Starting phenix.real_space_refine on Wed Aug 27 01:09:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5wln_8860/08_2025/5wln_8860.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wln_8860/08_2025/5wln_8860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5wln_8860/08_2025/5wln_8860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wln_8860/08_2025/5wln_8860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5wln_8860/08_2025/5wln_8860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wln_8860/08_2025/5wln_8860.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 sd= 0.044 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 75 5.16 5 C 27585 2.51 5 N 7980 2.21 5 O 8775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44415 Number of models: 1 Model: "" Number of chains: 1 Chain: "G" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Restraints were copied for chains: O, A, B, C, D, E, F, H, I, J, K, L, M, N Time building chain proxies: 4.64, per 1000 atoms: 0.10 Number of scatterers: 44415 At special positions: 0 Unit cell: (156.88, 156.88, 155.82, 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 75 16.00 O 8775 8.00 N 7980 7.00 C 27585 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 - 3.00 Amino acid : True - 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: 3.33 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10980 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 90 sheets defined 23.5% alpha, 52.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'G' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU G 190 " --> pdb=" O MET G 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN G 194 " --> pdb=" O GLU G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 238 Processing helix chain 'G' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU G 260 " --> pdb=" O ASP G 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR G 263 " --> pdb=" O THR G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 318 Processing helix chain 'G' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU G 377 " --> pdb=" O LEU G 373 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE G 549 " --> pdb=" O GLY G 546 " (cutoff:3.500A) Processing helix chain 'G' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU G 576 " --> pdb=" O ASP G 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE G 590 " --> pdb=" O ASP G 586 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU O 190 " --> pdb=" O MET O 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL O 191 " --> pdb=" O ASP O 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN O 194 " --> pdb=" O GLU O 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 238 Processing helix chain 'O' and resid 256 through 268 removed outlier: 3.689A pdb=" N LEU O 260 " --> pdb=" O ASP O 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR O 263 " --> pdb=" O THR O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 318 Processing helix chain 'O' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU O 377 " --> pdb=" O LEU O 373 " (cutoff:3.500A) Processing helix chain 'O' and resid 545 through 549 removed outlier: 3.643A pdb=" N PHE O 549 " --> pdb=" O GLY O 546 " (cutoff:3.500A) Processing helix chain 'O' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU O 576 " --> pdb=" O ASP O 572 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE O 590 " --> pdb=" O ASP O 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU A 190 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 238 Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 318 Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.953A pdb=" N GLU A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE A 549 " --> pdb=" O GLY A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 592 removed outlier: 3.673A pdb=" N LEU A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU B 190 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 238 Processing helix chain 'B' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 318 Processing helix chain 'B' and resid 368 through 381 removed outlier: 3.953A pdb=" N GLU B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE B 549 " --> pdb=" O GLY B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 592 removed outlier: 3.673A pdb=" N LEU B 576 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU C 190 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 238 Processing helix chain 'C' and resid 256 through 268 removed outlier: 3.689A pdb=" N LEU C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 263 " --> pdb=" O THR C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 318 Processing helix chain 'C' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE C 549 " --> pdb=" O GLY C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU C 576 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU D 190 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 238 Processing helix chain 'D' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR D 263 " --> pdb=" O THR D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 318 Processing helix chain 'D' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE D 549 " --> pdb=" O GLY D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU D 576 " --> pdb=" O ASP D 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 194 removed outlier: 4.440A pdb=" N GLU E 190 " --> pdb=" O MET E 186 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN E 194 " --> pdb=" O GLU E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 238 Processing helix chain 'E' and resid 256 through 268 removed outlier: 3.689A pdb=" N LEU E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR E 263 " --> pdb=" O THR E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 318 Processing helix chain 'E' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU E 377 " --> pdb=" O LEU E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 549 removed outlier: 3.645A pdb=" N PHE E 549 " --> pdb=" O GLY E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 592 removed outlier: 3.673A pdb=" N LEU E 576 " --> pdb=" O ASP E 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE E 590 " --> pdb=" O ASP E 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU F 190 " --> pdb=" O MET F 186 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 238 Processing helix chain 'F' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR F 263 " --> pdb=" O THR F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 318 Processing helix chain 'F' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU F 377 " --> pdb=" O LEU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE F 549 " --> pdb=" O GLY F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU F 576 " --> pdb=" O ASP F 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE F 590 " --> pdb=" O ASP F 586 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 194 removed outlier: 4.440A pdb=" N GLU H 190 " --> pdb=" O MET H 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL H 191 " --> pdb=" O ASP H 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN H 194 " --> pdb=" O GLU H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 238 Processing helix chain 'H' and resid 256 through 268 removed outlier: 3.689A pdb=" N LEU H 260 " --> pdb=" O ASP H 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR H 263 " --> pdb=" O THR H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 318 Processing helix chain 'H' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU H 377 " --> pdb=" O LEU H 373 " (cutoff:3.500A) Processing helix chain 'H' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE H 549 " --> pdb=" O GLY H 546 " (cutoff:3.500A) Processing helix chain 'H' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU H 576 " --> pdb=" O ASP H 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE H 590 " --> pdb=" O ASP H 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU I 190 " --> pdb=" O MET I 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL I 191 " --> pdb=" O ASP I 187 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN I 194 " --> pdb=" O GLU I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 238 Processing helix chain 'I' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU I 260 " --> pdb=" O ASP I 256 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR I 263 " --> pdb=" O THR I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 318 Processing helix chain 'I' and resid 368 through 381 removed outlier: 3.953A pdb=" N GLU I 377 " --> pdb=" O LEU I 373 " (cutoff:3.500A) Processing helix chain 'I' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE I 549 " --> pdb=" O GLY I 546 " (cutoff:3.500A) Processing helix chain 'I' and resid 572 through 592 removed outlier: 3.673A pdb=" N LEU I 576 " --> pdb=" O ASP I 572 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE I 590 " --> pdb=" O ASP I 586 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU J 190 " --> pdb=" O MET J 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL J 191 " --> pdb=" O ASP J 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN J 194 " --> pdb=" O GLU J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 238 Processing helix chain 'J' and resid 256 through 268 removed outlier: 3.689A pdb=" N LEU J 260 " --> pdb=" O ASP J 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR J 263 " --> pdb=" O THR J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 318 Processing helix chain 'J' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU J 377 " --> pdb=" O LEU J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE J 549 " --> pdb=" O GLY J 546 " (cutoff:3.500A) Processing helix chain 'J' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU J 576 " --> pdb=" O ASP J 572 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE J 590 " --> pdb=" O ASP J 586 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU K 190 " --> pdb=" O MET K 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL K 191 " --> pdb=" O ASP K 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN K 194 " --> pdb=" O GLU K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 238 Processing helix chain 'K' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU K 260 " --> pdb=" O ASP K 256 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR K 263 " --> pdb=" O THR K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 318 Processing helix chain 'K' and resid 368 through 381 removed outlier: 3.951A pdb=" N GLU K 377 " --> pdb=" O LEU K 373 " (cutoff:3.500A) Processing helix chain 'K' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE K 549 " --> pdb=" O GLY K 546 " (cutoff:3.500A) Processing helix chain 'K' and resid 572 through 592 removed outlier: 3.673A pdb=" N LEU K 576 " --> pdb=" O ASP K 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE K 590 " --> pdb=" O ASP K 586 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU L 190 " --> pdb=" O MET L 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL L 191 " --> pdb=" O ASP L 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN L 194 " --> pdb=" O GLU L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 238 Processing helix chain 'L' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU L 260 " --> pdb=" O ASP L 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR L 263 " --> pdb=" O THR L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 318 Processing helix chain 'L' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU L 377 " --> pdb=" O LEU L 373 " (cutoff:3.500A) Processing helix chain 'L' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE L 549 " --> pdb=" O GLY L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 592 removed outlier: 3.675A pdb=" N LEU L 576 " --> pdb=" O ASP L 572 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE L 590 " --> pdb=" O ASP L 586 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 194 removed outlier: 4.440A pdb=" N GLU M 190 " --> pdb=" O MET M 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL M 191 " --> pdb=" O ASP M 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN M 194 " --> pdb=" O GLU M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 238 Processing helix chain 'M' and resid 256 through 268 removed outlier: 3.689A pdb=" N LEU M 260 " --> pdb=" O ASP M 256 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR M 263 " --> pdb=" O THR M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 318 Processing helix chain 'M' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU M 377 " --> pdb=" O LEU M 373 " (cutoff:3.500A) Processing helix chain 'M' and resid 545 through 549 removed outlier: 3.645A pdb=" N PHE M 549 " --> pdb=" O GLY M 546 " (cutoff:3.500A) Processing helix chain 'M' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU M 576 " --> pdb=" O ASP M 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE M 590 " --> pdb=" O ASP M 586 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU N 190 " --> pdb=" O MET N 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL N 191 " --> pdb=" O ASP N 187 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN N 194 " --> pdb=" O GLU N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 238 Processing helix chain 'N' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU N 260 " --> pdb=" O ASP N 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR N 263 " --> pdb=" O THR N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 306 through 318 Processing helix chain 'N' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU N 377 " --> pdb=" O LEU N 373 " (cutoff:3.500A) Processing helix chain 'N' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE N 549 " --> pdb=" O GLY N 546 " (cutoff:3.500A) Processing helix chain 'N' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU N 576 " --> pdb=" O ASP N 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE N 590 " --> pdb=" O ASP N 586 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 175 through 178 Processing sheet with id=AA2, first strand: chain 'G' and resid 247 through 251 Processing sheet with id=AA3, first strand: chain 'G' and resid 326 through 350 removed outlier: 6.278A pdb=" N SER G 551 " --> pdb=" O GLU G 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU G 533 " --> pdb=" O SER G 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS G 553 " --> pdb=" O GLN G 531 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN G 531 " --> pdb=" O LYS G 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR G 555 " --> pdb=" O VAL G 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL G 529 " --> pdb=" O THR G 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR G 557 " --> pdb=" O ASP G 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP G 527 " --> pdb=" O THR G 557 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG G 559 " --> pdb=" O ILE G 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE G 525 " --> pdb=" O ARG G 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU G 561 " --> pdb=" O GLY G 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY G 523 " --> pdb=" O LEU G 561 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL G 563 " --> pdb=" O ILE G 521 " (cutoff:3.500A) removed outlier: 16.934A pdb=" N ILE G 519 " --> pdb=" O LEU H 422 " (cutoff:3.500A) removed outlier: 13.862A pdb=" N LEU H 422 " --> pdb=" O ILE G 519 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE G 521 " --> pdb=" O LEU H 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA H 407 " --> pdb=" O GLN H 341 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER H 551 " --> pdb=" O GLU H 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU H 533 " --> pdb=" O SER H 551 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS H 553 " --> pdb=" O GLN H 531 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN H 531 " --> pdb=" O LYS H 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR H 555 " --> pdb=" O VAL H 529 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL H 529 " --> pdb=" O THR H 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR H 557 " --> pdb=" O ASP H 527 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP H 527 " --> pdb=" O THR H 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG H 559 " --> pdb=" O ILE H 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE H 525 " --> pdb=" O ARG H 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU H 561 " --> pdb=" O GLY H 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY H 523 " --> pdb=" O LEU H 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL H 563 " --> pdb=" O ILE H 521 " (cutoff:3.500A) removed outlier: 16.784A pdb=" N ILE H 519 " --> pdb=" O LEU I 422 " (cutoff:3.500A) removed outlier: 13.731A pdb=" N LEU I 422 " --> pdb=" O ILE H 519 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE H 521 " --> pdb=" O LEU I 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA I 407 " --> pdb=" O GLN I 341 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER I 551 " --> pdb=" O GLU I 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU I 533 " --> pdb=" O SER I 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS I 553 " --> pdb=" O GLN I 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN I 531 " --> pdb=" O LYS I 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR I 555 " --> pdb=" O VAL I 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL I 529 " --> pdb=" O THR I 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR I 557 " --> pdb=" O ASP I 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP I 527 " --> pdb=" O THR I 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG I 559 " --> pdb=" O ILE I 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE I 525 " --> pdb=" O ARG I 559 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU I 561 " --> pdb=" O GLY I 523 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY I 523 " --> pdb=" O LEU I 561 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL I 563 " --> pdb=" O ILE I 521 " (cutoff:3.500A) removed outlier: 17.066A pdb=" N ILE I 519 " --> pdb=" O LEU J 422 " (cutoff:3.500A) removed outlier: 13.983A pdb=" N LEU J 422 " --> pdb=" O ILE I 519 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE I 521 " --> pdb=" O LEU J 420 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA J 407 " --> pdb=" O GLN J 341 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER J 551 " --> pdb=" O GLU J 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU J 533 " --> pdb=" O SER J 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS J 553 " --> pdb=" O GLN J 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN J 531 " --> pdb=" O LYS J 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR J 555 " --> pdb=" O VAL J 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL J 529 " --> pdb=" O THR J 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR J 557 " --> pdb=" O ASP J 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP J 527 " --> pdb=" O THR J 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG J 559 " --> pdb=" O ILE J 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE J 525 " --> pdb=" O ARG J 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU J 561 " --> pdb=" O GLY J 523 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY J 523 " --> pdb=" O LEU J 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL J 563 " --> pdb=" O ILE J 521 " (cutoff:3.500A) removed outlier: 16.868A pdb=" N ILE J 519 " --> pdb=" O LEU K 422 " (cutoff:3.500A) removed outlier: 13.838A pdb=" N LEU K 422 " --> pdb=" O ILE J 519 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE J 521 " --> pdb=" O LEU K 420 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN K 408 " --> pdb=" O GLU J 533 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA K 407 " --> pdb=" O GLN K 341 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER K 551 " --> pdb=" O GLU K 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU K 533 " --> pdb=" O SER K 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS K 553 " --> pdb=" O GLN K 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN K 531 " --> pdb=" O LYS K 553 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR K 555 " --> pdb=" O VAL K 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL K 529 " --> pdb=" O THR K 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR K 557 " --> pdb=" O ASP K 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP K 527 " --> pdb=" O THR K 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG K 559 " --> pdb=" O ILE K 525 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE K 525 " --> pdb=" O ARG K 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU K 561 " --> pdb=" O GLY K 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY K 523 " --> pdb=" O LEU K 561 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL K 563 " --> pdb=" O ILE K 521 " (cutoff:3.500A) removed outlier: 16.947A pdb=" N ILE K 519 " --> pdb=" O LEU L 422 " (cutoff:3.500A) removed outlier: 13.910A pdb=" N LEU L 422 " --> pdb=" O ILE K 519 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE K 521 " --> pdb=" O LEU L 420 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN L 408 " --> pdb=" O GLU K 533 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA L 407 " --> pdb=" O GLN L 341 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER L 551 " --> pdb=" O GLU L 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU L 533 " --> pdb=" O SER L 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS L 553 " --> pdb=" O GLN L 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN L 531 " --> pdb=" O LYS L 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR L 555 " --> pdb=" O VAL L 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL L 529 " --> pdb=" O THR L 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR L 557 " --> pdb=" O ASP L 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP L 527 " --> pdb=" O THR L 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG L 559 " --> pdb=" O ILE L 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE L 525 " --> pdb=" O ARG L 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU L 561 " --> pdb=" O GLY L 523 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY L 523 " --> pdb=" O LEU L 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL L 563 " --> pdb=" O ILE L 521 " (cutoff:3.500A) removed outlier: 17.013A pdb=" N ILE L 519 " --> pdb=" O LEU M 422 " (cutoff:3.500A) removed outlier: 13.965A pdb=" N LEU M 422 " --> pdb=" O ILE L 519 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE L 521 " --> pdb=" O LEU M 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA M 407 " --> pdb=" O GLN M 341 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER M 551 " --> pdb=" O GLU M 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU M 533 " --> pdb=" O SER M 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS M 553 " --> pdb=" O GLN M 531 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN M 531 " --> pdb=" O LYS M 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR M 555 " --> pdb=" O VAL M 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL M 529 " --> pdb=" O THR M 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR M 557 " --> pdb=" O ASP M 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP M 527 " --> pdb=" O THR M 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG M 559 " --> pdb=" O ILE M 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE M 525 " --> pdb=" O ARG M 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU M 561 " --> pdb=" O GLY M 523 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY M 523 " --> pdb=" O LEU M 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL M 563 " --> pdb=" O ILE M 521 " (cutoff:3.500A) removed outlier: 17.204A pdb=" N ILE M 519 " --> pdb=" O LEU N 422 " (cutoff:3.500A) removed outlier: 14.157A pdb=" N LEU N 422 " --> pdb=" O ILE M 519 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE M 521 " --> pdb=" O LEU N 420 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA N 407 " --> pdb=" O GLN N 341 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER N 551 " --> pdb=" O GLU N 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU N 533 " --> pdb=" O SER N 551 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS N 553 " --> pdb=" O GLN N 531 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN N 531 " --> pdb=" O LYS N 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR N 555 " --> pdb=" O VAL N 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL N 529 " --> pdb=" O THR N 555 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR N 557 " --> pdb=" O ASP N 527 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP N 527 " --> pdb=" O THR N 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG N 559 " --> pdb=" O ILE N 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE N 525 " --> pdb=" O ARG N 559 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU N 561 " --> pdb=" O GLY N 523 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY N 523 " --> pdb=" O LEU N 561 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL N 563 " --> pdb=" O ILE N 521 " (cutoff:3.500A) removed outlier: 16.786A pdb=" N ILE N 519 " --> pdb=" O LEU O 422 " (cutoff:3.500A) removed outlier: 13.602A pdb=" N LEU O 422 " --> pdb=" O ILE N 519 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE N 521 " --> pdb=" O LEU O 420 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN O 408 " --> pdb=" O GLU N 533 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS N 535 " --> pdb=" O SER O 406 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA O 407 " --> pdb=" O GLN O 341 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER O 551 " --> pdb=" O GLU O 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU O 533 " --> pdb=" O SER O 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS O 553 " --> pdb=" O GLN O 531 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN O 531 " --> pdb=" O LYS O 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR O 555 " --> pdb=" O VAL O 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL O 529 " --> pdb=" O THR O 555 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR O 557 " --> pdb=" O ASP O 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP O 527 " --> pdb=" O THR O 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG O 559 " --> pdb=" O ILE O 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE O 525 " --> pdb=" O ARG O 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU O 561 " --> pdb=" O GLY O 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY O 523 " --> pdb=" O LEU O 561 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL O 563 " --> pdb=" O ILE O 521 " (cutoff:3.500A) removed outlier: 16.922A pdb=" N ILE O 519 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 13.859A pdb=" N LEU A 422 " --> pdb=" O ILE O 519 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE O 521 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 407 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER A 551 " --> pdb=" O GLU A 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A 533 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS A 553 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN A 531 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR A 555 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A 529 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR A 557 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP A 527 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG A 559 " --> pdb=" O ILE A 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A 525 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 561 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY A 523 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 563 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 17.066A pdb=" N ILE A 519 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 13.968A pdb=" N LEU B 422 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE A 521 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B 407 " --> pdb=" O GLN B 341 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER B 551 " --> pdb=" O GLU B 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU B 533 " --> pdb=" O SER B 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS B 553 " --> pdb=" O GLN B 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN B 531 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR B 555 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL B 529 " --> pdb=" O THR B 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR B 557 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP B 527 " --> pdb=" O THR B 557 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG B 559 " --> pdb=" O ILE B 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE B 525 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 561 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY B 523 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL B 563 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP B 527 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 414 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 529 " --> pdb=" O ASN C 412 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN C 412 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 531 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 410 " --> pdb=" O GLN B 531 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 533 " --> pdb=" O ASN C 408 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN C 408 " --> pdb=" O GLU B 533 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS B 535 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER C 406 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 407 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER C 551 " --> pdb=" O GLU C 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU C 533 " --> pdb=" O SER C 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS C 553 " --> pdb=" O GLN C 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN C 531 " --> pdb=" O LYS C 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR C 555 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL C 529 " --> pdb=" O THR C 555 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR C 557 " --> pdb=" O ASP C 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP C 527 " --> pdb=" O THR C 557 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG C 559 " --> pdb=" O ILE C 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE C 525 " --> pdb=" O ARG C 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 561 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY C 523 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL C 563 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 16.673A pdb=" N ILE C 519 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 13.429A pdb=" N LEU D 422 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 521 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA D 407 " --> pdb=" O GLN D 341 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER D 551 " --> pdb=" O GLU D 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU D 533 " --> pdb=" O SER D 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS D 553 " --> pdb=" O GLN D 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN D 531 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR D 555 " --> pdb=" O VAL D 529 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL D 529 " --> pdb=" O THR D 555 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR D 557 " --> pdb=" O ASP D 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP D 527 " --> pdb=" O THR D 557 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG D 559 " --> pdb=" O ILE D 525 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE D 525 " --> pdb=" O ARG D 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU D 561 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY D 523 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL D 563 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 17.532A pdb=" N ILE D 519 " --> pdb=" O LEU E 422 " (cutoff:3.500A) removed outlier: 14.679A pdb=" N LEU E 422 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE D 521 " --> pdb=" O LEU E 420 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU E 420 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY D 523 " --> pdb=" O SER E 418 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER E 418 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER E 551 " --> pdb=" O GLU E 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU E 533 " --> pdb=" O SER E 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS E 553 " --> pdb=" O GLN E 531 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN E 531 " --> pdb=" O LYS E 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR E 555 " --> pdb=" O VAL E 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL E 529 " --> pdb=" O THR E 555 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR E 557 " --> pdb=" O ASP E 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP E 527 " --> pdb=" O THR E 557 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG E 559 " --> pdb=" O ILE E 525 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE E 525 " --> pdb=" O ARG E 559 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU E 561 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY E 523 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL E 563 " --> pdb=" O ILE E 521 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 519 through 535 current: chain 'F' and resid 551 through 570 removed outlier: 6.277A pdb=" N SER F 551 " --> pdb=" O GLU F 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU F 533 " --> pdb=" O SER F 551 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS F 553 " --> pdb=" O GLN F 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN F 531 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR F 555 " --> pdb=" O VAL F 529 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL F 529 " --> pdb=" O THR F 555 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR F 557 " --> pdb=" O ASP F 527 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP F 527 " --> pdb=" O THR F 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG F 559 " --> pdb=" O ILE F 525 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE F 525 " --> pdb=" O ARG F 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU F 561 " --> pdb=" O GLY F 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY F 523 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL F 563 " --> pdb=" O ILE F 521 " (cutoff:3.500A) removed outlier: 16.782A pdb=" N ILE F 519 " --> pdb=" O LEU G 422 " (cutoff:3.500A) removed outlier: 13.736A pdb=" N LEU G 422 " --> pdb=" O ILE F 519 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE F 521 " --> pdb=" O LEU G 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA G 407 " --> pdb=" O GLN G 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE G 350 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA G 407 " --> pdb=" O GLN G 341 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE G 398 " --> pdb=" O SER G 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE H 350 " --> pdb=" O THR H 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA H 407 " --> pdb=" O GLN H 341 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE H 398 " --> pdb=" O SER H 395 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE I 350 " --> pdb=" O THR I 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA I 407 " --> pdb=" O GLN I 341 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE I 398 " --> pdb=" O SER I 395 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE J 350 " --> pdb=" O THR J 358 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA J 407 " --> pdb=" O GLN J 341 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE J 398 " --> pdb=" O SER J 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE K 350 " --> pdb=" O THR K 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA K 407 " --> pdb=" O GLN K 341 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE K 398 " --> pdb=" O SER K 395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 358 through 359 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 358 through 359 current: chain 'L' and resid 389 through 395 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE M 350 " --> pdb=" O THR M 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA M 407 " --> pdb=" O GLN M 341 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE M 398 " --> pdb=" O SER M 395 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 358 through 359 removed outlier: 3.888A pdb=" N ILE N 350 " --> pdb=" O THR N 358 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA N 407 " --> pdb=" O GLN N 341 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE N 398 " --> pdb=" O SER N 395 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE O 350 " --> pdb=" O THR O 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA O 407 " --> pdb=" O GLN O 341 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE O 398 " --> pdb=" O SER O 395 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 358 through 359 removed outlier: 3.888A pdb=" N ILE A 350 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 407 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A 398 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 358 through 359 removed outlier: 3.886A pdb=" N ILE B 350 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE B 398 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 389 through 395 removed outlier: 3.935A pdb=" N PHE C 398 " --> pdb=" O SER C 395 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 407 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE C 350 " --> pdb=" O THR C 358 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 389 through 395 removed outlier: 3.935A pdb=" N PHE C 398 " --> pdb=" O SER C 395 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 407 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE C 350 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE C 350 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 418 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 420 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE B 521 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 14.524A pdb=" N LEU C 422 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 17.506A pdb=" N ILE B 519 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP B 527 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 414 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 529 " --> pdb=" O ASN C 412 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN C 412 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 531 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 410 " --> pdb=" O GLN B 531 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 533 " --> pdb=" O ASN C 408 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN C 408 " --> pdb=" O GLU B 533 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS B 535 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER C 406 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE C 398 " --> pdb=" O SER C 395 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE D 350 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA D 407 " --> pdb=" O GLN D 341 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE D 398 " --> pdb=" O SER D 395 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE E 350 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN E 408 " --> pdb=" O GLU D 533 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU D 533 " --> pdb=" O ASN E 408 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS E 410 " --> pdb=" O GLN D 531 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN D 531 " --> pdb=" O LYS E 410 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN E 412 " --> pdb=" O VAL D 529 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL D 529 " --> pdb=" O ASN E 412 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 414 " --> pdb=" O ASP D 527 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP D 527 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 17.532A pdb=" N ILE D 519 " --> pdb=" O LEU E 422 " (cutoff:3.500A) removed outlier: 14.679A pdb=" N LEU E 422 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE D 521 " --> pdb=" O LEU E 420 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU E 420 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY D 523 " --> pdb=" O SER E 418 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER E 418 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE E 398 " --> pdb=" O SER E 395 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 358 through 359 removed outlier: 3.888A pdb=" N ILE F 350 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA F 407 " --> pdb=" O GLN F 341 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE F 398 " --> pdb=" O SER F 395 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 429 through 431 Processing sheet with id=AC3, first strand: chain 'G' and resid 429 through 431 Processing sheet with id=AC4, first strand: chain 'G' and resid 434 through 437 Processing sheet with id=AC5, first strand: chain 'O' and resid 175 through 178 Processing sheet with id=AC6, first strand: chain 'O' and resid 247 through 251 Processing sheet with id=AC7, first strand: chain 'O' and resid 429 through 431 Processing sheet with id=AC8, first strand: chain 'O' and resid 429 through 431 Processing sheet with id=AC9, first strand: chain 'O' and resid 434 through 437 Processing sheet with id=AD1, first strand: chain 'A' and resid 175 through 178 Processing sheet with id=AD2, first strand: chain 'A' and resid 247 through 251 Processing sheet with id=AD3, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AD4, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AD5, first strand: chain 'A' and resid 434 through 437 Processing sheet with id=AD6, first strand: chain 'B' and resid 175 through 178 Processing sheet with id=AD7, first strand: chain 'B' and resid 247 through 251 Processing sheet with id=AD8, first strand: chain 'B' and resid 429 through 431 Processing sheet with id=AD9, first strand: chain 'B' and resid 429 through 431 Processing sheet with id=AE1, first strand: chain 'B' and resid 434 through 437 Processing sheet with id=AE2, first strand: chain 'C' and resid 175 through 178 Processing sheet with id=AE3, first strand: chain 'C' and resid 247 through 251 Processing sheet with id=AE4, first strand: chain 'C' and resid 429 through 431 Processing sheet with id=AE5, first strand: chain 'C' and resid 429 through 431 Processing sheet with id=AE6, first strand: chain 'C' and resid 434 through 437 Processing sheet with id=AE7, first strand: chain 'D' and resid 175 through 178 Processing sheet with id=AE8, first strand: chain 'D' and resid 247 through 251 Processing sheet with id=AE9, first strand: chain 'D' and resid 429 through 431 Processing sheet with id=AF1, first strand: chain 'D' and resid 510 through 513 Processing sheet with id=AF2, first strand: chain 'D' and resid 434 through 437 Processing sheet with id=AF3, first strand: chain 'E' and resid 175 through 178 Processing sheet with id=AF4, first strand: chain 'E' and resid 247 through 251 Processing sheet with id=AF5, first strand: chain 'E' and resid 434 through 437 Processing sheet with id=AF6, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AF7, first strand: chain 'F' and resid 247 through 251 Processing sheet with id=AF8, first strand: chain 'F' and resid 429 through 431 Processing sheet with id=AF9, first strand: chain 'F' and resid 429 through 431 Processing sheet with id=AG1, first strand: chain 'F' and resid 434 through 437 Processing sheet with id=AG2, first strand: chain 'H' and resid 175 through 178 Processing sheet with id=AG3, first strand: chain 'H' and resid 247 through 251 Processing sheet with id=AG4, first strand: chain 'H' and resid 429 through 431 Processing sheet with id=AG5, first strand: chain 'H' and resid 429 through 431 Processing sheet with id=AG6, first strand: chain 'H' and resid 434 through 437 Processing sheet with id=AG7, first strand: chain 'I' and resid 175 through 178 Processing sheet with id=AG8, first strand: chain 'I' and resid 247 through 251 Processing sheet with id=AG9, first strand: chain 'I' and resid 429 through 431 Processing sheet with id=AH1, first strand: chain 'I' and resid 429 through 431 Processing sheet with id=AH2, first strand: chain 'I' and resid 434 through 437 Processing sheet with id=AH3, first strand: chain 'J' and resid 175 through 178 Processing sheet with id=AH4, first strand: chain 'J' and resid 247 through 251 Processing sheet with id=AH5, first strand: chain 'J' and resid 429 through 431 Processing sheet with id=AH6, first strand: chain 'J' and resid 429 through 431 Processing sheet with id=AH7, first strand: chain 'J' and resid 434 through 437 Processing sheet with id=AH8, first strand: chain 'K' and resid 175 through 178 Processing sheet with id=AH9, first strand: chain 'K' and resid 247 through 251 Processing sheet with id=AI1, first strand: chain 'K' and resid 429 through 431 Processing sheet with id=AI2, first strand: chain 'K' and resid 429 through 431 Processing sheet with id=AI3, first strand: chain 'K' and resid 434 through 437 Processing sheet with id=AI4, first strand: chain 'L' and resid 175 through 178 Processing sheet with id=AI5, first strand: chain 'L' and resid 247 through 251 Processing sheet with id=AI6, first strand: chain 'L' and resid 429 through 431 Processing sheet with id=AI7, first strand: chain 'L' and resid 429 through 431 Processing sheet with id=AI8, first strand: chain 'L' and resid 434 through 437 Processing sheet with id=AI9, first strand: chain 'M' and resid 175 through 178 Processing sheet with id=AJ1, first strand: chain 'M' and resid 247 through 251 Processing sheet with id=AJ2, first strand: chain 'M' and resid 429 through 431 Processing sheet with id=AJ3, first strand: chain 'M' and resid 429 through 431 Processing sheet with id=AJ4, first strand: chain 'M' and resid 434 through 437 Processing sheet with id=AJ5, first strand: chain 'N' and resid 175 through 178 Processing sheet with id=AJ6, first strand: chain 'N' and resid 247 through 251 Processing sheet with id=AJ7, first strand: chain 'N' and resid 429 through 431 Processing sheet with id=AJ8, first strand: chain 'N' and resid 429 through 431 Processing sheet with id=AJ9, first strand: chain 'N' and resid 434 through 437 2904 hydrogen bonds defined for protein. 7992 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: 11.23 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13631 1.33 - 1.45: 5105 1.45 - 1.57: 25919 1.57 - 1.69: 0 1.69 - 1.80: 150 Bond restraints: 44805 Sorted by residual: bond pdb=" C ALA K 381 " pdb=" N PRO K 382 " ideal model delta sigma weight residual 1.334 1.400 -0.067 2.34e-02 1.83e+03 8.08e+00 bond pdb=" C ALA O 381 " pdb=" N PRO O 382 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 8.05e+00 bond pdb=" C ALA H 381 " pdb=" N PRO H 382 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 8.03e+00 bond pdb=" C ALA E 381 " pdb=" N PRO E 382 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 7.99e+00 bond pdb=" C ALA D 381 " pdb=" N PRO D 382 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 7.98e+00 ... (remaining 44800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 54024 1.60 - 3.21: 5246 3.21 - 4.81: 1051 4.81 - 6.41: 301 6.41 - 8.01: 128 Bond angle restraints: 60750 Sorted by residual: angle pdb=" C SER I 395 " pdb=" N SER I 396 " pdb=" CA SER I 396 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C SER F 395 " pdb=" N SER F 396 " pdb=" CA SER F 396 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C SER E 395 " pdb=" N SER E 396 " pdb=" CA SER E 396 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C SER C 395 " pdb=" N SER C 396 " pdb=" CA SER C 396 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C SER K 395 " pdb=" N SER K 396 " pdb=" CA SER K 396 " ideal model delta sigma weight residual 121.54 129.39 -7.85 1.91e+00 2.74e-01 1.69e+01 ... (remaining 60745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.18: 25885 14.18 - 28.37: 1461 28.37 - 42.55: 269 42.55 - 56.73: 30 56.73 - 70.91: 30 Dihedral angle restraints: 27675 sinusoidal: 10785 harmonic: 16890 Sorted by residual: dihedral pdb=" CA ALA M 242 " pdb=" C ALA M 242 " pdb=" N ARG M 243 " pdb=" CA ARG M 243 " ideal model delta harmonic sigma weight residual -180.00 -155.43 -24.57 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA ALA I 242 " pdb=" C ALA I 242 " pdb=" N ARG I 243 " pdb=" CA ARG I 243 " ideal model delta harmonic sigma weight residual -180.00 -155.44 -24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ALA B 242 " pdb=" C ALA B 242 " pdb=" N ARG B 243 " pdb=" CA ARG B 243 " ideal model delta harmonic sigma weight residual -180.00 -155.45 -24.55 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 27672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 5533 0.060 - 0.120: 1501 0.120 - 0.181: 391 0.181 - 0.241: 64 0.241 - 0.301: 56 Chirality restraints: 7545 Sorted by residual: chirality pdb=" CB ILE C 507 " pdb=" CA ILE C 507 " pdb=" CG1 ILE C 507 " pdb=" CG2 ILE C 507 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE I 507 " pdb=" CA ILE I 507 " pdb=" CG1 ILE I 507 " pdb=" CG2 ILE I 507 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB ILE H 507 " pdb=" CA ILE H 507 " pdb=" CG1 ILE H 507 " pdb=" CG2 ILE H 507 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 7542 not shown) Planarity restraints: 7905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 468 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.45e+00 pdb=" N PRO I 469 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO I 469 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 469 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 468 " 0.048 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO B 469 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 469 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 469 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR K 468 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO K 469 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO K 469 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO K 469 " 0.040 5.00e-02 4.00e+02 ... (remaining 7902 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5244 2.75 - 3.28: 41261 3.28 - 3.82: 67688 3.82 - 4.36: 78319 4.36 - 4.90: 141300 Nonbonded interactions: 333812 Sorted by model distance: nonbonded pdb=" NH2 ARG O 458 " pdb=" O THR N 498 " model vdw 2.206 3.120 nonbonded pdb=" O THR C 498 " pdb=" NH2 ARG D 458 " model vdw 2.214 3.120 nonbonded pdb=" OD1 ASP M 339 " pdb=" OG1 THR M 409 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP O 339 " pdb=" OG1 THR O 409 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP F 339 " pdb=" OG1 THR F 409 " model vdw 2.219 3.040 ... (remaining 333807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'O' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 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: 0.060 Extract box with map and model: 0.510 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 35.090 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.280 ------------------------------------------------------------------------------- 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 : 0.010 0.067 44805 Z= 0.432 Angle : 1.135 8.013 60750 Z= 0.603 Chirality : 0.064 0.301 7545 Planarity : 0.008 0.073 7905 Dihedral : 10.118 70.914 16695 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 0.31 % Allowed : 4.29 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.04 (0.09), residues: 5790 helix: -2.68 (0.10), residues: 1245 sheet: -2.88 (0.09), residues: 2610 loop : -4.09 (0.09), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 559 TYR 0.006 0.002 TYR A 584 PHE 0.015 0.003 PHE J 437 TRP 0.008 0.001 TRP D 184 HIS 0.009 0.004 HIS K 556 Details of bonding type rmsd covalent geometry : bond 0.00954 (44805) covalent geometry : angle 1.13451 (60750) hydrogen bonds : bond 0.10580 ( 2456) hydrogen bonds : angle 8.11423 ( 7992) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 797 time to evaluate : 1.527 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: G 271 MET cc_start: 0.7280 (mmm) cc_final: 0.6957 (mtm) REVERT: G 330 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6812 (tm-30) REVERT: G 355 MET cc_start: 0.5301 (tpt) cc_final: 0.5077 (tpt) REVERT: E 218 LEU cc_start: 0.8526 (tp) cc_final: 0.8296 (tp) REVERT: E 566 ARG cc_start: 0.7379 (tpt-90) cc_final: 0.6838 (mtt180) REVERT: F 271 MET cc_start: 0.7351 (mmm) cc_final: 0.6880 (mtm) REVERT: H 271 MET cc_start: 0.6982 (mmm) cc_final: 0.6684 (mtm) REVERT: I 181 ARG cc_start: 0.7297 (mtm110) cc_final: 0.7089 (mtm-85) REVERT: J 271 MET cc_start: 0.7112 (mmm) cc_final: 0.6806 (mtm) REVERT: J 511 ILE cc_start: 0.8673 (pp) cc_final: 0.8301 (mp) REVERT: K 511 ILE cc_start: 0.8522 (pp) cc_final: 0.8293 (mp) REVERT: L 271 MET cc_start: 0.7338 (mmm) cc_final: 0.6879 (mtt) REVERT: M 218 LEU cc_start: 0.8965 (tp) cc_final: 0.8645 (tt) REVERT: M 271 MET cc_start: 0.7292 (mmm) cc_final: 0.6943 (mtm) REVERT: M 355 MET cc_start: 0.5464 (tpt) cc_final: 0.5054 (tpt) REVERT: N 302 VAL cc_start: 0.9104 (t) cc_final: 0.8880 (m) outliers start: 15 outliers final: 15 residues processed: 812 average time/residue: 0.2560 time to fit residues: 332.6531 Evaluate side-chains 360 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 345 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain O residue 529 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain N residue 529 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 20.0000 chunk 41 optimal weight: 40.0000 chunk 265 optimal weight: 0.8980 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 0.9980 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 7.9990 chunk 223 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 608 ASN O 254 HIS ** O 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 517 GLN O 560 ASN O 608 ASN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 560 ASN A 608 ASN B 179 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN C 208 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN C 608 ASN D 254 HIS ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 ASN ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 608 ASN ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 ASN ** F 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 517 GLN F 608 ASN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 608 ASN I 179 ASN ** I 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 GLN I 608 ASN ** J 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 483 GLN J 517 GLN J 608 ASN ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 608 ASN ** L 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 494 GLN L 608 ASN ** M 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 483 GLN M 517 GLN M 608 ASN ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 434 ASN ** N 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 608 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.175241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.111299 restraints weight = 53550.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.116410 restraints weight = 23717.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.119531 restraints weight = 15687.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.121225 restraints weight = 12768.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.122239 restraints weight = 11526.768| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 44805 Z= 0.196 Angle : 0.756 11.883 60750 Z= 0.385 Chirality : 0.049 0.198 7545 Planarity : 0.007 0.066 7905 Dihedral : 6.496 27.900 6255 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.84 % Favored : 90.90 % Rotamer: Outliers : 2.82 % Allowed : 10.02 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.17 (0.09), residues: 5790 helix: -1.44 (0.13), residues: 1275 sheet: -2.44 (0.09), residues: 2700 loop : -3.90 (0.11), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 181 TYR 0.010 0.001 TYR J 175 PHE 0.022 0.002 PHE A 437 TRP 0.006 0.001 TRP D 348 HIS 0.006 0.002 HIS D 556 Details of bonding type rmsd covalent geometry : bond 0.00416 (44805) covalent geometry : angle 0.75588 (60750) hydrogen bonds : bond 0.03605 ( 2456) hydrogen bonds : angle 6.28426 ( 7992) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 438 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 271 MET cc_start: 0.7215 (mmm) cc_final: 0.6808 (mtm) REVERT: G 482 GLU cc_start: 0.7256 (tt0) cc_final: 0.6924 (mt-10) REVERT: O 369 ILE cc_start: 0.8143 (mm) cc_final: 0.7883 (mt) REVERT: A 237 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7128 (mt) REVERT: C 271 MET cc_start: 0.6335 (mtt) cc_final: 0.6025 (mtm) REVERT: C 340 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8212 (mp) REVERT: D 328 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8482 (tp) REVERT: D 533 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7603 (mp0) REVERT: E 218 LEU cc_start: 0.8685 (tp) cc_final: 0.8441 (tp) REVERT: E 566 ARG cc_start: 0.7483 (tpt-90) cc_final: 0.6274 (mtt180) REVERT: F 271 MET cc_start: 0.7358 (mmm) cc_final: 0.6780 (mtm) REVERT: F 333 ILE cc_start: 0.8968 (mp) cc_final: 0.8767 (mt) REVERT: H 181 ARG cc_start: 0.7614 (mtm110) cc_final: 0.7385 (mtm-85) REVERT: H 271 MET cc_start: 0.6875 (mmm) cc_final: 0.6569 (mtm) REVERT: H 507 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7655 (mp) REVERT: H 562 MET cc_start: 0.7934 (mtm) cc_final: 0.7603 (mpp) REVERT: I 181 ARG cc_start: 0.7488 (mtm110) cc_final: 0.7210 (mtm-85) REVERT: I 335 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7735 (tm-30) REVERT: J 271 MET cc_start: 0.7061 (mmm) cc_final: 0.6648 (mtm) REVERT: J 507 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7682 (mp) REVERT: J 548 LEU cc_start: 0.8730 (mp) cc_final: 0.8518 (tp) REVERT: K 181 ARG cc_start: 0.7477 (mtm110) cc_final: 0.7041 (mtm-85) REVERT: K 328 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8164 (tp) REVERT: K 340 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8342 (mp) REVERT: L 218 LEU cc_start: 0.8916 (tp) cc_final: 0.8662 (tt) REVERT: L 220 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8523 (pt) REVERT: L 271 MET cc_start: 0.7312 (mmm) cc_final: 0.6837 (mtm) REVERT: L 340 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8297 (mp) REVERT: M 218 LEU cc_start: 0.8977 (tp) cc_final: 0.8654 (tt) REVERT: M 271 MET cc_start: 0.7333 (mmm) cc_final: 0.6892 (mtm) REVERT: M 335 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7887 (tm-30) REVERT: N 214 ARG cc_start: 0.5940 (ttp80) cc_final: 0.4866 (mtt180) REVERT: N 428 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7861 (tm-30) outliers start: 138 outliers final: 73 residues processed: 553 average time/residue: 0.2595 time to fit residues: 235.0627 Evaluate side-chains 374 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 292 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 186 MET Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 435 VAL Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 529 VAL Chi-restraints excluded: chain O residue 541 ASP Chi-restraints excluded: chain O residue 552 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 379 ASN Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 507 ILE Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 507 ILE Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 340 ILE Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 396 SER Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 340 ILE Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 241 THR Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 396 SER Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 224 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 484 optimal weight: 10.0000 chunk 477 optimal weight: 8.9990 chunk 279 optimal weight: 20.0000 chunk 337 optimal weight: 4.9990 chunk 566 optimal weight: 8.9990 chunk 273 optimal weight: 20.0000 chunk 555 optimal weight: 8.9990 chunk 197 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN C 560 ASN ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 ASN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.165688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.102062 restraints weight = 55178.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.106265 restraints weight = 25994.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.108750 restraints weight = 17841.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.110001 restraints weight = 14809.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.110832 restraints weight = 13543.123| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 44805 Z= 0.347 Angle : 0.869 9.106 60750 Z= 0.444 Chirality : 0.051 0.200 7545 Planarity : 0.007 0.065 7905 Dihedral : 6.817 37.516 6255 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.42 % Favored : 86.58 % Rotamer: Outliers : 4.40 % Allowed : 11.64 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.78 (0.10), residues: 5790 helix: -0.88 (0.13), residues: 1290 sheet: -2.26 (0.09), residues: 2580 loop : -3.75 (0.11), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 505 TYR 0.015 0.002 TYR E 584 PHE 0.019 0.002 PHE O 362 TRP 0.010 0.002 TRP B 348 HIS 0.012 0.004 HIS O 556 Details of bonding type rmsd covalent geometry : bond 0.00760 (44805) covalent geometry : angle 0.86929 (60750) hydrogen bonds : bond 0.04331 ( 2456) hydrogen bonds : angle 6.23288 ( 7992) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 346 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 218 LEU cc_start: 0.8840 (tp) cc_final: 0.8606 (tt) REVERT: G 271 MET cc_start: 0.7222 (mmm) cc_final: 0.6937 (mtm) REVERT: G 482 GLU cc_start: 0.7413 (tt0) cc_final: 0.7097 (mt-10) REVERT: G 547 ARG cc_start: 0.8714 (mmm160) cc_final: 0.7933 (tpm170) REVERT: O 212 ASP cc_start: 0.6823 (m-30) cc_final: 0.6304 (m-30) REVERT: C 271 MET cc_start: 0.6683 (mtt) cc_final: 0.6399 (mtm) REVERT: D 335 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7776 (tm-30) REVERT: E 218 LEU cc_start: 0.8854 (tp) cc_final: 0.8573 (tp) REVERT: F 214 ARG cc_start: 0.5947 (ttp80) cc_final: 0.4411 (mtt180) REVERT: F 271 MET cc_start: 0.7381 (mmm) cc_final: 0.6820 (mtm) REVERT: F 330 GLU cc_start: 0.7685 (mt-10) cc_final: 0.6991 (pp20) REVERT: F 547 ARG cc_start: 0.8556 (mmm160) cc_final: 0.8125 (tpp-160) REVERT: H 181 ARG cc_start: 0.7639 (mtm110) cc_final: 0.7358 (mtm-85) REVERT: H 271 MET cc_start: 0.7281 (mmm) cc_final: 0.6843 (mtm) REVERT: I 181 ARG cc_start: 0.7492 (mtm110) cc_final: 0.7236 (mtm-85) REVERT: I 507 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7849 (mp) REVERT: J 271 MET cc_start: 0.7170 (mmm) cc_final: 0.6786 (mtm) REVERT: J 511 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8395 (pt) REVERT: K 181 ARG cc_start: 0.7517 (mtm110) cc_final: 0.7285 (mtp180) REVERT: K 547 ARG cc_start: 0.8547 (mmm160) cc_final: 0.7916 (tpp-160) REVERT: L 218 LEU cc_start: 0.8922 (tp) cc_final: 0.8621 (tt) REVERT: L 271 MET cc_start: 0.7396 (mmm) cc_final: 0.6855 (mtt) REVERT: L 547 ARG cc_start: 0.8698 (mmm160) cc_final: 0.8115 (tpp-160) REVERT: M 218 LEU cc_start: 0.8923 (tp) cc_final: 0.8675 (tt) REVERT: M 271 MET cc_start: 0.7395 (mmm) cc_final: 0.6932 (mtm) outliers start: 215 outliers final: 145 residues processed: 538 average time/residue: 0.2640 time to fit residues: 236.7131 Evaluate side-chains 433 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 286 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 396 SER Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 511 ILE Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 409 THR Chi-restraints excluded: chain O residue 481 ILE Chi-restraints excluded: chain O residue 507 ILE Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 529 VAL Chi-restraints excluded: chain O residue 541 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 379 ASN Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 396 SER Chi-restraints excluded: chain H residue 409 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 507 ILE Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 396 SER Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 507 ILE Chi-restraints excluded: chain I residue 518 VAL Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 396 SER Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain J residue 507 ILE Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 340 ILE Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 511 ILE Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 186 MET Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 340 ILE Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain L residue 409 THR Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain M residue 186 MET Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 241 THR Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 396 SER Chi-restraints excluded: chain M residue 409 THR Chi-restraints excluded: chain M residue 491 ASN Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 256 ASP Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 396 SER Chi-restraints excluded: chain N residue 409 THR Chi-restraints excluded: chain N residue 491 ASN Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 363 optimal weight: 3.9990 chunk 464 optimal weight: 3.9990 chunk 445 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 270 optimal weight: 1.9990 chunk 391 optimal weight: 20.0000 chunk 351 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 481 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 483 GLN ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.179120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.115050 restraints weight = 55665.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.121086 restraints weight = 26085.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.122327 restraints weight = 17622.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.123047 restraints weight = 14179.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.123418 restraints weight = 14107.500| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 44805 Z= 0.171 Angle : 0.710 9.234 60750 Z= 0.360 Chirality : 0.047 0.191 7545 Planarity : 0.006 0.060 7905 Dihedral : 6.057 29.653 6255 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.22 % Favored : 90.69 % Rotamer: Outliers : 4.13 % Allowed : 13.27 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.46 (0.10), residues: 5790 helix: -0.40 (0.14), residues: 1290 sheet: -2.17 (0.09), residues: 2715 loop : -3.64 (0.12), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 181 TYR 0.018 0.001 TYR B 175 PHE 0.034 0.002 PHE K 437 TRP 0.006 0.001 TRP O 348 HIS 0.005 0.001 HIS D 556 Details of bonding type rmsd covalent geometry : bond 0.00365 (44805) covalent geometry : angle 0.71038 (60750) hydrogen bonds : bond 0.03402 ( 2456) hydrogen bonds : angle 5.82493 ( 7992) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 335 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 271 MET cc_start: 0.7227 (mmm) cc_final: 0.6880 (mtm) REVERT: G 484 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: G 547 ARG cc_start: 0.8760 (mmm160) cc_final: 0.7961 (tpm170) REVERT: O 212 ASP cc_start: 0.6794 (m-30) cc_final: 0.6323 (m-30) REVERT: O 488 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8190 (mp) REVERT: A 482 GLU cc_start: 0.7047 (tt0) cc_final: 0.6784 (mt-10) REVERT: B 547 ARG cc_start: 0.8564 (mmm160) cc_final: 0.7818 (tpp-160) REVERT: C 258 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7430 (mmtt) REVERT: C 271 MET cc_start: 0.6726 (mtt) cc_final: 0.6513 (mtm) REVERT: D 328 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8356 (tp) REVERT: D 335 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7752 (tm-30) REVERT: D 340 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8291 (mp) REVERT: E 218 LEU cc_start: 0.8878 (tp) cc_final: 0.8593 (tp) REVERT: E 221 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6972 (tt) REVERT: E 547 ARG cc_start: 0.7454 (tpp80) cc_final: 0.7239 (ttm170) REVERT: F 214 ARG cc_start: 0.5910 (ttp80) cc_final: 0.4375 (mtt180) REVERT: F 227 ARG cc_start: 0.5887 (mmp80) cc_final: 0.5535 (mmm160) REVERT: F 271 MET cc_start: 0.7338 (mmm) cc_final: 0.6751 (mtm) REVERT: H 181 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7192 (mtm-85) REVERT: H 186 MET cc_start: 0.6476 (ptt) cc_final: 0.6264 (ptm) REVERT: H 271 MET cc_start: 0.7184 (mmm) cc_final: 0.6796 (mtm) REVERT: J 271 MET cc_start: 0.7391 (mmm) cc_final: 0.7043 (mtm) REVERT: K 181 ARG cc_start: 0.7433 (mtm110) cc_final: 0.7199 (mtp180) REVERT: K 328 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8014 (tp) REVERT: K 480 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7379 (mp0) REVERT: L 218 LEU cc_start: 0.8906 (tp) cc_final: 0.8627 (tt) REVERT: L 220 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8172 (pt) REVERT: L 271 MET cc_start: 0.7339 (mmm) cc_final: 0.6844 (mtm) REVERT: L 547 ARG cc_start: 0.8635 (mmm160) cc_final: 0.8050 (tpp-160) REVERT: M 218 LEU cc_start: 0.8946 (tp) cc_final: 0.8681 (tt) REVERT: M 271 MET cc_start: 0.7335 (mmm) cc_final: 0.6856 (mtm) REVERT: N 221 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7729 (tt) REVERT: N 340 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8502 (mp) outliers start: 202 outliers final: 113 residues processed: 507 average time/residue: 0.2254 time to fit residues: 191.5043 Evaluate side-chains 407 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 284 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 186 MET Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 409 THR Chi-restraints excluded: chain O residue 435 VAL Chi-restraints excluded: chain O residue 484 GLU Chi-restraints excluded: chain O residue 488 LEU Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 529 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 175 TYR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 409 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 369 ILE Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 396 SER Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 570 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 409 THR Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 409 THR Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 409 THR Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 102 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 561 optimal weight: 10.0000 chunk 425 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 390 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 584 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 526 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 483 GLN O 179 ASN ** O 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN C 560 ASN ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 483 GLN L 517 GLN ** M 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.180629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.120830 restraints weight = 55173.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.123793 restraints weight = 26129.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.124091 restraints weight = 17589.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.125415 restraints weight = 16312.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.125525 restraints weight = 14156.712| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 44805 Z= 0.155 Angle : 0.682 14.089 60750 Z= 0.342 Chirality : 0.046 0.182 7545 Planarity : 0.006 0.060 7905 Dihedral : 5.594 22.159 6255 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.71 % Favored : 90.21 % Rotamer: Outliers : 3.95 % Allowed : 14.48 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.10), residues: 5790 helix: -0.02 (0.14), residues: 1290 sheet: -1.90 (0.09), residues: 2700 loop : -3.53 (0.12), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 181 TYR 0.009 0.001 TYR E 584 PHE 0.025 0.001 PHE N 437 TRP 0.008 0.001 TRP O 348 HIS 0.003 0.001 HIS D 556 Details of bonding type rmsd covalent geometry : bond 0.00330 (44805) covalent geometry : angle 0.68160 (60750) hydrogen bonds : bond 0.03209 ( 2456) hydrogen bonds : angle 5.56011 ( 7992) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 340 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 271 MET cc_start: 0.7359 (mmm) cc_final: 0.6956 (mtm) REVERT: G 547 ARG cc_start: 0.8568 (mmm160) cc_final: 0.7806 (tpm170) REVERT: O 212 ASP cc_start: 0.6934 (m-30) cc_final: 0.6529 (m-30) REVERT: O 488 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8188 (mp) REVERT: A 237 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6655 (mp) REVERT: B 488 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8383 (mp) REVERT: C 258 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7474 (mmtt) REVERT: C 271 MET cc_start: 0.6651 (mtt) cc_final: 0.6430 (mtm) REVERT: C 301 LEU cc_start: 0.8813 (mt) cc_final: 0.8499 (mm) REVERT: C 405 LEU cc_start: 0.7817 (tt) cc_final: 0.7006 (mt) REVERT: C 482 GLU cc_start: 0.6884 (tt0) cc_final: 0.6679 (mt-10) REVERT: D 328 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8243 (tp) REVERT: D 335 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7709 (tm-30) REVERT: D 340 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8266 (mp) REVERT: D 495 ARG cc_start: 0.6565 (ptt180) cc_final: 0.6331 (ptt180) REVERT: E 218 LEU cc_start: 0.8893 (tp) cc_final: 0.8595 (tp) REVERT: E 221 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6867 (tt) REVERT: F 214 ARG cc_start: 0.5575 (ttp80) cc_final: 0.4331 (mtt180) REVERT: F 271 MET cc_start: 0.7400 (mmm) cc_final: 0.6832 (mtm) REVERT: F 488 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8196 (mp) REVERT: H 181 ARG cc_start: 0.7377 (mtm110) cc_final: 0.7091 (mtm-85) REVERT: H 220 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8073 (pt) REVERT: H 271 MET cc_start: 0.7265 (mmm) cc_final: 0.6963 (mtp) REVERT: I 218 LEU cc_start: 0.8716 (tp) cc_final: 0.8464 (tp) REVERT: I 484 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6957 (pt0) REVERT: J 271 MET cc_start: 0.7424 (mmm) cc_final: 0.7137 (mtm) REVERT: K 181 ARG cc_start: 0.7274 (mtm110) cc_final: 0.6944 (mtm-85) REVERT: K 328 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8075 (tp) REVERT: L 218 LEU cc_start: 0.8951 (tp) cc_final: 0.8666 (tt) REVERT: L 220 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8271 (pt) REVERT: L 271 MET cc_start: 0.7294 (mmm) cc_final: 0.7078 (mtm) REVERT: M 218 LEU cc_start: 0.9037 (tp) cc_final: 0.8743 (tt) REVERT: M 271 MET cc_start: 0.7376 (mmm) cc_final: 0.6930 (mtm) REVERT: M 428 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7872 (tm-30) REVERT: N 221 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7714 (tt) REVERT: N 340 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8500 (mp) outliers start: 193 outliers final: 118 residues processed: 500 average time/residue: 0.2606 time to fit residues: 219.6417 Evaluate side-chains 437 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 305 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain O residue 175 TYR Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 409 THR Chi-restraints excluded: chain O residue 435 VAL Chi-restraints excluded: chain O residue 488 LEU Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 529 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain C residue 175 TYR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 484 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 562 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 409 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 369 ILE Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 484 GLU Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 570 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 409 THR Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 369 ILE Chi-restraints excluded: chain M residue 409 THR Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 301 LEU Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 409 THR Chi-restraints excluded: chain N residue 491 ASN Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 65 optimal weight: 0.8980 chunk 296 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 507 optimal weight: 20.0000 chunk 385 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 450 optimal weight: 9.9990 chunk 225 optimal weight: 0.7980 chunk 354 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 GLN E 494 GLN F 326 GLN H 326 GLN H 483 GLN ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.179659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.117001 restraints weight = 55237.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.121921 restraints weight = 26045.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.123068 restraints weight = 16089.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.123789 restraints weight = 14881.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.123981 restraints weight = 13777.603| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 44805 Z= 0.173 Angle : 0.682 11.144 60750 Z= 0.342 Chirality : 0.046 0.178 7545 Planarity : 0.006 0.106 7905 Dihedral : 5.527 23.447 6255 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.79 % Favored : 90.14 % Rotamer: Outliers : 4.27 % Allowed : 14.74 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.93 (0.10), residues: 5790 helix: 0.10 (0.14), residues: 1290 sheet: -1.76 (0.09), residues: 2715 loop : -3.54 (0.12), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 547 TYR 0.007 0.001 TYR O 584 PHE 0.026 0.001 PHE N 437 TRP 0.008 0.001 TRP O 348 HIS 0.005 0.002 HIS D 556 Details of bonding type rmsd covalent geometry : bond 0.00373 (44805) covalent geometry : angle 0.68177 (60750) hydrogen bonds : bond 0.03245 ( 2456) hydrogen bonds : angle 5.46655 ( 7992) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 331 time to evaluate : 1.808 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: G 271 MET cc_start: 0.7238 (mmm) cc_final: 0.7022 (mtm) REVERT: O 196 MET cc_start: 0.7232 (tpp) cc_final: 0.6539 (tpt) REVERT: O 212 ASP cc_start: 0.7048 (m-30) cc_final: 0.6658 (m-30) REVERT: O 488 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8210 (mp) REVERT: A 237 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6660 (mp) REVERT: A 488 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8291 (mp) REVERT: B 488 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8382 (mp) REVERT: C 258 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7408 (mmtt) REVERT: C 271 MET cc_start: 0.6771 (mtt) cc_final: 0.6539 (mtm) REVERT: C 301 LEU cc_start: 0.8802 (mt) cc_final: 0.8480 (mm) REVERT: C 547 ARG cc_start: 0.8531 (tpp-160) cc_final: 0.7570 (ttm170) REVERT: D 328 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8270 (tp) REVERT: D 335 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7671 (tm-30) REVERT: D 340 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8261 (mp) REVERT: E 218 LEU cc_start: 0.8790 (tp) cc_final: 0.8446 (tp) REVERT: E 221 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6879 (tt) REVERT: F 227 ARG cc_start: 0.5947 (mmp80) cc_final: 0.5651 (mmm160) REVERT: F 241 THR cc_start: 0.5742 (OUTLIER) cc_final: 0.5497 (p) REVERT: F 271 MET cc_start: 0.7375 (mmm) cc_final: 0.6795 (mtm) REVERT: F 488 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8363 (mp) REVERT: H 181 ARG cc_start: 0.7451 (mtm110) cc_final: 0.7250 (mtm-85) REVERT: I 218 LEU cc_start: 0.8583 (tp) cc_final: 0.8356 (tp) REVERT: J 271 MET cc_start: 0.7307 (mmm) cc_final: 0.7074 (mtm) REVERT: K 181 ARG cc_start: 0.7339 (mtm110) cc_final: 0.6986 (mtm-85) REVERT: K 271 MET cc_start: 0.6859 (mtm) cc_final: 0.6168 (mtm) REVERT: K 328 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8064 (tp) REVERT: L 218 LEU cc_start: 0.8895 (tp) cc_final: 0.8623 (tt) REVERT: L 220 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8337 (pt) REVERT: L 271 MET cc_start: 0.7250 (mmm) cc_final: 0.7037 (mtm) REVERT: M 218 LEU cc_start: 0.8886 (tp) cc_final: 0.8677 (tp) REVERT: M 271 MET cc_start: 0.7355 (mmm) cc_final: 0.6928 (mtm) REVERT: N 221 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7445 (tt) outliers start: 209 outliers final: 136 residues processed: 504 average time/residue: 0.2509 time to fit residues: 216.6784 Evaluate side-chains 447 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 298 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 409 THR Chi-restraints excluded: chain O residue 435 VAL Chi-restraints excluded: chain O residue 484 GLU Chi-restraints excluded: chain O residue 488 LEU Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 529 VAL Chi-restraints excluded: chain O residue 541 ASP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 175 TYR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 484 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 562 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 409 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 369 ILE Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 541 ASP Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 484 GLU Chi-restraints excluded: chain J residue 488 LEU Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 409 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 570 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 409 THR Chi-restraints excluded: chain L residue 477 LEU Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 369 ILE Chi-restraints excluded: chain M residue 409 THR Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 301 LEU Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 409 THR Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 414 optimal weight: 6.9990 chunk 251 optimal weight: 0.9980 chunk 392 optimal weight: 40.0000 chunk 27 optimal weight: 0.7980 chunk 306 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 320 optimal weight: 9.9990 chunk 534 optimal weight: 0.8980 chunk 274 optimal weight: 9.9990 chunk 326 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 ASN ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 379 ASN ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.173513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.109361 restraints weight = 53063.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.114758 restraints weight = 21565.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.117923 restraints weight = 14019.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.119645 restraints weight = 11444.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.120586 restraints weight = 10337.812| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 44805 Z= 0.147 Angle : 0.671 11.051 60750 Z= 0.333 Chirality : 0.046 0.182 7545 Planarity : 0.006 0.056 7905 Dihedral : 5.291 21.211 6255 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.76 % Favored : 91.21 % Rotamer: Outliers : 3.80 % Allowed : 15.64 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.75 (0.10), residues: 5790 helix: 0.28 (0.14), residues: 1290 sheet: -1.62 (0.09), residues: 2715 loop : -3.52 (0.12), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 547 TYR 0.008 0.001 TYR E 584 PHE 0.029 0.002 PHE F 437 TRP 0.007 0.001 TRP M 348 HIS 0.003 0.001 HIS D 556 Details of bonding type rmsd covalent geometry : bond 0.00317 (44805) covalent geometry : angle 0.67135 (60750) hydrogen bonds : bond 0.03118 ( 2456) hydrogen bonds : angle 5.35198 ( 7992) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 330 time to evaluate : 2.093 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: G 484 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: O 196 MET cc_start: 0.7164 (tpp) cc_final: 0.6541 (tpt) REVERT: O 227 ARG cc_start: 0.6017 (mmp80) cc_final: 0.5652 (mmp80) REVERT: O 488 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8225 (mp) REVERT: A 482 GLU cc_start: 0.7095 (tt0) cc_final: 0.6694 (mt-10) REVERT: B 488 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8321 (mp) REVERT: C 258 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7462 (mmtt) REVERT: C 271 MET cc_start: 0.6741 (mtt) cc_final: 0.6501 (mtm) REVERT: C 301 LEU cc_start: 0.8745 (mt) cc_final: 0.8414 (mm) REVERT: C 405 LEU cc_start: 0.7588 (tt) cc_final: 0.6760 (mt) REVERT: C 547 ARG cc_start: 0.8329 (tpp-160) cc_final: 0.7564 (ttm170) REVERT: D 335 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7974 (tm-30) REVERT: D 340 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7954 (mp) REVERT: E 218 LEU cc_start: 0.8667 (tp) cc_final: 0.8379 (tp) REVERT: F 241 THR cc_start: 0.5544 (OUTLIER) cc_final: 0.5316 (p) REVERT: F 271 MET cc_start: 0.7361 (mmm) cc_final: 0.6790 (mtm) REVERT: F 488 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8261 (mp) REVERT: F 495 ARG cc_start: 0.7353 (mmp80) cc_final: 0.7123 (mmp80) REVERT: H 181 ARG cc_start: 0.7465 (mtm110) cc_final: 0.7242 (mtm-85) REVERT: I 218 LEU cc_start: 0.8462 (tp) cc_final: 0.8236 (tp) REVERT: K 181 ARG cc_start: 0.7392 (mtm110) cc_final: 0.7142 (mtm-85) REVERT: K 271 MET cc_start: 0.6802 (mtm) cc_final: 0.6182 (mtm) REVERT: K 328 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8035 (tp) REVERT: L 218 LEU cc_start: 0.8729 (tp) cc_final: 0.8462 (tt) REVERT: L 220 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8237 (pt) REVERT: M 218 LEU cc_start: 0.8727 (tp) cc_final: 0.8442 (tt) REVERT: M 271 MET cc_start: 0.7249 (mmm) cc_final: 0.6827 (mtm) REVERT: M 584 TYR cc_start: 0.8537 (t80) cc_final: 0.8201 (t80) REVERT: N 340 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8187 (mp) outliers start: 186 outliers final: 130 residues processed: 482 average time/residue: 0.2561 time to fit residues: 210.0901 Evaluate side-chains 437 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 297 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain O residue 175 TYR Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 390 ILE Chi-restraints excluded: chain O residue 409 THR Chi-restraints excluded: chain O residue 435 VAL Chi-restraints excluded: chain O residue 488 LEU Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 529 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain C residue 175 TYR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 484 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 409 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 369 ILE Chi-restraints excluded: chain I residue 429 ILE Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 541 ASP Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 330 GLU Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain J residue 484 GLU Chi-restraints excluded: chain J residue 488 LEU Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 570 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 409 THR Chi-restraints excluded: chain L residue 477 LEU Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 369 ILE Chi-restraints excluded: chain M residue 409 THR Chi-restraints excluded: chain M residue 481 ILE Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 409 THR Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 174 optimal weight: 6.9990 chunk 426 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 79 optimal weight: 30.0000 chunk 497 optimal weight: 2.9990 chunk 342 optimal weight: 6.9990 chunk 564 optimal weight: 9.9990 chunk 567 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 325 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 374 GLN ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 ASN F 560 ASN ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.165596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.102840 restraints weight = 55414.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.106779 restraints weight = 33298.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.107887 restraints weight = 22585.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.108771 restraints weight = 19726.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.108884 restraints weight = 18915.304| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 44805 Z= 0.249 Angle : 0.753 13.131 60750 Z= 0.376 Chirality : 0.048 0.184 7545 Planarity : 0.006 0.053 7905 Dihedral : 5.738 29.098 6255 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % Rotamer: Outliers : 3.80 % Allowed : 15.85 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.94 (0.10), residues: 5790 helix: 0.16 (0.14), residues: 1305 sheet: -1.76 (0.09), residues: 2685 loop : -3.62 (0.12), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 547 TYR 0.008 0.001 TYR A 584 PHE 0.026 0.002 PHE N 437 TRP 0.010 0.001 TRP O 348 HIS 0.007 0.003 HIS E 556 Details of bonding type rmsd covalent geometry : bond 0.00546 (44805) covalent geometry : angle 0.75300 (60750) hydrogen bonds : bond 0.03541 ( 2456) hydrogen bonds : angle 5.52964 ( 7992) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 342 time to evaluate : 1.810 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: G 547 ARG cc_start: 0.8605 (mmm160) cc_final: 0.7816 (tpm170) REVERT: O 196 MET cc_start: 0.7275 (tpp) cc_final: 0.6651 (tpt) REVERT: O 488 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8493 (mp) REVERT: A 362 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6553 (t80) REVERT: A 488 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8553 (mp) REVERT: A 547 ARG cc_start: 0.8572 (mmm160) cc_final: 0.8204 (tpp-160) REVERT: B 482 GLU cc_start: 0.7071 (tt0) cc_final: 0.6820 (mt-10) REVERT: B 488 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8724 (mp) REVERT: B 507 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7934 (mp) REVERT: C 271 MET cc_start: 0.6878 (mtt) cc_final: 0.6603 (mtm) REVERT: C 547 ARG cc_start: 0.8462 (tpp-160) cc_final: 0.7630 (ttm170) REVERT: E 218 LEU cc_start: 0.8760 (tp) cc_final: 0.8425 (tp) REVERT: F 241 THR cc_start: 0.5801 (OUTLIER) cc_final: 0.5584 (p) REVERT: F 271 MET cc_start: 0.7417 (mmm) cc_final: 0.6875 (mtm) REVERT: F 330 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6810 (pp20) REVERT: F 488 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8497 (mp) REVERT: H 181 ARG cc_start: 0.7576 (mtm110) cc_final: 0.7321 (mtm-85) REVERT: I 218 LEU cc_start: 0.8463 (tp) cc_final: 0.8255 (tp) REVERT: K 181 ARG cc_start: 0.7424 (mtm110) cc_final: 0.7191 (mtp180) REVERT: L 192 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7948 (mm) REVERT: L 218 LEU cc_start: 0.8852 (tp) cc_final: 0.8597 (tt) REVERT: L 220 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8386 (pt) REVERT: M 218 LEU cc_start: 0.8801 (tp) cc_final: 0.8510 (tt) REVERT: M 271 MET cc_start: 0.7300 (mmm) cc_final: 0.6895 (mtm) REVERT: M 296 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7808 (tm-30) REVERT: M 584 TYR cc_start: 0.8530 (t80) cc_final: 0.8163 (t80) REVERT: N 186 MET cc_start: 0.8675 (pmm) cc_final: 0.8452 (pmm) REVERT: N 330 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6555 (pp20) outliers start: 186 outliers final: 141 residues processed: 492 average time/residue: 0.2593 time to fit residues: 215.8563 Evaluate side-chains 460 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 309 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain O residue 175 TYR Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 390 ILE Chi-restraints excluded: chain O residue 409 THR Chi-restraints excluded: chain O residue 435 VAL Chi-restraints excluded: chain O residue 484 GLU Chi-restraints excluded: chain O residue 488 LEU Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 529 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain C residue 175 TYR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 484 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 409 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 369 ILE Chi-restraints excluded: chain I residue 429 ILE Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 541 ASP Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 330 GLU Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain J residue 484 GLU Chi-restraints excluded: chain J residue 488 LEU Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 409 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 541 ASP Chi-restraints excluded: chain K residue 570 VAL Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 409 THR Chi-restraints excluded: chain L residue 477 LEU Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 369 ILE Chi-restraints excluded: chain M residue 409 THR Chi-restraints excluded: chain M residue 481 ILE Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 301 LEU Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 330 GLU Chi-restraints excluded: chain N residue 333 ILE Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 409 THR Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 484 GLU Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 108 optimal weight: 0.7980 chunk 390 optimal weight: 20.0000 chunk 337 optimal weight: 3.9990 chunk 531 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 275 optimal weight: 20.0000 chunk 165 optimal weight: 5.9990 chunk 411 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 520 optimal weight: 0.8980 chunk 456 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 326 GLN ** O 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 483 GLN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 483 GLN ** L 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.166462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.103595 restraints weight = 54930.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.107579 restraints weight = 32829.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.108494 restraints weight = 22239.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.109273 restraints weight = 19751.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.109602 restraints weight = 18976.137| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 44805 Z= 0.219 Angle : 0.738 12.385 60750 Z= 0.366 Chirality : 0.047 0.227 7545 Planarity : 0.006 0.054 7905 Dihedral : 5.657 28.805 6255 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 3.37 % Allowed : 16.54 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.10), residues: 5790 helix: -0.13 (0.14), residues: 1395 sheet: -1.71 (0.09), residues: 2655 loop : -3.81 (0.11), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 547 TYR 0.009 0.001 TYR D 175 PHE 0.028 0.002 PHE E 564 TRP 0.008 0.001 TRP D 348 HIS 0.006 0.002 HIS E 556 Details of bonding type rmsd covalent geometry : bond 0.00478 (44805) covalent geometry : angle 0.73754 (60750) hydrogen bonds : bond 0.03416 ( 2456) hydrogen bonds : angle 5.48351 ( 7992) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 321 time to evaluate : 1.816 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: G 547 ARG cc_start: 0.8453 (mmm160) cc_final: 0.7616 (tpm170) REVERT: O 196 MET cc_start: 0.7190 (tpp) cc_final: 0.6584 (tpt) REVERT: O 488 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8508 (mp) REVERT: A 227 ARG cc_start: 0.5591 (mmp80) cc_final: 0.5018 (ttm-80) REVERT: A 362 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.6009 (t80) REVERT: A 488 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8583 (mp) REVERT: B 218 LEU cc_start: 0.8752 (tp) cc_final: 0.8536 (tp) REVERT: B 488 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8755 (mp) REVERT: B 507 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7908 (mp) REVERT: C 258 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7281 (mptt) REVERT: C 271 MET cc_start: 0.6938 (mtt) cc_final: 0.6652 (mtm) REVERT: C 301 LEU cc_start: 0.8849 (mt) cc_final: 0.8506 (mm) REVERT: C 547 ARG cc_start: 0.8395 (tpp-160) cc_final: 0.7617 (ttm170) REVERT: D 227 ARG cc_start: 0.6577 (mmp80) cc_final: 0.6048 (mmp80) REVERT: E 218 LEU cc_start: 0.8779 (tp) cc_final: 0.8458 (tp) REVERT: E 230 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7163 (pp) REVERT: F 271 MET cc_start: 0.7343 (mmm) cc_final: 0.6870 (mtm) REVERT: F 330 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6785 (pp20) REVERT: F 488 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8501 (mp) REVERT: H 181 ARG cc_start: 0.7605 (mtm110) cc_final: 0.7337 (mtm-85) REVERT: I 218 LEU cc_start: 0.8461 (tp) cc_final: 0.8257 (tp) REVERT: K 181 ARG cc_start: 0.7346 (mtm110) cc_final: 0.7135 (mtp180) REVERT: K 328 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7990 (tp) REVERT: L 218 LEU cc_start: 0.8751 (tp) cc_final: 0.8506 (tt) REVERT: L 220 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8428 (pt) REVERT: L 241 THR cc_start: 0.5923 (OUTLIER) cc_final: 0.5668 (p) REVERT: M 218 LEU cc_start: 0.8722 (tp) cc_final: 0.8440 (tt) REVERT: M 271 MET cc_start: 0.7281 (mmm) cc_final: 0.6895 (mtm) REVERT: M 296 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7834 (tm-30) REVERT: M 584 TYR cc_start: 0.8436 (t80) cc_final: 0.8095 (t80) REVERT: N 186 MET cc_start: 0.8756 (pmm) cc_final: 0.8497 (pmm) REVERT: N 330 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6629 (pp20) REVERT: N 340 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8484 (mp) outliers start: 165 outliers final: 132 residues processed: 465 average time/residue: 0.2513 time to fit residues: 198.4402 Evaluate side-chains 448 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 303 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 390 ILE Chi-restraints excluded: chain O residue 435 VAL Chi-restraints excluded: chain O residue 484 GLU Chi-restraints excluded: chain O residue 488 LEU Chi-restraints excluded: chain O residue 529 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain C residue 175 TYR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 484 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 409 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 369 ILE Chi-restraints excluded: chain I residue 429 ILE Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 541 ASP Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain J residue 330 GLU Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain J residue 484 GLU Chi-restraints excluded: chain J residue 488 LEU Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain K residue 175 TYR Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 334 VAL Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 409 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 570 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 409 THR Chi-restraints excluded: chain L residue 477 LEU Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 369 ILE Chi-restraints excluded: chain M residue 409 THR Chi-restraints excluded: chain M residue 456 VAL Chi-restraints excluded: chain M residue 481 ILE Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain M residue 589 VAL Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 301 LEU Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 330 GLU Chi-restraints excluded: chain N residue 333 ILE Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 409 THR Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 38 optimal weight: 8.9990 chunk 357 optimal weight: 7.9990 chunk 584 optimal weight: 0.0050 chunk 553 optimal weight: 5.9990 chunk 409 optimal weight: 5.9990 chunk 320 optimal weight: 10.0000 chunk 386 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 554 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 179 ASN ** O 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 179 ASN ** J 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.166503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.103921 restraints weight = 55242.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.108012 restraints weight = 31894.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.109089 restraints weight = 21328.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.109662 restraints weight = 19076.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.110080 restraints weight = 18278.830| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 44805 Z= 0.204 Angle : 0.727 13.472 60750 Z= 0.360 Chirality : 0.047 0.237 7545 Planarity : 0.006 0.055 7905 Dihedral : 5.578 27.103 6255 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 3.23 % Allowed : 16.77 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.88 (0.10), residues: 5790 helix: 0.24 (0.14), residues: 1305 sheet: -1.72 (0.09), residues: 2685 loop : -3.64 (0.12), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 181 TYR 0.012 0.001 TYR I 182 PHE 0.031 0.002 PHE I 437 TRP 0.009 0.001 TRP D 348 HIS 0.006 0.002 HIS A 556 Details of bonding type rmsd covalent geometry : bond 0.00448 (44805) covalent geometry : angle 0.72743 (60750) hydrogen bonds : bond 0.03347 ( 2456) hydrogen bonds : angle 5.43351 ( 7992) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 309 time to evaluate : 1.612 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: G 547 ARG cc_start: 0.8461 (mmm160) cc_final: 0.7672 (tpm170) REVERT: O 227 ARG cc_start: 0.6589 (mmp80) cc_final: 0.6253 (mmp80) REVERT: O 488 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8630 (mp) REVERT: A 362 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.6036 (t80) REVERT: A 488 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8627 (mp) REVERT: A 504 LYS cc_start: 0.8226 (tttp) cc_final: 0.8014 (tttt) REVERT: B 218 LEU cc_start: 0.8712 (tp) cc_final: 0.8498 (tp) REVERT: B 482 GLU cc_start: 0.7090 (tt0) cc_final: 0.6790 (mt-10) REVERT: B 488 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8748 (mp) REVERT: B 507 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7859 (mp) REVERT: C 547 ARG cc_start: 0.8333 (tpp-160) cc_final: 0.7559 (ttm170) REVERT: E 218 LEU cc_start: 0.8765 (tp) cc_final: 0.8462 (tp) REVERT: E 230 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7185 (pp) REVERT: E 362 PHE cc_start: 0.6985 (m-80) cc_final: 0.6692 (m-80) REVERT: F 271 MET cc_start: 0.7335 (mmm) cc_final: 0.6846 (mtm) REVERT: F 488 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8583 (mp) REVERT: K 181 ARG cc_start: 0.7468 (mtm110) cc_final: 0.7242 (mtp180) REVERT: K 328 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8021 (tp) REVERT: K 488 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8724 (mp) REVERT: L 218 LEU cc_start: 0.8732 (tp) cc_final: 0.8497 (tt) REVERT: L 220 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8471 (pt) REVERT: L 241 THR cc_start: 0.5741 (OUTLIER) cc_final: 0.5511 (p) REVERT: M 218 LEU cc_start: 0.8682 (tp) cc_final: 0.8402 (tt) REVERT: M 271 MET cc_start: 0.7259 (mmm) cc_final: 0.6855 (mtm) REVERT: M 296 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7852 (tm-30) REVERT: M 584 TYR cc_start: 0.8464 (t80) cc_final: 0.8124 (t80) REVERT: N 186 MET cc_start: 0.8839 (pmm) cc_final: 0.8589 (pmm) REVERT: N 330 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6538 (pp20) REVERT: N 340 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8387 (mp) outliers start: 158 outliers final: 132 residues processed: 437 average time/residue: 0.2451 time to fit residues: 181.8748 Evaluate side-chains 444 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 299 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain O residue 175 TYR Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 390 ILE Chi-restraints excluded: chain O residue 484 GLU Chi-restraints excluded: chain O residue 488 LEU Chi-restraints excluded: chain O residue 529 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 175 TYR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 484 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 409 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 369 ILE Chi-restraints excluded: chain I residue 429 ILE Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain J residue 330 GLU Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 409 THR Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain J residue 484 GLU Chi-restraints excluded: chain J residue 488 LEU Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 593 THR Chi-restraints excluded: chain K residue 175 TYR Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 334 VAL Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 409 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 570 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain L residue 477 LEU Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 369 ILE Chi-restraints excluded: chain M residue 409 THR Chi-restraints excluded: chain M residue 456 VAL Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 301 LEU Chi-restraints excluded: chain N residue 330 GLU Chi-restraints excluded: chain N residue 333 ILE Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 409 THR Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 558 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 286 optimal weight: 1.9990 chunk 480 optimal weight: 7.9990 chunk 400 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 392 optimal weight: 30.0000 chunk 463 optimal weight: 7.9990 chunk 358 optimal weight: 5.9990 chunk 451 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 ASN ** L 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.168007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.105938 restraints weight = 55173.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.108716 restraints weight = 35596.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.109905 restraints weight = 23651.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.111474 restraints weight = 20804.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.111651 restraints weight = 18785.042| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 44805 Z= 0.175 Angle : 0.709 13.212 60750 Z= 0.349 Chirality : 0.046 0.287 7545 Planarity : 0.006 0.055 7905 Dihedral : 5.425 24.468 6255 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 3.19 % Allowed : 16.97 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.77 (0.10), residues: 5790 helix: 0.39 (0.14), residues: 1290 sheet: -1.65 (0.09), residues: 2685 loop : -3.59 (0.11), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 227 TYR 0.010 0.001 TYR D 175 PHE 0.029 0.002 PHE E 437 TRP 0.007 0.001 TRP D 348 HIS 0.004 0.001 HIS O 556 Details of bonding type rmsd covalent geometry : bond 0.00381 (44805) covalent geometry : angle 0.70876 (60750) hydrogen bonds : bond 0.03220 ( 2456) hydrogen bonds : angle 5.34805 ( 7992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8227.50 seconds wall clock time: 143 minutes 0.19 seconds (8580.19 seconds total)