 (tp30) cc_final: 0.6860 (tp30) REVERT: A 586 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8472 (mm) REVERT: A 592 PHE cc_start: 0.7325 (t80) cc_final: 0.7059 (t80) REVERT: A 609 GLN cc_start: 0.8040 (tp40) cc_final: 0.7418 (tp40) REVERT: A 694 LYS cc_start: 0.8266 (tmtt) cc_final: 0.7764 (tptp) REVERT: A 695 ILE cc_start: 0.8784 (pt) cc_final: 0.8528 (pt) REVERT: B 100 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7235 (mt-10) REVERT: B 156 ASN cc_start: 0.7401 (m110) cc_final: 0.7141 (m110) REVERT: B 197 GLU cc_start: 0.7032 (mp0) cc_final: 0.6720 (mp0) REVERT: B 200 GLN cc_start: 0.8128 (tt0) cc_final: 0.7574 (mt0) REVERT: B 363 LYS cc_start: 0.7486 (mppt) cc_final: 0.6970 (mppt) REVERT: B 392 ARG cc_start: 0.7948 (ttp-170) cc_final: 0.7740 (ttp-170) REVERT: B 416 GLU cc_start: 0.6269 (mp0) cc_final: 0.5965 (mp0) REVERT: B 454 ASP cc_start: 0.7406 (m-30) cc_final: 0.7125 (m-30) REVERT: B 520 GLU cc_start: 0.7116 (tp30) cc_final: 0.6698 (tp30) REVERT: B 540 THR cc_start: 0.8471 (t) cc_final: 0.8167 (t) REVERT: B 694 LYS cc_start: 0.8406 (tmtt) cc_final: 0.8015 (tptp) REVERT: C 100 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: C 149 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7158 (mm-30) REVERT: C 169 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7736 (mt) REVERT: C 173 LYS cc_start: 0.8339 (mtmm) cc_final: 0.7893 (mtmm) REVERT: C 195 SER cc_start: 0.8003 (m) cc_final: 0.7548 (t) REVERT: C 196 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6305 (tm-30) REVERT: C 197 GLU cc_start: 0.6990 (mp0) cc_final: 0.6358 (mp0) REVERT: C 200 GLN cc_start: 0.8008 (tt0) cc_final: 0.7623 (tt0) REVERT: C 247 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6528 (tm-30) REVERT: C 248 LYS cc_start: 0.8466 (mmtp) cc_final: 0.7948 (mttp) REVERT: C 392 ARG cc_start: 0.8033 (ttm170) cc_final: 0.7636 (ttp-110) REVERT: C 444 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8265 (mt) REVERT: C 544 GLU cc_start: 0.6813 (tm-30) cc_final: 0.6544 (tm-30) REVERT: C 694 LYS cc_start: 0.8186 (tmtt) cc_final: 0.7742 (tmtt) REVERT: D 100 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: D 156 ASN cc_start: 0.7652 (m110) cc_final: 0.7327 (m110) REVERT: D 157 ARG cc_start: 0.8037 (mtt180) cc_final: 0.7617 (mtm180) REVERT: D 189 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7724 (tm-30) REVERT: D 195 SER cc_start: 0.7961 (m) cc_final: 0.7601 (t) REVERT: D 196 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6352 (tm-30) REVERT: D 197 GLU cc_start: 0.7088 (mp0) cc_final: 0.6643 (mp0) REVERT: D 200 GLN cc_start: 0.7924 (tt0) cc_final: 0.7553 (tt0) REVERT: D 201 ARG cc_start: 0.7647 (mtp180) cc_final: 0.7374 (ttp80) REVERT: D 247 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6618 (tm-30) REVERT: D 248 LYS cc_start: 0.8372 (mmtp) cc_final: 0.7854 (mttp) REVERT: D 352 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7275 (mm-30) REVERT: D 363 LYS cc_start: 0.7475 (mppt) cc_final: 0.7061 (mppt) REVERT: D 392 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7627 (ttp-110) REVERT: D 395 ARG cc_start: 0.7560 (ptp-110) cc_final: 0.7296 (ttp-110) REVERT: D 448 GLU cc_start: 0.7119 (tt0) cc_final: 0.6298 (mm-30) REVERT: D 485 SER cc_start: 0.7813 (t) cc_final: 0.7223 (t) REVERT: D 520 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6902 (tm-30) REVERT: D 540 THR cc_start: 0.8609 (t) cc_final: 0.8343 (t) REVERT: D 609 GLN cc_start: 0.8128 (tp40) cc_final: 0.7773 (tp40) REVERT: D 694 LYS cc_start: 0.8138 (tmtt) cc_final: 0.7719 (tptt) REVERT: D 695 ILE cc_start: 0.8559 (pt) cc_final: 0.8338 (pt) REVERT: E 100 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7536 (mm-30) REVERT: E 157 ARG cc_start: 0.8250 (mtm-85) cc_final: 0.8022 (ttm110) REVERT: E 196 GLU cc_start: 0.6961 (tm-30) cc_final: 0.5800 (tm-30) REVERT: E 200 GLN cc_start: 0.8004 (mt0) cc_final: 0.7351 (mt0) REVERT: E 247 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6601 (tm-30) REVERT: E 296 VAL cc_start: 0.7454 (m) cc_final: 0.6918 (t) REVERT: E 349 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7970 (mp) REVERT: E 376 ARG cc_start: 0.6732 (mtt-85) cc_final: 0.6508 (mtt-85) REVERT: E 540 THR cc_start: 0.8447 (m) cc_final: 0.8066 (t) REVERT: E 544 GLU cc_start: 0.6960 (tm-30) cc_final: 0.6646 (tm-30) REVERT: E 694 LYS cc_start: 0.8416 (tmtt) cc_final: 0.7810 (tptt) REVERT: F 133 LEU cc_start: 0.8399 (mp) cc_final: 0.8185 (mm) REVERT: F 156 ASN cc_start: 0.7435 (m110) cc_final: 0.7124 (m110) REVERT: F 196 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6233 (tm-30) REVERT: F 197 GLU cc_start: 0.7135 (mp0) cc_final: 0.6800 (mp0) REVERT: F 200 GLN cc_start: 0.8126 (tt0) cc_final: 0.7568 (mt0) REVERT: F 201 ARG cc_start: 0.7516 (mtp180) cc_final: 0.7175 (mtp85) REVERT: F 247 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6615 (tm-30) REVERT: F 352 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7326 (mm-30) REVERT: F 363 LYS cc_start: 0.7425 (mppt) cc_final: 0.6923 (mppt) REVERT: F 444 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8471 (mt) REVERT: F 450 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6381 (mt-10) REVERT: F 454 ASP cc_start: 0.7438 (m-30) cc_final: 0.7107 (m-30) REVERT: F 520 GLU cc_start: 0.7047 (tp30) cc_final: 0.6640 (tp30) REVERT: F 540 THR cc_start: 0.8593 (t) cc_final: 0.8289 (t) REVERT: F 544 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6946 (tm-30) REVERT: F 592 PHE cc_start: 0.7484 (t80) cc_final: 0.7236 (t80) REVERT: F 609 GLN cc_start: 0.7856 (tp40) cc_final: 0.7306 (tp40) REVERT: F 612 MET cc_start: 0.7282 (tpp) cc_final: 0.6688 (tpp) REVERT: F 638 TRP cc_start: 0.6958 (m-90) cc_final: 0.6531 (m-90) REVERT: F 694 LYS cc_start: 0.8347 (tmtt) cc_final: 0.7952 (tptp) REVERT: G 100 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7471 (mm-30) REVERT: G 157 ARG cc_start: 0.8276 (mtp180) cc_final: 0.8002 (ttm110) REVERT: G 196 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6403 (tm-30) REVERT: G 200 GLN cc_start: 0.7968 (tt0) cc_final: 0.7647 (tt0) REVERT: G 247 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6602 (tm-30) REVERT: G 325 ASP cc_start: 0.6633 (t70) cc_final: 0.6424 (t70) REVERT: G 349 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7815 (mp) REVERT: G 392 ARG cc_start: 0.8055 (ttm170) cc_final: 0.7567 (ttp-110) REVERT: G 444 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8437 (mt) REVERT: G 592 PHE cc_start: 0.7417 (t80) cc_final: 0.7081 (t80) REVERT: G 694 LYS cc_start: 0.8297 (tmtt) cc_final: 0.7811 (tmtt) REVERT: H 100 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7742 (mm-30) REVERT: H 156 ASN cc_start: 0.7505 (m110) cc_final: 0.7226 (m110) REVERT: H 159 ARG cc_start: 0.8087 (tpt90) cc_final: 0.7773 (tpt90) REVERT: H 196 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6840 (tm-30) REVERT: H 197 GLU cc_start: 0.7051 (mp0) cc_final: 0.6705 (mp0) REVERT: H 201 ARG cc_start: 0.7589 (mtp180) cc_final: 0.7274 (mtp85) REVERT: H 209 ASP cc_start: 0.7577 (t0) cc_final: 0.7276 (t0) REVERT: H 247 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6636 (tm-30) REVERT: H 352 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7124 (mm-30) REVERT: H 363 LYS cc_start: 0.7485 (mppt) cc_final: 0.7240 (tppt) REVERT: H 485 SER cc_start: 0.7942 (t) cc_final: 0.7445 (t) REVERT: H 540 THR cc_start: 0.8401 (m) cc_final: 0.7949 (t) REVERT: H 544 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6816 (tm-30) REVERT: H 592 PHE cc_start: 0.7723 (t80) cc_final: 0.7387 (t80) REVERT: H 612 MET cc_start: 0.6909 (tpp) cc_final: 0.6454 (tpp) REVERT: H 693 GLU cc_start: 0.7092 (tp30) cc_final: 0.6844 (tp30) REVERT: H 694 LYS cc_start: 0.8402 (tptt) cc_final: 0.8160 (tptt) outliers start: 143 outliers final: 90 residues processed: 1105 average time/residue: 0.5548 time to fit residues: 932.0890 Evaluate side-chains 1103 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 999 time to evaluate : 4.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 191 MET Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 458 LYS Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 654 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Chi-restraints excluded: chain H residue 687 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 440 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 260 optimal weight: 4.9990 chunk 333 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 384 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 chunk 454 optimal weight: 0.6980 chunk 284 optimal weight: 5.9990 chunk 277 optimal weight: 0.7980 chunk 210 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 522 GLN A 585 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 422 GLN D 522 GLN D 585 GLN D 587 HIS D 685 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 585 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN F 585 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN G 585 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37552 Z= 0.212 Angle : 0.641 13.186 50728 Z= 0.314 Chirality : 0.041 0.187 5848 Planarity : 0.004 0.047 6536 Dihedral : 4.532 23.760 5128 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.42 % Allowed : 20.87 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 4624 helix: 0.46 (0.10), residues: 3144 sheet: -2.51 (0.39), residues: 160 loop : -2.04 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 662 HIS 0.018 0.001 HIS D 685 PHE 0.024 0.001 PHE E 565 TYR 0.026 0.001 TYR A 479 ARG 0.010 0.000 ARG E 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1025 time to evaluate : 4.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: A 155 GLU cc_start: 0.6865 (mp0) cc_final: 0.6654 (mp0) REVERT: A 157 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.8010 (ttm110) REVERT: A 195 SER cc_start: 0.8038 (m) cc_final: 0.7722 (t) REVERT: A 196 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6375 (tm-30) REVERT: A 197 GLU cc_start: 0.6966 (mp0) cc_final: 0.6735 (mp0) REVERT: A 200 GLN cc_start: 0.8038 (tt0) cc_final: 0.7639 (tt0) REVERT: A 376 ARG cc_start: 0.6568 (mtm-85) cc_final: 0.6289 (mtm-85) REVERT: A 444 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8295 (mt) REVERT: A 483 ASP cc_start: 0.7972 (t0) cc_final: 0.7678 (t0) REVERT: A 520 GLU cc_start: 0.7186 (tp30) cc_final: 0.6876 (tp30) REVERT: A 586 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8459 (mm) REVERT: A 592 PHE cc_start: 0.7309 (t80) cc_final: 0.7016 (t80) REVERT: A 609 GLN cc_start: 0.8036 (tp40) cc_final: 0.7414 (tp40) REVERT: A 694 LYS cc_start: 0.8244 (tmtt) cc_final: 0.7833 (tptp) REVERT: A 695 ILE cc_start: 0.8787 (pt) cc_final: 0.8531 (pt) REVERT: B 100 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: B 156 ASN cc_start: 0.7359 (m110) cc_final: 0.7135 (m110) REVERT: B 197 GLU cc_start: 0.7047 (mp0) cc_final: 0.6719 (mp0) REVERT: B 200 GLN cc_start: 0.8140 (tt0) cc_final: 0.7587 (mt0) REVERT: B 363 LYS cc_start: 0.7450 (mppt) cc_final: 0.6973 (mppt) REVERT: B 392 ARG cc_start: 0.7920 (ttp-170) cc_final: 0.7699 (ttp-170) REVERT: B 416 GLU cc_start: 0.6290 (mp0) cc_final: 0.5962 (mp0) REVERT: B 418 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7668 (mm-40) REVERT: B 454 ASP cc_start: 0.7390 (m-30) cc_final: 0.7119 (m-30) REVERT: B 520 GLU cc_start: 0.7114 (tp30) cc_final: 0.6704 (tp30) REVERT: B 540 THR cc_start: 0.8463 (t) cc_final: 0.8154 (t) REVERT: B 592 PHE cc_start: 0.7419 (t80) cc_final: 0.7165 (t80) REVERT: B 694 LYS cc_start: 0.8421 (tmtt) cc_final: 0.8083 (tptp) REVERT: C 100 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: C 169 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7737 (mt) REVERT: C 173 LYS cc_start: 0.8324 (mtmm) cc_final: 0.7885 (mtmm) REVERT: C 195 SER cc_start: 0.8005 (m) cc_final: 0.7555 (t) REVERT: C 196 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6288 (tm-30) REVERT: C 197 GLU cc_start: 0.6995 (mp0) cc_final: 0.6356 (mp0) REVERT: C 200 GLN cc_start: 0.7996 (tt0) cc_final: 0.7591 (tt0) REVERT: C 247 GLU cc_start: 0.6981 (tm-30) cc_final: 0.6541 (tm-30) REVERT: C 248 LYS cc_start: 0.8460 (mmtp) cc_final: 0.7953 (mttp) REVERT: C 376 ARG cc_start: 0.6690 (mtm-85) cc_final: 0.6469 (mtm-85) REVERT: C 392 ARG cc_start: 0.8009 (ttm170) cc_final: 0.7597 (ttp-110) REVERT: C 413 LYS cc_start: 0.8122 (mmmm) cc_final: 0.7633 (mmtm) REVERT: C 444 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8266 (mt) REVERT: C 544 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6540 (tm-30) REVERT: C 694 LYS cc_start: 0.8211 (tmtt) cc_final: 0.7756 (tmtt) REVERT: D 100 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: D 156 ASN cc_start: 0.7653 (m110) cc_final: 0.7328 (m110) REVERT: D 189 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7751 (tm-30) REVERT: D 195 SER cc_start: 0.7966 (m) cc_final: 0.7609 (t) REVERT: D 196 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6434 (tm-30) REVERT: D 197 GLU cc_start: 0.7096 (mp0) cc_final: 0.6665 (mp0) REVERT: D 200 GLN cc_start: 0.7907 (tt0) cc_final: 0.7540 (tt0) REVERT: D 201 ARG cc_start: 0.7650 (mtp180) cc_final: 0.7370 (ttp80) REVERT: D 248 LYS cc_start: 0.8358 (mmtp) cc_final: 0.8023 (mttp) REVERT: D 352 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7290 (mm-30) REVERT: D 362 THR cc_start: 0.5768 (OUTLIER) cc_final: 0.5274 (m) REVERT: D 363 LYS cc_start: 0.7462 (mppt) cc_final: 0.7012 (mppt) REVERT: D 392 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7371 (ttm170) REVERT: D 395 ARG cc_start: 0.7518 (ptp-110) cc_final: 0.7285 (ttp-110) REVERT: D 448 GLU cc_start: 0.7116 (tt0) cc_final: 0.6305 (mm-30) REVERT: D 485 SER cc_start: 0.7816 (t) cc_final: 0.7224 (t) REVERT: D 495 ASP cc_start: 0.7459 (t0) cc_final: 0.7236 (t0) REVERT: D 520 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6886 (tm-30) REVERT: D 540 THR cc_start: 0.8603 (t) cc_final: 0.8331 (t) REVERT: D 609 GLN cc_start: 0.8128 (tp40) cc_final: 0.7777 (tp40) REVERT: D 694 LYS cc_start: 0.8123 (tmtt) cc_final: 0.7682 (tptt) REVERT: D 695 ILE cc_start: 0.8559 (pt) cc_final: 0.8333 (pt) REVERT: E 100 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7472 (mm-30) REVERT: E 196 GLU cc_start: 0.7017 (tm-30) cc_final: 0.5797 (tm-30) REVERT: E 200 GLN cc_start: 0.7990 (mt0) cc_final: 0.7308 (mt0) REVERT: E 247 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6608 (tm-30) REVERT: E 296 VAL cc_start: 0.7439 (m) cc_final: 0.6905 (t) REVERT: E 376 ARG cc_start: 0.6716 (mtt-85) cc_final: 0.6485 (mtt-85) REVERT: E 544 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6663 (tm-30) REVERT: E 694 LYS cc_start: 0.8413 (tmtt) cc_final: 0.7828 (tptt) REVERT: F 156 ASN cc_start: 0.7440 (m110) cc_final: 0.7150 (m110) REVERT: F 193 LYS cc_start: 0.7386 (tttt) cc_final: 0.7145 (tppp) REVERT: F 196 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6672 (tm-30) REVERT: F 197 GLU cc_start: 0.6995 (mp0) cc_final: 0.6701 (mp0) REVERT: F 201 ARG cc_start: 0.7527 (mtp180) cc_final: 0.7184 (mtp85) REVERT: F 247 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6596 (tm-30) REVERT: F 248 LYS cc_start: 0.8397 (mmtp) cc_final: 0.7993 (mttp) REVERT: F 352 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7328 (mm-30) REVERT: F 363 LYS cc_start: 0.7352 (mppt) cc_final: 0.7112 (tppt) REVERT: F 392 ARG cc_start: 0.8051 (ttm170) cc_final: 0.7739 (ttp-110) REVERT: F 444 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8476 (mt) REVERT: F 450 GLU cc_start: 0.6629 (mt-10) cc_final: 0.6390 (mt-10) REVERT: F 454 ASP cc_start: 0.7425 (m-30) cc_final: 0.7101 (m-30) REVERT: F 540 THR cc_start: 0.8586 (t) cc_final: 0.8281 (t) REVERT: F 544 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6949 (tm-30) REVERT: F 592 PHE cc_start: 0.7454 (t80) cc_final: 0.7221 (t80) REVERT: F 609 GLN cc_start: 0.7842 (tp40) cc_final: 0.7296 (tp40) REVERT: F 612 MET cc_start: 0.7250 (tpp) cc_final: 0.6650 (tpp) REVERT: F 638 TRP cc_start: 0.6891 (m-90) cc_final: 0.6498 (m-90) REVERT: F 694 LYS cc_start: 0.8359 (tmtt) cc_final: 0.8095 (tptt) REVERT: G 100 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7018 (mt-10) REVERT: G 157 ARG cc_start: 0.8261 (mtp180) cc_final: 0.7992 (ttm110) REVERT: G 196 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6440 (tm-30) REVERT: G 200 GLN cc_start: 0.7967 (tt0) cc_final: 0.7650 (tt0) REVERT: G 247 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6627 (tm-30) REVERT: G 325 ASP cc_start: 0.6631 (t70) cc_final: 0.6427 (t70) REVERT: G 444 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8412 (mt) REVERT: G 592 PHE cc_start: 0.7396 (t80) cc_final: 0.7066 (t80) REVERT: G 694 LYS cc_start: 0.8291 (tmtt) cc_final: 0.7822 (tmtt) REVERT: H 100 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7547 (mm-30) REVERT: H 156 ASN cc_start: 0.7441 (m110) cc_final: 0.7193 (m110) REVERT: H 159 ARG cc_start: 0.8077 (tpt90) cc_final: 0.7803 (tpt90) REVERT: H 193 LYS cc_start: 0.7368 (tttt) cc_final: 0.7119 (tppp) REVERT: H 196 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6796 (tm-30) REVERT: H 197 GLU cc_start: 0.7045 (mp0) cc_final: 0.6685 (mp0) REVERT: H 201 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7290 (mtp85) REVERT: H 209 ASP cc_start: 0.7567 (t0) cc_final: 0.7279 (t0) REVERT: H 247 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6641 (tm-30) REVERT: H 352 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7112 (mm-30) REVERT: H 363 LYS cc_start: 0.7467 (mppt) cc_final: 0.7174 (tppt) REVERT: H 454 ASP cc_start: 0.7470 (m-30) cc_final: 0.7114 (m-30) REVERT: H 485 SER cc_start: 0.7987 (t) cc_final: 0.7501 (t) REVERT: H 540 THR cc_start: 0.8375 (m) cc_final: 0.7914 (t) REVERT: H 544 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6823 (tm-30) REVERT: H 592 PHE cc_start: 0.7691 (t80) cc_final: 0.7409 (t80) REVERT: H 612 MET cc_start: 0.6860 (tpp) cc_final: 0.6408 (tpp) REVERT: H 693 GLU cc_start: 0.7097 (tp30) cc_final: 0.6837 (tp30) REVERT: H 694 LYS cc_start: 0.8373 (tptt) cc_final: 0.8132 (tptt) outliers start: 134 outliers final: 90 residues processed: 1091 average time/residue: 0.5655 time to fit residues: 939.1307 Evaluate side-chains 1104 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1000 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 191 MET Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 457 MET Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 457 MET Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 654 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 281 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 271 optimal weight: 0.1980 chunk 137 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 289 optimal weight: 4.9990 chunk 309 optimal weight: 0.7980 chunk 224 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 357 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 522 GLN A 585 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN D 585 GLN D 587 HIS D 685 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN F 585 GLN G 81 GLN G 422 GLN G 522 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 37552 Z= 0.237 Angle : 0.649 12.687 50728 Z= 0.318 Chirality : 0.042 0.164 5848 Planarity : 0.004 0.047 6536 Dihedral : 4.520 23.805 5128 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.39 % Allowed : 21.53 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4624 helix: 0.47 (0.10), residues: 3168 sheet: -2.43 (0.39), residues: 160 loop : -2.03 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 662 HIS 0.020 0.001 HIS D 685 PHE 0.024 0.001 PHE E 565 TYR 0.018 0.001 TYR B 568 ARG 0.011 0.000 ARG E 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1030 time to evaluate : 4.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.6887 (mp0) cc_final: 0.6683 (mp0) REVERT: A 157 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7998 (ttm110) REVERT: A 195 SER cc_start: 0.8012 (m) cc_final: 0.7745 (t) REVERT: A 196 GLU cc_start: 0.7097 (tm-30) cc_final: 0.5848 (tm-30) REVERT: A 197 GLU cc_start: 0.6983 (mp0) cc_final: 0.6740 (mp0) REVERT: A 200 GLN cc_start: 0.8041 (tt0) cc_final: 0.7109 (mt0) REVERT: A 376 ARG cc_start: 0.6575 (mtm-85) cc_final: 0.6333 (mtm-85) REVERT: A 392 ARG cc_start: 0.7859 (ttm170) cc_final: 0.7444 (ttp-110) REVERT: A 483 ASP cc_start: 0.7974 (t0) cc_final: 0.7690 (t0) REVERT: A 520 GLU cc_start: 0.7206 (tp30) cc_final: 0.6875 (tp30) REVERT: A 586 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8392 (mm) REVERT: A 592 PHE cc_start: 0.7320 (t80) cc_final: 0.7028 (t80) REVERT: A 609 GLN cc_start: 0.8054 (tp40) cc_final: 0.7408 (tp40) REVERT: A 694 LYS cc_start: 0.8253 (tmtt) cc_final: 0.7825 (tptp) REVERT: A 695 ILE cc_start: 0.8782 (pt) cc_final: 0.8526 (pt) REVERT: B 100 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: B 156 ASN cc_start: 0.7367 (m110) cc_final: 0.7116 (m110) REVERT: B 197 GLU cc_start: 0.7049 (mp0) cc_final: 0.6754 (mp0) REVERT: B 200 GLN cc_start: 0.8154 (tt0) cc_final: 0.7579 (mt0) REVERT: B 289 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7498 (mtm-85) REVERT: B 363 LYS cc_start: 0.7497 (mppt) cc_final: 0.7016 (mppt) REVERT: B 392 ARG cc_start: 0.7918 (ttp-170) cc_final: 0.7691 (ttp-170) REVERT: B 416 GLU cc_start: 0.6271 (mp0) cc_final: 0.5987 (mp0) REVERT: B 454 ASP cc_start: 0.7402 (m-30) cc_final: 0.7100 (m-30) REVERT: B 520 GLU cc_start: 0.7120 (tp30) cc_final: 0.6709 (tp30) REVERT: B 540 THR cc_start: 0.8466 (t) cc_final: 0.8157 (t) REVERT: B 592 PHE cc_start: 0.7422 (t80) cc_final: 0.7167 (t80) REVERT: B 694 LYS cc_start: 0.8440 (tmtt) cc_final: 0.8085 (tptp) REVERT: C 100 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: C 159 ARG cc_start: 0.8242 (tpt90) cc_final: 0.7990 (tpt90) REVERT: C 169 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7762 (mt) REVERT: C 173 LYS cc_start: 0.8323 (mtmm) cc_final: 0.7870 (mtmm) REVERT: C 195 SER cc_start: 0.8014 (m) cc_final: 0.7572 (t) REVERT: C 196 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6298 (tm-30) REVERT: C 197 GLU cc_start: 0.6998 (mp0) cc_final: 0.6471 (mp0) REVERT: C 200 GLN cc_start: 0.7998 (tt0) cc_final: 0.7595 (tt0) REVERT: C 247 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6559 (tm-30) REVERT: C 248 LYS cc_start: 0.8471 (mmtp) cc_final: 0.7959 (mttp) REVERT: C 376 ARG cc_start: 0.6651 (mtm-85) cc_final: 0.6425 (mtm-85) REVERT: C 392 ARG cc_start: 0.8003 (ttm170) cc_final: 0.7590 (ttp-110) REVERT: C 413 LYS cc_start: 0.8151 (mmmm) cc_final: 0.7485 (mmtm) REVERT: C 444 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8269 (mt) REVERT: C 544 GLU cc_start: 0.6834 (tm-30) cc_final: 0.6553 (tm-30) REVERT: C 694 LYS cc_start: 0.8250 (tmtt) cc_final: 0.7785 (tmtt) REVERT: D 100 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7239 (mt-10) REVERT: D 153 VAL cc_start: 0.7947 (t) cc_final: 0.7559 (t) REVERT: D 156 ASN cc_start: 0.7667 (m110) cc_final: 0.7345 (m110) REVERT: D 189 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7764 (tm-30) REVERT: D 195 SER cc_start: 0.7985 (m) cc_final: 0.7615 (t) REVERT: D 196 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6451 (tm-30) REVERT: D 197 GLU cc_start: 0.7088 (mp0) cc_final: 0.6693 (mp0) REVERT: D 200 GLN cc_start: 0.7905 (tt0) cc_final: 0.7587 (tt0) REVERT: D 201 ARG cc_start: 0.7657 (mtp180) cc_final: 0.7389 (ttp80) REVERT: D 248 LYS cc_start: 0.8349 (mmtp) cc_final: 0.8003 (mttp) REVERT: D 352 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7289 (mm-30) REVERT: D 362 THR cc_start: 0.5854 (OUTLIER) cc_final: 0.5424 (m) REVERT: D 363 LYS cc_start: 0.7483 (mppt) cc_final: 0.7040 (mppt) REVERT: D 392 ARG cc_start: 0.7926 (ttm170) cc_final: 0.7359 (ttm170) REVERT: D 395 ARG cc_start: 0.7529 (ptp-110) cc_final: 0.7293 (ttp-110) REVERT: D 448 GLU cc_start: 0.7127 (tt0) cc_final: 0.6313 (mm-30) REVERT: D 485 SER cc_start: 0.7803 (t) cc_final: 0.7212 (t) REVERT: D 495 ASP cc_start: 0.7494 (t0) cc_final: 0.7280 (t0) REVERT: D 520 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6888 (tm-30) REVERT: D 540 THR cc_start: 0.8603 (t) cc_final: 0.8332 (t) REVERT: D 592 PHE cc_start: 0.7522 (t80) cc_final: 0.7305 (t80) REVERT: D 609 GLN cc_start: 0.8126 (tp40) cc_final: 0.7767 (tp40) REVERT: D 694 LYS cc_start: 0.8191 (tmtt) cc_final: 0.7764 (tptt) REVERT: D 695 ILE cc_start: 0.8585 (pt) cc_final: 0.8354 (pt) REVERT: E 96 PHE cc_start: 0.6606 (t80) cc_final: 0.6140 (t80) REVERT: E 196 GLU cc_start: 0.7008 (tm-30) cc_final: 0.5801 (tm-30) REVERT: E 197 GLU cc_start: 0.6605 (mp0) cc_final: 0.6371 (mp0) REVERT: E 200 GLN cc_start: 0.7928 (mt0) cc_final: 0.7240 (mt0) REVERT: E 247 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6607 (tm-30) REVERT: E 296 VAL cc_start: 0.7472 (m) cc_final: 0.6906 (t) REVERT: E 544 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6684 (tm-30) REVERT: E 694 LYS cc_start: 0.8407 (tmtt) cc_final: 0.7802 (tmtt) REVERT: F 156 ASN cc_start: 0.7452 (m110) cc_final: 0.7166 (m110) REVERT: F 193 LYS cc_start: 0.7385 (tttt) cc_final: 0.7148 (tppp) REVERT: F 196 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6544 (tm-30) REVERT: F 197 GLU cc_start: 0.7015 (mp0) cc_final: 0.6721 (mp0) REVERT: F 201 ARG cc_start: 0.7544 (mtp180) cc_final: 0.7191 (mtp85) REVERT: F 247 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6595 (tm-30) REVERT: F 248 LYS cc_start: 0.8383 (mmtp) cc_final: 0.7993 (mttp) REVERT: F 352 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7301 (mm-30) REVERT: F 363 LYS cc_start: 0.7397 (mppt) cc_final: 0.7162 (tppt) REVERT: F 444 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8475 (mt) REVERT: F 450 GLU cc_start: 0.6628 (mt-10) cc_final: 0.6395 (mt-10) REVERT: F 454 ASP cc_start: 0.7398 (m-30) cc_final: 0.7084 (m-30) REVERT: F 540 THR cc_start: 0.8591 (t) cc_final: 0.8290 (t) REVERT: F 544 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6980 (tm-30) REVERT: F 592 PHE cc_start: 0.7481 (t80) cc_final: 0.7237 (t80) REVERT: F 609 GLN cc_start: 0.7784 (tp40) cc_final: 0.7260 (tp40) REVERT: F 612 MET cc_start: 0.7257 (tpp) cc_final: 0.6656 (tpp) REVERT: F 638 TRP cc_start: 0.6899 (m-90) cc_final: 0.6487 (m-90) REVERT: F 694 LYS cc_start: 0.8375 (tmtt) cc_final: 0.8025 (tptp) REVERT: G 100 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7044 (mt-10) REVERT: G 157 ARG cc_start: 0.8272 (mtp180) cc_final: 0.7991 (ttm110) REVERT: G 196 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6730 (tm-30) REVERT: G 247 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6664 (tm-30) REVERT: G 349 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7939 (mp) REVERT: G 392 ARG cc_start: 0.8044 (ttm170) cc_final: 0.7735 (ttp-110) REVERT: G 444 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8409 (mt) REVERT: G 483 ASP cc_start: 0.7979 (t0) cc_final: 0.7624 (t70) REVERT: G 592 PHE cc_start: 0.7397 (t80) cc_final: 0.7065 (t80) REVERT: G 694 LYS cc_start: 0.8288 (tmtt) cc_final: 0.7824 (tmtt) REVERT: H 100 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7479 (mm-30) REVERT: H 156 ASN cc_start: 0.7363 (m110) cc_final: 0.7118 (m110) REVERT: H 159 ARG cc_start: 0.8051 (tpt90) cc_final: 0.7819 (tpt90) REVERT: H 196 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6600 (tm-30) REVERT: H 197 GLU cc_start: 0.7057 (mp0) cc_final: 0.6626 (mp0) REVERT: H 209 ASP cc_start: 0.7589 (t0) cc_final: 0.7258 (t0) REVERT: H 247 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6597 (tm-30) REVERT: H 352 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7124 (mm-30) REVERT: H 363 LYS cc_start: 0.7436 (mppt) cc_final: 0.7220 (tppt) REVERT: H 454 ASP cc_start: 0.7449 (m-30) cc_final: 0.7095 (m-30) REVERT: H 485 SER cc_start: 0.8028 (t) cc_final: 0.7533 (t) REVERT: H 540 THR cc_start: 0.8381 (m) cc_final: 0.7917 (t) REVERT: H 544 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6818 (tm-30) REVERT: H 592 PHE cc_start: 0.7723 (t80) cc_final: 0.7398 (t80) REVERT: H 609 GLN cc_start: 0.7653 (tp40) cc_final: 0.7140 (tp40) REVERT: H 612 MET cc_start: 0.6815 (tpp) cc_final: 0.6373 (tpp) REVERT: H 693 GLU cc_start: 0.7084 (tp30) cc_final: 0.6827 (tp30) REVERT: H 694 LYS cc_start: 0.8369 (tptt) cc_final: 0.8141 (tptt) outliers start: 133 outliers final: 94 residues processed: 1095 average time/residue: 0.5578 time to fit residues: 930.0491 Evaluate side-chains 1108 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1002 time to evaluate : 4.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 191 MET Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 457 MET Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 457 MET Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 654 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 413 optimal weight: 10.0000 chunk 435 optimal weight: 0.0000 chunk 397 optimal weight: 0.9990 chunk 423 optimal weight: 0.9980 chunk 255 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 332 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 383 optimal weight: 1.9990 chunk 400 optimal weight: 0.5980 chunk 422 optimal weight: 0.8980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN A 585 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN D 585 GLN D 587 HIS D 685 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN G 522 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 422 GLN H 522 GLN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37552 Z= 0.207 Angle : 0.657 14.644 50728 Z= 0.318 Chirality : 0.041 0.167 5848 Planarity : 0.004 0.045 6536 Dihedral : 4.439 23.431 5128 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.04 % Allowed : 22.47 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 4624 helix: 0.57 (0.10), residues: 3168 sheet: -2.38 (0.40), residues: 160 loop : -1.97 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 253 HIS 0.015 0.001 HIS D 685 PHE 0.022 0.001 PHE G 565 TYR 0.026 0.002 TYR A 479 ARG 0.010 0.000 ARG F 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1037 time to evaluate : 4.303 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 157 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7993 (ttm110) REVERT: A 195 SER cc_start: 0.7995 (m) cc_final: 0.7719 (t) REVERT: A 196 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6601 (tm-30) REVERT: A 197 GLU cc_start: 0.6963 (mp0) cc_final: 0.6692 (mp0) REVERT: A 376 ARG cc_start: 0.6563 (mtm-85) cc_final: 0.6350 (mtm-85) REVERT: A 392 ARG cc_start: 0.7848 (ttm170) cc_final: 0.7488 (ttp-110) REVERT: A 469 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6581 (mm-30) REVERT: A 483 ASP cc_start: 0.7959 (t0) cc_final: 0.7708 (t0) REVERT: A 511 ASP cc_start: 0.7580 (p0) cc_final: 0.7376 (p0) REVERT: A 586 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8416 (mm) REVERT: A 592 PHE cc_start: 0.7363 (t80) cc_final: 0.7070 (t80) REVERT: A 609 GLN cc_start: 0.8045 (tp40) cc_final: 0.7397 (tp40) REVERT: A 694 LYS cc_start: 0.8234 (tmtt) cc_final: 0.7811 (tptp) REVERT: A 695 ILE cc_start: 0.8782 (pt) cc_final: 0.8527 (pt) REVERT: B 100 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: B 156 ASN cc_start: 0.7357 (m110) cc_final: 0.7115 (m110) REVERT: B 197 GLU cc_start: 0.7053 (mp0) cc_final: 0.6753 (mp0) REVERT: B 200 GLN cc_start: 0.8140 (tt0) cc_final: 0.7574 (mt0) REVERT: B 289 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7492 (mtm-85) REVERT: B 363 LYS cc_start: 0.7449 (mppt) cc_final: 0.7012 (mppt) REVERT: B 392 ARG cc_start: 0.7902 (ttp-170) cc_final: 0.7665 (ttp-170) REVERT: B 416 GLU cc_start: 0.6277 (mp0) cc_final: 0.5979 (mp0) REVERT: B 422 GLN cc_start: 0.7989 (mt0) cc_final: 0.7696 (tt0) REVERT: B 454 ASP cc_start: 0.7411 (m-30) cc_final: 0.7073 (m-30) REVERT: B 520 GLU cc_start: 0.7114 (tp30) cc_final: 0.6705 (tp30) REVERT: B 540 THR cc_start: 0.8457 (t) cc_final: 0.8137 (t) REVERT: B 592 PHE cc_start: 0.7429 (t80) cc_final: 0.7166 (t80) REVERT: B 694 LYS cc_start: 0.8442 (tmtt) cc_final: 0.8094 (tptp) REVERT: C 100 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: C 149 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7265 (mm-30) REVERT: C 159 ARG cc_start: 0.8169 (tpt90) cc_final: 0.7956 (tpt90) REVERT: C 169 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8073 (mt) REVERT: C 195 SER cc_start: 0.7989 (m) cc_final: 0.7564 (t) REVERT: C 196 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6268 (tm-30) REVERT: C 197 GLU cc_start: 0.6992 (mp0) cc_final: 0.6450 (mp0) REVERT: C 200 GLN cc_start: 0.7985 (tt0) cc_final: 0.7571 (tt0) REVERT: C 248 LYS cc_start: 0.8414 (mmtp) cc_final: 0.8196 (mttm) REVERT: C 249 ARG cc_start: 0.7907 (tpp80) cc_final: 0.7658 (tpp80) REVERT: C 361 LYS cc_start: 0.7053 (mmmt) cc_final: 0.6758 (mmmt) REVERT: C 376 ARG cc_start: 0.6641 (mtm-85) cc_final: 0.6427 (mtm-85) REVERT: C 392 ARG cc_start: 0.7982 (ttm170) cc_final: 0.7591 (ttp-110) REVERT: C 413 LYS cc_start: 0.8143 (mmmm) cc_final: 0.7534 (mmtm) REVERT: C 444 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8261 (mt) REVERT: C 544 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6545 (tm-30) REVERT: C 693 GLU cc_start: 0.7188 (tp30) cc_final: 0.6919 (tp30) REVERT: C 694 LYS cc_start: 0.8274 (tmtt) cc_final: 0.7800 (tmtt) REVERT: D 100 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: D 153 VAL cc_start: 0.7961 (t) cc_final: 0.7600 (t) REVERT: D 156 ASN cc_start: 0.7663 (m110) cc_final: 0.7372 (m110) REVERT: D 189 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7778 (tm-30) REVERT: D 195 SER cc_start: 0.7958 (m) cc_final: 0.7593 (t) REVERT: D 196 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6438 (tm-30) REVERT: D 197 GLU cc_start: 0.7083 (mp0) cc_final: 0.6682 (mp0) REVERT: D 200 GLN cc_start: 0.7872 (tt0) cc_final: 0.7558 (tt0) REVERT: D 201 ARG cc_start: 0.7653 (mtp180) cc_final: 0.7377 (ttp80) REVERT: D 248 LYS cc_start: 0.8335 (mmtp) cc_final: 0.7996 (mttp) REVERT: D 352 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7292 (mm-30) REVERT: D 363 LYS cc_start: 0.7463 (mppt) cc_final: 0.6996 (mppt) REVERT: D 395 ARG cc_start: 0.7487 (ptp-110) cc_final: 0.7259 (ttp-110) REVERT: D 448 GLU cc_start: 0.7104 (tt0) cc_final: 0.6314 (mm-30) REVERT: D 485 SER cc_start: 0.7808 (t) cc_final: 0.7228 (t) REVERT: D 520 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6889 (tm-30) REVERT: D 540 THR cc_start: 0.8598 (t) cc_final: 0.8316 (t) REVERT: D 592 PHE cc_start: 0.7510 (t80) cc_final: 0.7303 (t80) REVERT: D 609 GLN cc_start: 0.8114 (tp40) cc_final: 0.7755 (tp40) REVERT: D 694 LYS cc_start: 0.8140 (tmtt) cc_final: 0.7729 (tptt) REVERT: D 695 ILE cc_start: 0.8575 (pt) cc_final: 0.8361 (pt) REVERT: E 96 PHE cc_start: 0.7077 (t80) cc_final: 0.6638 (t80) REVERT: E 176 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6698 (mm-30) REVERT: E 196 GLU cc_start: 0.7019 (tm-30) cc_final: 0.5797 (tm-30) REVERT: E 200 GLN cc_start: 0.7909 (mt0) cc_final: 0.7201 (mt0) REVERT: E 247 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6599 (tm-30) REVERT: E 296 VAL cc_start: 0.7488 (m) cc_final: 0.6943 (t) REVERT: E 544 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6696 (tm-30) REVERT: E 694 LYS cc_start: 0.8412 (tmtt) cc_final: 0.7799 (tmtt) REVERT: F 156 ASN cc_start: 0.7458 (m110) cc_final: 0.7197 (m110) REVERT: F 193 LYS cc_start: 0.7381 (tttt) cc_final: 0.7155 (tppp) REVERT: F 197 GLU cc_start: 0.7016 (mp0) cc_final: 0.6701 (mp0) REVERT: F 200 GLN cc_start: 0.8143 (tt0) cc_final: 0.7685 (mt0) REVERT: F 201 ARG cc_start: 0.7539 (mtp180) cc_final: 0.7186 (mtp85) REVERT: F 247 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6588 (tm-30) REVERT: F 248 LYS cc_start: 0.8343 (mmtp) cc_final: 0.7964 (mttp) REVERT: F 352 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7299 (mm-30) REVERT: F 363 LYS cc_start: 0.7383 (mppt) cc_final: 0.7146 (tppt) REVERT: F 392 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7717 (ttp-110) REVERT: F 444 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8478 (mt) REVERT: F 450 GLU cc_start: 0.6618 (mt-10) cc_final: 0.6385 (mt-10) REVERT: F 454 ASP cc_start: 0.7399 (m-30) cc_final: 0.7083 (m-30) REVERT: F 540 THR cc_start: 0.8575 (t) cc_final: 0.8270 (t) REVERT: F 544 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6999 (tm-30) REVERT: F 592 PHE cc_start: 0.7444 (t80) cc_final: 0.7193 (t80) REVERT: F 609 GLN cc_start: 0.7788 (tp40) cc_final: 0.7243 (tp40) REVERT: F 612 MET cc_start: 0.7208 (tpp) cc_final: 0.6615 (tpp) REVERT: F 638 TRP cc_start: 0.6889 (m-90) cc_final: 0.6485 (m-90) REVERT: F 694 LYS cc_start: 0.8361 (tmtt) cc_final: 0.8107 (tptt) REVERT: G 100 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7086 (mt-10) REVERT: G 157 ARG cc_start: 0.8252 (mtp180) cc_final: 0.7970 (ttm110) REVERT: G 196 GLU cc_start: 0.7055 (tm-30) cc_final: 0.5970 (tm-30) REVERT: G 200 GLN cc_start: 0.7987 (tt0) cc_final: 0.7259 (mt0) REVERT: G 247 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6668 (tm-30) REVERT: G 392 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7749 (ttp-110) REVERT: G 444 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8406 (mt) REVERT: G 479 TYR cc_start: 0.7935 (m-80) cc_final: 0.7717 (m-80) REVERT: G 483 ASP cc_start: 0.7997 (t0) cc_final: 0.7675 (t0) REVERT: G 543 ARG cc_start: 0.7021 (mmt90) cc_final: 0.6819 (mmt90) REVERT: G 592 PHE cc_start: 0.7380 (t80) cc_final: 0.7017 (t80) REVERT: G 694 LYS cc_start: 0.8373 (tmtt) cc_final: 0.7911 (tmtt) REVERT: H 100 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7427 (mm-30) REVERT: H 156 ASN cc_start: 0.7382 (m110) cc_final: 0.7131 (m110) REVERT: H 159 ARG cc_start: 0.8027 (tpt90) cc_final: 0.7754 (tpt90) REVERT: H 196 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6663 (tm-30) REVERT: H 197 GLU cc_start: 0.7050 (mp0) cc_final: 0.6639 (mp0) REVERT: H 209 ASP cc_start: 0.7583 (t0) cc_final: 0.7269 (t0) REVERT: H 247 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6584 (tm-30) REVERT: H 352 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7119 (mm-30) REVERT: H 454 ASP cc_start: 0.7441 (m-30) cc_final: 0.7118 (m-30) REVERT: H 485 SER cc_start: 0.8058 (t) cc_final: 0.7575 (t) REVERT: H 540 THR cc_start: 0.8381 (m) cc_final: 0.7919 (t) REVERT: H 544 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6859 (tm-30) REVERT: H 609 GLN cc_start: 0.7649 (tp40) cc_final: 0.7135 (tp40) REVERT: H 612 MET cc_start: 0.6809 (tpp) cc_final: 0.6366 (tpp) REVERT: H 693 GLU cc_start: 0.7076 (tp30) cc_final: 0.6757 (tp30) REVERT: H 694 LYS cc_start: 0.8384 (tptt) cc_final: 0.8103 (tptt) outliers start: 119 outliers final: 89 residues processed: 1103 average time/residue: 0.5591 time to fit residues: 936.3960 Evaluate side-chains 1114 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1015 time to evaluate : 4.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 191 MET Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 457 MET Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 457 MET Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 282 GLU Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 654 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 278 optimal weight: 0.9980 chunk 448 optimal weight: 0.0470 chunk 273 optimal weight: 0.4980 chunk 212 optimal weight: 0.6980 chunk 311 optimal weight: 2.9990 chunk 470 optimal weight: 0.5980 chunk 432 optimal weight: 0.0870 chunk 374 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 289 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN D 522 GLN D 587 HIS D 685 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 585 GLN H 81 GLN H 422 GLN H 522 GLN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37552 Z= 0.181 Angle : 0.661 15.360 50728 Z= 0.317 Chirality : 0.041 0.172 5848 Planarity : 0.004 0.060 6536 Dihedral : 4.320 23.157 5128 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.47 % Allowed : 23.34 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 4624 helix: 0.67 (0.10), residues: 3176 sheet: -2.34 (0.38), residues: 168 loop : -1.96 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 253 HIS 0.028 0.001 HIS D 685 PHE 0.016 0.001 PHE G 96 TYR 0.026 0.001 TYR A 479 ARG 0.010 0.000 ARG D 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9248 Ramachandran restraints generated. 4624 Oldfield, 0 Emsley, 4624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1046 time to evaluate : 3.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 SER cc_start: 0.7921 (m) cc_final: 0.7656 (t) REVERT: A 196 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6600 (tm-30) REVERT: A 197 GLU cc_start: 0.6984 (mp0) cc_final: 0.6709 (mp0) REVERT: A 376 ARG cc_start: 0.6552 (mtm-85) cc_final: 0.6351 (mtm-85) REVERT: A 392 ARG cc_start: 0.7843 (ttm170) cc_final: 0.7493 (ttp-110) REVERT: A 469 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6556 (mm-30) REVERT: A 483 ASP cc_start: 0.7949 (t0) cc_final: 0.7716 (t0) REVERT: A 511 ASP cc_start: 0.7544 (p0) cc_final: 0.7344 (p0) REVERT: A 520 GLU cc_start: 0.7229 (tp30) cc_final: 0.6894 (tp30) REVERT: A 586 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8436 (mm) REVERT: A 592 PHE cc_start: 0.7325 (t80) cc_final: 0.7058 (t80) REVERT: A 609 GLN cc_start: 0.8032 (tp40) cc_final: 0.7374 (tp40) REVERT: A 682 LYS cc_start: 0.6923 (tptp) cc_final: 0.6608 (tptp) REVERT: A 694 LYS cc_start: 0.8195 (tmtt) cc_final: 0.7763 (tptp) REVERT: A 695 ILE cc_start: 0.8763 (pt) cc_final: 0.8495 (pt) REVERT: B 100 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: B 156 ASN cc_start: 0.7363 (m110) cc_final: 0.7132 (m110) REVERT: B 197 GLU cc_start: 0.7042 (mp0) cc_final: 0.6724 (mp0) REVERT: B 200 GLN cc_start: 0.8119 (tt0) cc_final: 0.7563 (mt0) REVERT: B 289 ARG cc_start: 0.7798 (ttm-80) cc_final: 0.7479 (mtm-85) REVERT: B 356 LYS cc_start: 0.7662 (tmtt) cc_final: 0.7393 (tptp) REVERT: B 363 LYS cc_start: 0.7297 (mppt) cc_final: 0.6886 (mppt) REVERT: B 392 ARG cc_start: 0.7851 (ttp-170) cc_final: 0.7615 (ttp-170) REVERT: B 416 GLU cc_start: 0.6265 (mp0) cc_final: 0.5954 (mp0) REVERT: B 422 GLN cc_start: 0.7968 (mt0) cc_final: 0.7692 (tt0) REVERT: B 454 ASP cc_start: 0.7356 (m-30) cc_final: 0.6992 (m-30) REVERT: B 520 GLU cc_start: 0.7108 (tp30) cc_final: 0.6689 (tp30) REVERT: B 540 THR cc_start: 0.8440 (t) cc_final: 0.8111 (t) REVERT: B 592 PHE cc_start: 0.7372 (t80) cc_final: 0.7118 (t80) REVERT: B 694 LYS cc_start: 0.8427 (tmtt) cc_final: 0.8087 (tptp) REVERT: C 100 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: C 149 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7240 (mm-30) REVERT: C 159 ARG cc_start: 0.8149 (tpt90) cc_final: 0.7933 (tpt90) REVERT: C 169 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7983 (mt) REVERT: C 173 LYS cc_start: 0.8336 (mtmm) cc_final: 0.7903 (mtmm) REVERT: C 195 SER cc_start: 0.7926 (m) cc_final: 0.7567 (t) REVERT: C 196 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6389 (tm-30) REVERT: C 197 GLU cc_start: 0.6985 (mp0) cc_final: 0.6438 (mp0) REVERT: C 200 GLN cc_start: 0.7932 (tt0) cc_final: 0.7638 (tt0) REVERT: C 248 LYS cc_start: 0.8381 (mmtp) cc_final: 0.8150 (mttm) REVERT: C 376 ARG cc_start: 0.6622 (mtm-85) cc_final: 0.6394 (mtm-85) REVERT: C 392 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7588 (ttp-110) REVERT: C 413 LYS cc_start: 0.8103 (mmmm) cc_final: 0.7528 (mmtm) REVERT: C 423 GLN cc_start: 0.8019 (mt0) cc_final: 0.7818 (mt0) REVERT: C 444 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8245 (mt) REVERT: C 543 ARG cc_start: 0.7213 (mmt90) cc_final: 0.6912 (mmt90) REVERT: C 544 GLU cc_start: 0.6871 (tm-30) cc_final: 0.6591 (tm-30) REVERT: C 693 GLU cc_start: 0.7163 (tp30) cc_final: 0.6891 (tp30) REVERT: C 694 LYS cc_start: 0.8267 (tmtt) cc_final: 0.7797 (tmtt) REVERT: D 100 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: D 153 VAL cc_start: 0.7967 (t) cc_final: 0.7625 (t) REVERT: D 156 ASN cc_start: 0.7665 (m110) cc_final: 0.7389 (m110) REVERT: D 159 ARG cc_start: 0.7773 (tpt90) cc_final: 0.7252 (tpt90) REVERT: D 189 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7769 (tm-30) REVERT: D 195 SER cc_start: 0.7811 (m) cc_final: 0.7456 (t) REVERT: D 196 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6448 (tm-30) REVERT: D 197 GLU cc_start: 0.6994 (mp0) cc_final: 0.6595 (mp0) REVERT: D 200 GLN cc_start: 0.7812 (tt0) cc_final: 0.7499 (tt0) REVERT: D 201 ARG cc_start: 0.7647 (mtp180) cc_final: 0.7370 (ttp80) REVERT: D 248 LYS cc_start: 0.8321 (mmtp) cc_final: 0.7960 (mttp) REVERT: D 352 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7293 (mm-30) REVERT: D 356 LYS cc_start: 0.7943 (tmtt) cc_final: 0.7637 (tptp) REVERT: D 363 LYS cc_start: 0.7318 (mppt) cc_final: 0.7091 (tppt) REVERT: D 392 ARG cc_start: 0.7865 (ttp-170) cc_final: 0.7664 (ttp-110) REVERT: D 395 ARG cc_start: 0.7442 (ptp-110) cc_final: 0.7228 (ttp-110) REVERT: D 448 GLU cc_start: 0.7078 (tt0) cc_final: 0.6506 (mm-30) REVERT: D 485 SER cc_start: 0.7812 (t) cc_final: 0.7232 (t) REVERT: D 520 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6880 (tm-30) REVERT: D 540 THR cc_start: 0.8582 (t) cc_final: 0.8297 (t) REVERT: D 609 GLN cc_start: 0.8090 (tp40) cc_final: 0.7731 (tp40) REVERT: D 694 LYS cc_start: 0.8113 (tmtt) cc_final: 0.7710 (tptt) REVERT: D 695 ILE cc_start: 0.8568 (pt) cc_final: 0.8345 (pt) REVERT: E 96 PHE cc_start: 0.6995 (t80) cc_final: 0.6301 (t80) REVERT: E 176 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6684 (mm-30) REVERT: E 196 GLU cc_start: 0.7060 (tm-30) cc_final: 0.5823 (tm-30) REVERT: E 197 GLU cc_start: 0.6634 (mp0) cc_final: 0.6389 (mp0) REVERT: E 200 GLN cc_start: 0.7883 (mt0) cc_final: 0.7183 (mt0) REVERT: E 296 VAL cc_start: 0.7419 (m) cc_final: 0.6842 (t) REVERT: E 479 TYR cc_start: 0.7493 (m-80) cc_final: 0.7261 (m-10) REVERT: E 544 GLU cc_start: 0.6981 (tm-30) cc_final: 0.6699 (tm-30) REVERT: E 694 LYS cc_start: 0.8395 (tmtt) cc_final: 0.7780 (tmtt) REVERT: F 156 ASN cc_start: 0.7453 (m110) cc_final: 0.7205 (m110) REVERT: F 193 LYS cc_start: 0.7384 (tttt) cc_final: 0.7177 (tppp) REVERT: F 196 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6726 (tm-30) REVERT: F 197 GLU cc_start: 0.7001 (mp0) cc_final: 0.6707 (mp0) REVERT: F 247 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6604 (tm-30) REVERT: F 248 LYS cc_start: 0.8325 (mmtp) cc_final: 0.7979 (mttp) REVERT: F 352 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7296 (mm-30) REVERT: F 363 LYS cc_start: 0.7314 (mppt) cc_final: 0.7107 (tppt) REVERT: F 444 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8465 (mt) REVERT: F 450 GLU cc_start: 0.6558 (mt-10) cc_final: 0.6293 (mt-10) REVERT: F 454 ASP cc_start: 0.7397 (m-30) cc_final: 0.7094 (m-30) REVERT: F 540 THR cc_start: 0.8564 (t) cc_final: 0.8257 (t) REVERT: F 592 PHE cc_start: 0.7399 (t80) cc_final: 0.7178 (t80) REVERT: F 609 GLN cc_start: 0.7819 (tp40) cc_final: 0.7271 (tp40) REVERT: F 612 MET cc_start: 0.7108 (tpp) cc_final: 0.6596 (tpp) REVERT: F 638 TRP cc_start: 0.6944 (m-90) cc_final: 0.6551 (m-90) REVERT: F 694 LYS cc_start: 0.8339 (tmtt) cc_final: 0.8090 (tptt) REVERT: G 100 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7219 (mt-10) REVERT: G 157 ARG cc_start: 0.8231 (mtp180) cc_final: 0.7943 (ttm110) REVERT: G 196 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6576 (tm-30) REVERT: G 247 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6668 (tm-30) REVERT: G 380 TYR cc_start: 0.7822 (m-80) cc_final: 0.7569 (m-10) REVERT: G 392 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7738 (ttp-110) REVERT: G 444 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8366 (mm) REVERT: G 479 TYR cc_start: 0.7882 (m-80) cc_final: 0.7671 (m-80) REVERT: G 483 ASP cc_start: 0.7999 (t0) cc_final: 0.7696 (t0) REVERT: G 525 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6814 (mm-30) REVERT: G 592 PHE cc_start: 0.7328 (t80) cc_final: 0.7001 (t80) REVERT: G 693 GLU cc_start: 0.7172 (tp30) cc_final: 0.6836 (tp30) REVERT: G 694 LYS cc_start: 0.8357 (tmtt) cc_final: 0.7909 (tmtt) REVERT: H 100 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: H 156 ASN cc_start: 0.7365 (m110) cc_final: 0.7117 (m110) REVERT: H 159 ARG cc_start: 0.8036 (tpt90) cc_final: 0.7834 (tpt90) REVERT: H 196 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6684 (tm-30) REVERT: H 197 GLU cc_start: 0.7049 (mp0) cc_final: 0.6622 (mp0) REVERT: H 209 ASP cc_start: 0.7575 (t0) cc_final: 0.7272 (t0) REVERT: H 247 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6595 (tm-30) REVERT: H 352 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7091 (mm-30) REVERT: H 454 ASP cc_start: 0.7366 (m-30) cc_final: 0.7152 (m-30) REVERT: H 540 THR cc_start: 0.8339 (m) cc_final: 0.7864 (t) REVERT: H 544 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6860 (tm-30) REVERT: H 609 GLN cc_start: 0.7631 (tp40) cc_final: 0.7136 (tp40) REVERT: H 612 MET cc_start: 0.6781 (tpp) cc_final: 0.6326 (tpp) REVERT: H 693 GLU cc_start: 0.7054 (tp30) cc_final: 0.6731 (tp30) REVERT: H 694 LYS cc_start: 0.8376 (tptt) cc_final: 0.8100 (tptt) outliers start: 97 outliers final: 67 residues processed: 1095 average time/residue: 0.5565 time to fit residues: 923.6792 Evaluate side-chains 1090 residues out of total 3920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1013 time to evaluate : 4.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 191 MET Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 457 MET Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 457 MET Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 GLU Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 654 VAL Chi-restraints excluded: chain H residue 656 ILE Chi-restraints excluded: chain H residue 685 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 297 optimal weight: 0.7980 chunk 398 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 345 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 375 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 385 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN A 585 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN C 522 GLN C 585 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN D 522 GLN D 585 GLN D 685 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 GLN G 422 GLN G 585 GLN G 652 ASN H 422 GLN H 522 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.153090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.126653 restraints weight = 56597.953| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.42 r_work: 0.3497 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37552 Z= 0.229 Angle : 0.675 14.229 50728 Z= 0.326 Chirality : 0.042 0.169 5848 Planarity : 0.004 0.046 6536 Dihedral : 4.375 23.433 5128 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.37 % Allowed : 23.52 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.13), residues: 4624 helix: 0.62 (0.10), residues: 3176 sheet: -2.29 (0.38), residues: 168 loop : -1.94 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 638 HIS 0.018 0.001 HIS D 685 PHE 0.027 0.001 PHE E 96 TYR 0.034 0.002 TYR A 479 ARG 0.010 0.000 ARG F 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13576.85 seconds wall clock time: 243 minutes 42.33 seconds (14622.33 seconds total)