Starting phenix.real_space_refine on Wed Feb 14 02:44:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/02_2024/8f3d_28846_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/02_2024/8f3d_28846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/02_2024/8f3d_28846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/02_2024/8f3d_28846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/02_2024/8f3d_28846_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/02_2024/8f3d_28846_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 306 5.16 5 C 36504 2.51 5 N 10254 2.21 5 O 10782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 183": "NH1" <-> "NH2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "E ARG 183": "NH1" <-> "NH2" Residue "E GLU 259": "OE1" <-> "OE2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "F ARG 183": "NH1" <-> "NH2" Residue "F GLU 259": "OE1" <-> "OE2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H GLU 261": "OE1" <-> "OE2" Residue "H GLU 308": "OE1" <-> "OE2" Residue "H GLU 314": "OE1" <-> "OE2" Residue "H GLU 545": "OE1" <-> "OE2" Residue "H GLU 648": "OE1" <-> "OE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "I GLU 261": "OE1" <-> "OE2" Residue "I GLU 308": "OE1" <-> "OE2" Residue "I GLU 314": "OE1" <-> "OE2" Residue "I GLU 545": "OE1" <-> "OE2" Residue "I GLU 648": "OE1" <-> "OE2" Residue "J GLU 34": "OE1" <-> "OE2" Residue "J GLU 261": "OE1" <-> "OE2" Residue "J GLU 308": "OE1" <-> "OE2" Residue "J GLU 314": "OE1" <-> "OE2" Residue "J GLU 545": "OE1" <-> "OE2" Residue "J GLU 648": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 261": "OE1" <-> "OE2" Residue "K GLU 308": "OE1" <-> "OE2" Residue "K GLU 314": "OE1" <-> "OE2" Residue "K GLU 545": "OE1" <-> "OE2" Residue "K GLU 648": "OE1" <-> "OE2" Residue "L GLU 34": "OE1" <-> "OE2" Residue "L GLU 261": "OE1" <-> "OE2" Residue "L GLU 308": "OE1" <-> "OE2" Residue "L GLU 314": "OE1" <-> "OE2" Residue "L GLU 545": "OE1" <-> "OE2" Residue "L GLU 648": "OE1" <-> "OE2" Residue "M GLU 34": "OE1" <-> "OE2" Residue "M GLU 261": "OE1" <-> "OE2" Residue "M GLU 308": "OE1" <-> "OE2" Residue "M GLU 314": "OE1" <-> "OE2" Residue "M GLU 545": "OE1" <-> "OE2" Residue "M GLU 648": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 57846 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "B" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "C" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "D" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "E" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "F" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "H" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "I" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "J" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "K" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "L" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "M" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.38, per 1000 atoms: 0.37 Number of scatterers: 57846 At special positions: 0 Unit cell: (155.1, 166.1, 232.1, 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 306 16.00 O 10782 8.00 N 10254 7.00 C 36504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.49 Conformation dependent library (CDL) restraints added in 7.8 seconds 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13596 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 228 helices and 60 sheets defined 28.7% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.06 Creating SS restraints... Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 178 through 185 removed outlier: 3.771A pdb=" N VAL A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 219 Processing helix chain 'A' and resid 225 through 231 removed outlier: 3.618A pdb=" N ARG A 230 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 328 through 331 No H-bonds generated for 'chain 'A' and resid 328 through 331' Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.927A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.586A pdb=" N ALA A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 372' Processing helix chain 'A' and resid 391 through 394 No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 427 through 439 Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.732A pdb=" N GLY A 468 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 470 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 491 Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 571 through 584 Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 608 through 610 No H-bonds generated for 'chain 'A' and resid 608 through 610' Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.582A pdb=" N LEU A 637 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 663 removed outlier: 3.994A pdb=" N ASP A 655 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 178 through 185 removed outlier: 3.774A pdb=" N VAL B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG B 183 " --> pdb=" O ARG B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 219 Processing helix chain 'B' and resid 225 through 231 removed outlier: 3.620A pdb=" N ARG B 230 " --> pdb=" O ARG B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 328 through 331 No H-bonds generated for 'chain 'B' and resid 328 through 331' Processing helix chain 'B' and resid 338 through 350 removed outlier: 3.927A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.586A pdb=" N ALA B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 372' Processing helix chain 'B' and resid 391 through 394 No H-bonds generated for 'chain 'B' and resid 391 through 394' Processing helix chain 'B' and resid 427 through 439 Processing helix chain 'B' and resid 443 through 450 Processing helix chain 'B' and resid 464 through 470 removed outlier: 3.732A pdb=" N GLY B 468 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE B 470 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 491 Processing helix chain 'B' and resid 531 through 547 Processing helix chain 'B' and resid 564 through 568 Processing helix chain 'B' and resid 571 through 584 Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 608 through 610 No H-bonds generated for 'chain 'B' and resid 608 through 610' Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.581A pdb=" N LEU B 637 " --> pdb=" O THR B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 663 removed outlier: 3.995A pdb=" N ASP B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'C' and resid 162 through 175 Processing helix chain 'C' and resid 178 through 185 removed outlier: 3.772A pdb=" N VAL C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 219 Processing helix chain 'C' and resid 225 through 231 removed outlier: 3.618A pdb=" N ARG C 230 " --> pdb=" O ARG C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 310 Processing helix chain 'C' and resid 328 through 331 No H-bonds generated for 'chain 'C' and resid 328 through 331' Processing helix chain 'C' and resid 338 through 350 removed outlier: 3.929A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.586A pdb=" N ALA C 372 " --> pdb=" O ALA C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 372' Processing helix chain 'C' and resid 391 through 394 No H-bonds generated for 'chain 'C' and resid 391 through 394' Processing helix chain 'C' and resid 427 through 439 Processing helix chain 'C' and resid 443 through 450 Processing helix chain 'C' and resid 464 through 470 removed outlier: 3.732A pdb=" N GLY C 468 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE C 470 " --> pdb=" O LEU C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 491 Processing helix chain 'C' and resid 531 through 547 Processing helix chain 'C' and resid 564 through 568 Processing helix chain 'C' and resid 571 through 584 Processing helix chain 'C' and resid 600 through 605 Processing helix chain 'C' and resid 608 through 610 No H-bonds generated for 'chain 'C' and resid 608 through 610' Processing helix chain 'C' and resid 630 through 637 removed outlier: 3.582A pdb=" N LEU C 637 " --> pdb=" O THR C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 663 removed outlier: 3.993A pdb=" N ASP C 655 " --> pdb=" O ALA C 651 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS C 656 " --> pdb=" O ALA C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'D' and resid 162 through 175 Processing helix chain 'D' and resid 178 through 185 removed outlier: 3.773A pdb=" N VAL D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 219 Processing helix chain 'D' and resid 225 through 231 removed outlier: 3.618A pdb=" N ARG D 230 " --> pdb=" O ARG D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 310 Processing helix chain 'D' and resid 328 through 331 No H-bonds generated for 'chain 'D' and resid 328 through 331' Processing helix chain 'D' and resid 338 through 350 removed outlier: 3.927A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER D 349 " --> pdb=" O GLU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 372 removed outlier: 3.586A pdb=" N ALA D 372 " --> pdb=" O ALA D 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 372' Processing helix chain 'D' and resid 391 through 394 No H-bonds generated for 'chain 'D' and resid 391 through 394' Processing helix chain 'D' and resid 427 through 439 Processing helix chain 'D' and resid 443 through 450 Processing helix chain 'D' and resid 464 through 470 removed outlier: 3.730A pdb=" N GLY D 468 " --> pdb=" O ARG D 465 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE D 470 " --> pdb=" O LEU D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 491 Processing helix chain 'D' and resid 531 through 547 Processing helix chain 'D' and resid 564 through 568 Processing helix chain 'D' and resid 571 through 584 Processing helix chain 'D' and resid 600 through 605 Processing helix chain 'D' and resid 608 through 610 No H-bonds generated for 'chain 'D' and resid 608 through 610' Processing helix chain 'D' and resid 630 through 637 removed outlier: 3.580A pdb=" N LEU D 637 " --> pdb=" O THR D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 663 removed outlier: 3.994A pdb=" N ASP D 655 " --> pdb=" O ALA D 651 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS D 656 " --> pdb=" O ALA D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'E' and resid 162 through 175 Processing helix chain 'E' and resid 178 through 185 removed outlier: 3.772A pdb=" N VAL E 182 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG E 183 " --> pdb=" O ARG E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 219 Processing helix chain 'E' and resid 225 through 231 removed outlier: 3.619A pdb=" N ARG E 230 " --> pdb=" O ARG E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 310 Processing helix chain 'E' and resid 328 through 331 No H-bonds generated for 'chain 'E' and resid 328 through 331' Processing helix chain 'E' and resid 338 through 350 removed outlier: 3.927A pdb=" N PHE E 342 " --> pdb=" O PHE E 338 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER E 349 " --> pdb=" O GLU E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 372 removed outlier: 3.586A pdb=" N ALA E 372 " --> pdb=" O ALA E 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 368 through 372' Processing helix chain 'E' and resid 391 through 394 No H-bonds generated for 'chain 'E' and resid 391 through 394' Processing helix chain 'E' and resid 427 through 439 Processing helix chain 'E' and resid 443 through 450 Processing helix chain 'E' and resid 464 through 470 removed outlier: 3.731A pdb=" N GLY E 468 " --> pdb=" O ARG E 465 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE E 470 " --> pdb=" O LEU E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 491 Processing helix chain 'E' and resid 531 through 547 Processing helix chain 'E' and resid 564 through 568 Processing helix chain 'E' and resid 571 through 584 Processing helix chain 'E' and resid 600 through 605 Processing helix chain 'E' and resid 608 through 610 No H-bonds generated for 'chain 'E' and resid 608 through 610' Processing helix chain 'E' and resid 630 through 637 removed outlier: 3.582A pdb=" N LEU E 637 " --> pdb=" O THR E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 663 removed outlier: 3.993A pdb=" N ASP E 655 " --> pdb=" O ALA E 651 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS E 656 " --> pdb=" O ALA E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 685 through 695 Processing helix chain 'F' and resid 162 through 175 Processing helix chain 'F' and resid 178 through 185 removed outlier: 3.773A pdb=" N VAL F 182 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 219 Processing helix chain 'F' and resid 225 through 231 removed outlier: 3.619A pdb=" N ARG F 230 " --> pdb=" O ARG F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 310 Processing helix chain 'F' and resid 328 through 331 No H-bonds generated for 'chain 'F' and resid 328 through 331' Processing helix chain 'F' and resid 338 through 350 removed outlier: 3.927A pdb=" N PHE F 342 " --> pdb=" O PHE F 338 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER F 349 " --> pdb=" O GLU F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 372 removed outlier: 3.585A pdb=" N ALA F 372 " --> pdb=" O ALA F 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 368 through 372' Processing helix chain 'F' and resid 391 through 394 No H-bonds generated for 'chain 'F' and resid 391 through 394' Processing helix chain 'F' and resid 427 through 439 Processing helix chain 'F' and resid 443 through 450 Processing helix chain 'F' and resid 464 through 470 removed outlier: 3.732A pdb=" N GLY F 468 " --> pdb=" O ARG F 465 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE F 470 " --> pdb=" O LEU F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 491 Processing helix chain 'F' and resid 531 through 547 Processing helix chain 'F' and resid 564 through 568 Processing helix chain 'F' and resid 571 through 584 Processing helix chain 'F' and resid 600 through 605 Processing helix chain 'F' and resid 608 through 610 No H-bonds generated for 'chain 'F' and resid 608 through 610' Processing helix chain 'F' and resid 630 through 637 removed outlier: 3.582A pdb=" N LEU F 637 " --> pdb=" O THR F 633 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 663 removed outlier: 3.992A pdb=" N ASP F 655 " --> pdb=" O ALA F 651 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS F 656 " --> pdb=" O ALA F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 685 through 695 Processing helix chain 'H' and resid 23 through 34 removed outlier: 3.629A pdb=" N THR H 31 " --> pdb=" O ARG H 27 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS H 32 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU H 34 " --> pdb=" O ARG H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 54 No H-bonds generated for 'chain 'H' and resid 52 through 54' Processing helix chain 'H' and resid 74 through 83 Processing helix chain 'H' and resid 95 through 98 removed outlier: 4.461A pdb=" N GLU H 98 " --> pdb=" O PHE H 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 95 through 98' Processing helix chain 'H' and resid 100 through 109 Processing helix chain 'H' and resid 118 through 125 Processing helix chain 'H' and resid 127 through 137 Processing helix chain 'H' and resid 152 through 159 removed outlier: 3.738A pdb=" N ALA H 156 " --> pdb=" O VAL H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 199 Processing helix chain 'H' and resid 260 through 277 Processing helix chain 'H' and resid 308 through 315 Processing helix chain 'H' and resid 325 through 334 Processing helix chain 'H' and resid 418 through 431 Processing helix chain 'H' and resid 441 through 449 Processing helix chain 'H' and resid 453 through 455 No H-bonds generated for 'chain 'H' and resid 453 through 455' Processing helix chain 'H' and resid 462 through 467 removed outlier: 4.086A pdb=" N HIS H 466 " --> pdb=" O PHE H 462 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU H 467 " --> pdb=" O ILE H 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 462 through 467' Processing helix chain 'H' and resid 478 through 490 removed outlier: 3.610A pdb=" N ALA H 482 " --> pdb=" O PRO H 478 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU H 489 " --> pdb=" O ALA H 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 34 removed outlier: 3.630A pdb=" N THR I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS I 32 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG I 33 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU I 34 " --> pdb=" O ARG I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 54 No H-bonds generated for 'chain 'I' and resid 52 through 54' Processing helix chain 'I' and resid 74 through 83 Processing helix chain 'I' and resid 95 through 98 removed outlier: 4.461A pdb=" N GLU I 98 " --> pdb=" O PHE I 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 95 through 98' Processing helix chain 'I' and resid 100 through 109 Processing helix chain 'I' and resid 118 through 125 Processing helix chain 'I' and resid 127 through 137 Processing helix chain 'I' and resid 152 through 159 removed outlier: 3.738A pdb=" N ALA I 156 " --> pdb=" O VAL I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 199 Processing helix chain 'I' and resid 260 through 277 Processing helix chain 'I' and resid 308 through 315 Processing helix chain 'I' and resid 325 through 334 Processing helix chain 'I' and resid 418 through 431 Processing helix chain 'I' and resid 441 through 449 Processing helix chain 'I' and resid 453 through 455 No H-bonds generated for 'chain 'I' and resid 453 through 455' Processing helix chain 'I' and resid 462 through 467 removed outlier: 4.087A pdb=" N HIS I 466 " --> pdb=" O PHE I 462 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU I 467 " --> pdb=" O ILE I 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 462 through 467' Processing helix chain 'I' and resid 478 through 490 removed outlier: 3.609A pdb=" N ALA I 482 " --> pdb=" O PRO I 478 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU I 489 " --> pdb=" O ALA I 485 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 34 removed outlier: 3.629A pdb=" N THR J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS J 32 " --> pdb=" O VAL J 28 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG J 33 " --> pdb=" O PHE J 29 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU J 34 " --> pdb=" O ARG J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 54 No H-bonds generated for 'chain 'J' and resid 52 through 54' Processing helix chain 'J' and resid 74 through 83 Processing helix chain 'J' and resid 95 through 98 removed outlier: 4.461A pdb=" N GLU J 98 " --> pdb=" O PHE J 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 95 through 98' Processing helix chain 'J' and resid 100 through 109 Processing helix chain 'J' and resid 118 through 125 Processing helix chain 'J' and resid 127 through 137 Processing helix chain 'J' and resid 152 through 159 removed outlier: 3.738A pdb=" N ALA J 156 " --> pdb=" O VAL J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 199 Processing helix chain 'J' and resid 260 through 277 Processing helix chain 'J' and resid 308 through 315 Processing helix chain 'J' and resid 325 through 334 Processing helix chain 'J' and resid 418 through 431 Processing helix chain 'J' and resid 441 through 449 Processing helix chain 'J' and resid 453 through 455 No H-bonds generated for 'chain 'J' and resid 453 through 455' Processing helix chain 'J' and resid 462 through 467 removed outlier: 4.087A pdb=" N HIS J 466 " --> pdb=" O PHE J 462 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU J 467 " --> pdb=" O ILE J 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 462 through 467' Processing helix chain 'J' and resid 478 through 490 removed outlier: 3.610A pdb=" N ALA J 482 " --> pdb=" O PRO J 478 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU J 489 " --> pdb=" O ALA J 485 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 34 removed outlier: 3.630A pdb=" N THR K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS K 32 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU K 34 " --> pdb=" O ARG K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 54 No H-bonds generated for 'chain 'K' and resid 52 through 54' Processing helix chain 'K' and resid 74 through 83 Processing helix chain 'K' and resid 95 through 98 removed outlier: 4.461A pdb=" N GLU K 98 " --> pdb=" O PHE K 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 95 through 98' Processing helix chain 'K' and resid 100 through 109 Processing helix chain 'K' and resid 118 through 125 Processing helix chain 'K' and resid 127 through 137 Processing helix chain 'K' and resid 152 through 159 removed outlier: 3.738A pdb=" N ALA K 156 " --> pdb=" O VAL K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 199 Processing helix chain 'K' and resid 260 through 277 Processing helix chain 'K' and resid 308 through 315 Processing helix chain 'K' and resid 325 through 334 Processing helix chain 'K' and resid 418 through 431 Processing helix chain 'K' and resid 441 through 449 Processing helix chain 'K' and resid 453 through 455 No H-bonds generated for 'chain 'K' and resid 453 through 455' Processing helix chain 'K' and resid 462 through 467 removed outlier: 4.087A pdb=" N HIS K 466 " --> pdb=" O PHE K 462 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU K 467 " --> pdb=" O ILE K 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 462 through 467' Processing helix chain 'K' and resid 478 through 490 removed outlier: 3.609A pdb=" N ALA K 482 " --> pdb=" O PRO K 478 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU K 489 " --> pdb=" O ALA K 485 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 34 removed outlier: 3.630A pdb=" N THR L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS L 32 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG L 33 " --> pdb=" O PHE L 29 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU L 34 " --> pdb=" O ARG L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 54 No H-bonds generated for 'chain 'L' and resid 52 through 54' Processing helix chain 'L' and resid 74 through 83 Processing helix chain 'L' and resid 95 through 98 removed outlier: 4.461A pdb=" N GLU L 98 " --> pdb=" O PHE L 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 95 through 98' Processing helix chain 'L' and resid 100 through 109 Processing helix chain 'L' and resid 118 through 125 Processing helix chain 'L' and resid 127 through 137 Processing helix chain 'L' and resid 152 through 159 removed outlier: 3.737A pdb=" N ALA L 156 " --> pdb=" O VAL L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 199 Processing helix chain 'L' and resid 260 through 277 Processing helix chain 'L' and resid 308 through 315 Processing helix chain 'L' and resid 325 through 334 Processing helix chain 'L' and resid 418 through 431 Processing helix chain 'L' and resid 441 through 449 Processing helix chain 'L' and resid 453 through 455 No H-bonds generated for 'chain 'L' and resid 453 through 455' Processing helix chain 'L' and resid 462 through 467 removed outlier: 4.087A pdb=" N HIS L 466 " --> pdb=" O PHE L 462 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU L 467 " --> pdb=" O ILE L 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 462 through 467' Processing helix chain 'L' and resid 478 through 490 removed outlier: 3.610A pdb=" N ALA L 482 " --> pdb=" O PRO L 478 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU L 489 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 34 removed outlier: 3.629A pdb=" N THR M 31 " --> pdb=" O ARG M 27 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS M 32 " --> pdb=" O VAL M 28 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG M 33 " --> pdb=" O PHE M 29 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU M 34 " --> pdb=" O ARG M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 54 No H-bonds generated for 'chain 'M' and resid 52 through 54' Processing helix chain 'M' and resid 74 through 83 Processing helix chain 'M' and resid 95 through 98 removed outlier: 4.462A pdb=" N GLU M 98 " --> pdb=" O PHE M 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 95 through 98' Processing helix chain 'M' and resid 100 through 109 Processing helix chain 'M' and resid 118 through 125 Processing helix chain 'M' and resid 127 through 137 Processing helix chain 'M' and resid 152 through 159 removed outlier: 3.738A pdb=" N ALA M 156 " --> pdb=" O VAL M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 199 Processing helix chain 'M' and resid 260 through 277 Processing helix chain 'M' and resid 308 through 315 Processing helix chain 'M' and resid 325 through 334 Processing helix chain 'M' and resid 418 through 431 Processing helix chain 'M' and resid 441 through 449 Processing helix chain 'M' and resid 453 through 455 No H-bonds generated for 'chain 'M' and resid 453 through 455' Processing helix chain 'M' and resid 462 through 467 removed outlier: 4.087A pdb=" N HIS M 466 " --> pdb=" O PHE M 462 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU M 467 " --> pdb=" O ILE M 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 462 through 467' Processing helix chain 'M' and resid 478 through 490 removed outlier: 3.609A pdb=" N ALA M 482 " --> pdb=" O PRO M 478 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU M 489 " --> pdb=" O ALA M 485 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 266 through 273 removed outlier: 7.758A pdb=" N VAL A 281 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE A 315 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASN A 283 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU A 317 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 356 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL A 318 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 358 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU A 376 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL A 359 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE A 378 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N HIS A 422 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 508 through 514 removed outlier: 3.536A pdb=" N GLY A 511 " --> pdb=" O ILE A 522 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE A 523 " --> pdb=" O PRO A 550 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 552 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASN A 525 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU A 554 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE A 614 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N LEU A 593 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE A 616 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 266 through 273 removed outlier: 7.757A pdb=" N VAL B 281 " --> pdb=" O PRO B 313 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE B 315 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASN B 283 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU B 317 " --> pdb=" O ASN B 283 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE B 356 " --> pdb=" O TYR B 316 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL B 318 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 358 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU B 376 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL B 359 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE B 378 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N HIS B 422 " --> pdb=" O ILE B 379 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 508 through 514 removed outlier: 3.536A pdb=" N GLY B 511 " --> pdb=" O ILE B 522 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE B 523 " --> pdb=" O PRO B 550 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 552 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASN B 525 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU B 554 " --> pdb=" O ASN B 525 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE B 614 " --> pdb=" O THR B 591 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N LEU B 593 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N PHE B 616 " --> pdb=" O LEU B 593 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 266 through 273 removed outlier: 7.758A pdb=" N VAL C 281 " --> pdb=" O PRO C 313 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE C 315 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASN C 283 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU C 317 " --> pdb=" O ASN C 283 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE C 356 " --> pdb=" O TYR C 316 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL C 318 " --> pdb=" O ILE C 356 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 358 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU C 376 " --> pdb=" O ALA C 357 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL C 359 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 378 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS C 422 " --> pdb=" O ILE C 379 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 508 through 514 removed outlier: 3.536A pdb=" N GLY C 511 " --> pdb=" O ILE C 522 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE C 523 " --> pdb=" O PRO C 550 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU C 552 " --> pdb=" O ILE C 523 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASN C 525 " --> pdb=" O LEU C 552 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU C 554 " --> pdb=" O ASN C 525 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE C 614 " --> pdb=" O THR C 591 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N LEU C 593 " --> pdb=" O PHE C 614 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N PHE C 616 " --> pdb=" O LEU C 593 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 266 through 273 removed outlier: 7.759A pdb=" N VAL D 281 " --> pdb=" O PRO D 313 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE D 315 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASN D 283 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU D 317 " --> pdb=" O ASN D 283 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE D 356 " --> pdb=" O TYR D 316 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL D 318 " --> pdb=" O ILE D 356 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL D 358 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU D 376 " --> pdb=" O ALA D 357 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL D 359 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE D 378 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS D 422 " --> pdb=" O ILE D 379 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 508 through 514 removed outlier: 3.534A pdb=" N GLY D 511 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE D 523 " --> pdb=" O PRO D 550 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU D 552 " --> pdb=" O ILE D 523 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ASN D 525 " --> pdb=" O LEU D 552 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU D 554 " --> pdb=" O ASN D 525 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE D 614 " --> pdb=" O THR D 591 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N LEU D 593 " --> pdb=" O PHE D 614 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE D 616 " --> pdb=" O LEU D 593 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 266 through 273 removed outlier: 7.758A pdb=" N VAL E 281 " --> pdb=" O PRO E 313 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE E 315 " --> pdb=" O VAL E 281 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASN E 283 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU E 317 " --> pdb=" O ASN E 283 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE E 356 " --> pdb=" O TYR E 316 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL E 318 " --> pdb=" O ILE E 356 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL E 358 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU E 376 " --> pdb=" O ALA E 357 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL E 359 " --> pdb=" O GLU E 376 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE E 378 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS E 422 " --> pdb=" O ILE E 379 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 508 through 514 removed outlier: 3.536A pdb=" N GLY E 511 " --> pdb=" O ILE E 522 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE E 523 " --> pdb=" O PRO E 550 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU E 552 " --> pdb=" O ILE E 523 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASN E 525 " --> pdb=" O LEU E 552 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU E 554 " --> pdb=" O ASN E 525 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE E 614 " --> pdb=" O THR E 591 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N LEU E 593 " --> pdb=" O PHE E 614 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE E 616 " --> pdb=" O LEU E 593 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 266 through 273 removed outlier: 7.757A pdb=" N VAL F 281 " --> pdb=" O PRO F 313 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE F 315 " --> pdb=" O VAL F 281 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASN F 283 " --> pdb=" O ILE F 315 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU F 317 " --> pdb=" O ASN F 283 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE F 356 " --> pdb=" O TYR F 316 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL F 318 " --> pdb=" O ILE F 356 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL F 358 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU F 376 " --> pdb=" O ALA F 357 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL F 359 " --> pdb=" O GLU F 376 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE F 378 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS F 422 " --> pdb=" O ILE F 379 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 508 through 514 removed outlier: 3.536A pdb=" N GLY F 511 " --> pdb=" O ILE F 522 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE F 523 " --> pdb=" O PRO F 550 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU F 552 " --> pdb=" O ILE F 523 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASN F 525 " --> pdb=" O LEU F 552 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU F 554 " --> pdb=" O ASN F 525 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE F 614 " --> pdb=" O THR F 591 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N LEU F 593 " --> pdb=" O PHE F 614 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE F 616 " --> pdb=" O LEU F 593 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 16 through 18 removed outlier: 6.629A pdb=" N ALA H 88 " --> pdb=" O LEU H 17 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'H' and resid 41 through 43 Processing sheet with id= O, first strand: chain 'H' and resid 218 through 226 removed outlier: 3.535A pdb=" N THR H 284 " --> pdb=" O ASN H 302 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU H 300 " --> pdb=" O GLU H 286 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE H 288 " --> pdb=" O PHE H 298 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE H 298 " --> pdb=" O ILE H 288 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 386 through 392 removed outlier: 4.185A pdb=" N ALA H 409 " --> pdb=" O VAL H 356 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL H 249 " --> pdb=" O ARG H 355 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL H 249 " --> pdb=" O VAL H 242 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL H 242 " --> pdb=" O VAL H 249 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 507 through 514 Processing sheet with id= R, first strand: chain 'H' and resid 532 through 537 removed outlier: 4.244A pdb=" N ILE H 561 " --> pdb=" O ALA H 581 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN H 563 " --> pdb=" O ALA H 579 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 585 through 590 Processing sheet with id= T, first strand: chain 'H' and resid 664 through 666 Processing sheet with id= U, first strand: chain 'I' and resid 16 through 18 removed outlier: 6.630A pdb=" N ALA I 88 " --> pdb=" O LEU I 17 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'I' and resid 41 through 43 Processing sheet with id= W, first strand: chain 'I' and resid 218 through 226 removed outlier: 3.536A pdb=" N THR I 284 " --> pdb=" O ASN I 302 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU I 300 " --> pdb=" O GLU I 286 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE I 288 " --> pdb=" O PHE I 298 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE I 298 " --> pdb=" O ILE I 288 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 386 through 392 removed outlier: 4.186A pdb=" N ALA I 409 " --> pdb=" O VAL I 356 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL I 249 " --> pdb=" O ARG I 355 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL I 249 " --> pdb=" O VAL I 242 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL I 242 " --> pdb=" O VAL I 249 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 507 through 514 Processing sheet with id= Z, first strand: chain 'I' and resid 532 through 537 removed outlier: 4.243A pdb=" N ILE I 561 " --> pdb=" O ALA I 581 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN I 563 " --> pdb=" O ALA I 579 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 585 through 590 Processing sheet with id= AB, first strand: chain 'I' and resid 664 through 666 Processing sheet with id= AC, first strand: chain 'J' and resid 16 through 18 removed outlier: 6.630A pdb=" N ALA J 88 " --> pdb=" O LEU J 17 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'J' and resid 41 through 43 Processing sheet with id= AE, first strand: chain 'J' and resid 218 through 226 removed outlier: 3.535A pdb=" N THR J 284 " --> pdb=" O ASN J 302 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU J 300 " --> pdb=" O GLU J 286 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE J 288 " --> pdb=" O PHE J 298 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE J 298 " --> pdb=" O ILE J 288 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 386 through 392 removed outlier: 4.186A pdb=" N ALA J 409 " --> pdb=" O VAL J 356 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL J 249 " --> pdb=" O ARG J 355 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL J 249 " --> pdb=" O VAL J 242 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL J 242 " --> pdb=" O VAL J 249 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 507 through 514 Processing sheet with id= AH, first strand: chain 'J' and resid 532 through 537 removed outlier: 4.243A pdb=" N ILE J 561 " --> pdb=" O ALA J 581 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN J 563 " --> pdb=" O ALA J 579 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 585 through 590 Processing sheet with id= AJ, first strand: chain 'J' and resid 664 through 666 Processing sheet with id= AK, first strand: chain 'K' and resid 16 through 18 removed outlier: 6.630A pdb=" N ALA K 88 " --> pdb=" O LEU K 17 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'K' and resid 41 through 43 Processing sheet with id= AM, first strand: chain 'K' and resid 218 through 226 removed outlier: 3.536A pdb=" N THR K 284 " --> pdb=" O ASN K 302 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU K 300 " --> pdb=" O GLU K 286 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE K 288 " --> pdb=" O PHE K 298 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE K 298 " --> pdb=" O ILE K 288 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'K' and resid 386 through 392 removed outlier: 4.186A pdb=" N ALA K 409 " --> pdb=" O VAL K 356 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL K 249 " --> pdb=" O ARG K 355 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL K 249 " --> pdb=" O VAL K 242 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL K 242 " --> pdb=" O VAL K 249 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'K' and resid 507 through 514 Processing sheet with id= AP, first strand: chain 'K' and resid 532 through 537 removed outlier: 4.244A pdb=" N ILE K 561 " --> pdb=" O ALA K 581 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN K 563 " --> pdb=" O ALA K 579 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'K' and resid 585 through 590 Processing sheet with id= AR, first strand: chain 'K' and resid 664 through 666 Processing sheet with id= AS, first strand: chain 'L' and resid 16 through 18 removed outlier: 6.630A pdb=" N ALA L 88 " --> pdb=" O LEU L 17 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'L' and resid 41 through 43 Processing sheet with id= AU, first strand: chain 'L' and resid 218 through 226 removed outlier: 3.535A pdb=" N THR L 284 " --> pdb=" O ASN L 302 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU L 300 " --> pdb=" O GLU L 286 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE L 288 " --> pdb=" O PHE L 298 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE L 298 " --> pdb=" O ILE L 288 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'L' and resid 386 through 392 removed outlier: 4.186A pdb=" N ALA L 409 " --> pdb=" O VAL L 356 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL L 249 " --> pdb=" O ARG L 355 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL L 249 " --> pdb=" O VAL L 242 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL L 242 " --> pdb=" O VAL L 249 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'L' and resid 507 through 514 Processing sheet with id= AX, first strand: chain 'L' and resid 532 through 537 removed outlier: 4.244A pdb=" N ILE L 561 " --> pdb=" O ALA L 581 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN L 563 " --> pdb=" O ALA L 579 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'L' and resid 585 through 590 Processing sheet with id= AZ, first strand: chain 'L' and resid 664 through 666 Processing sheet with id= BA, first strand: chain 'M' and resid 16 through 18 removed outlier: 6.630A pdb=" N ALA M 88 " --> pdb=" O LEU M 17 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'M' and resid 41 through 43 Processing sheet with id= BC, first strand: chain 'M' and resid 218 through 226 removed outlier: 3.535A pdb=" N THR M 284 " --> pdb=" O ASN M 302 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU M 300 " --> pdb=" O GLU M 286 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE M 288 " --> pdb=" O PHE M 298 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE M 298 " --> pdb=" O ILE M 288 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'M' and resid 386 through 392 removed outlier: 4.186A pdb=" N ALA M 409 " --> pdb=" O VAL M 356 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL M 249 " --> pdb=" O ARG M 355 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL M 249 " --> pdb=" O VAL M 242 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL M 242 " --> pdb=" O VAL M 249 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'M' and resid 507 through 514 Processing sheet with id= BF, first strand: chain 'M' and resid 532 through 537 removed outlier: 4.243A pdb=" N ILE M 561 " --> pdb=" O ALA M 581 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN M 563 " --> pdb=" O ALA M 579 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'M' and resid 585 through 590 Processing sheet with id= BH, first strand: chain 'M' and resid 664 through 666 1641 hydrogen bonds defined for protein. 4527 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: 19.53 Time building geometry restraints manager: 19.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18910 1.34 - 1.46: 9055 1.46 - 1.58: 30559 1.58 - 1.70: 0 1.70 - 1.82: 486 Bond restraints: 59010 Sorted by residual: bond pdb=" CA LEU E 178 " pdb=" C LEU E 178 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.33e+01 bond pdb=" CA LEU A 178 " pdb=" C LEU A 178 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.33e+01 bond pdb=" CA LEU B 178 " pdb=" C LEU B 178 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.32e+01 bond pdb=" CA LEU D 178 " pdb=" C LEU D 178 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.31e+01 bond pdb=" CA GLU A 143 " pdb=" C GLU A 143 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.34e-02 5.57e+03 1.30e+01 ... (remaining 59005 not shown) Histogram of bond angle deviations from ideal: 94.77 - 102.62: 245 102.62 - 110.47: 15015 110.47 - 118.33: 30384 118.33 - 126.18: 33406 126.18 - 134.03: 726 Bond angle restraints: 79776 Sorted by residual: angle pdb=" N ARG D 144 " pdb=" CA ARG D 144 " pdb=" C ARG D 144 " ideal model delta sigma weight residual 111.71 97.86 13.85 1.15e+00 7.56e-01 1.45e+02 angle pdb=" N ARG C 144 " pdb=" CA ARG C 144 " pdb=" C ARG C 144 " ideal model delta sigma weight residual 111.71 97.91 13.80 1.15e+00 7.56e-01 1.44e+02 angle pdb=" N ARG F 144 " pdb=" CA ARG F 144 " pdb=" C ARG F 144 " ideal model delta sigma weight residual 111.71 97.92 13.79 1.15e+00 7.56e-01 1.44e+02 angle pdb=" N ARG B 144 " pdb=" CA ARG B 144 " pdb=" C ARG B 144 " ideal model delta sigma weight residual 111.71 97.92 13.79 1.15e+00 7.56e-01 1.44e+02 angle pdb=" N ARG E 144 " pdb=" CA ARG E 144 " pdb=" C ARG E 144 " ideal model delta sigma weight residual 111.71 97.92 13.79 1.15e+00 7.56e-01 1.44e+02 ... (remaining 79771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 31910 16.05 - 32.09: 2905 32.09 - 48.14: 603 48.14 - 64.19: 144 64.19 - 80.23: 24 Dihedral angle restraints: 35586 sinusoidal: 14322 harmonic: 21264 Sorted by residual: dihedral pdb=" CA GLU C 499 " pdb=" C GLU C 499 " pdb=" N PHE C 500 " pdb=" CA PHE C 500 " ideal model delta harmonic sigma weight residual 180.00 156.21 23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLU F 499 " pdb=" C GLU F 499 " pdb=" N PHE F 500 " pdb=" CA PHE F 500 " ideal model delta harmonic sigma weight residual 180.00 156.26 23.74 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLU D 499 " pdb=" C GLU D 499 " pdb=" N PHE D 500 " pdb=" CA PHE D 500 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 35583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 6485 0.048 - 0.096: 1710 0.096 - 0.145: 558 0.145 - 0.193: 54 0.193 - 0.241: 19 Chirality restraints: 8826 Sorted by residual: chirality pdb=" CA GLU M 362 " pdb=" N GLU M 362 " pdb=" C GLU M 362 " pdb=" CB GLU M 362 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA GLU I 362 " pdb=" N GLU I 362 " pdb=" C GLU I 362 " pdb=" CB GLU I 362 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA GLU H 362 " pdb=" N GLU H 362 " pdb=" C GLU H 362 " pdb=" CB GLU H 362 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 8823 not shown) Planarity restraints: 10464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTI D 801 " 0.015 2.00e-02 2.50e+03 3.64e-02 1.99e+01 pdb=" C4 BTI D 801 " -0.043 2.00e-02 2.50e+03 pdb=" C5 BTI D 801 " -0.011 2.00e-02 2.50e+03 pdb=" N2 BTI D 801 " 0.053 2.00e-02 2.50e+03 pdb=" N3 BTI D 801 " 0.031 2.00e-02 2.50e+03 pdb=" O3 BTI D 801 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI B 801 " -0.015 2.00e-02 2.50e+03 3.60e-02 1.95e+01 pdb=" C4 BTI B 801 " 0.042 2.00e-02 2.50e+03 pdb=" C5 BTI B 801 " 0.011 2.00e-02 2.50e+03 pdb=" N2 BTI B 801 " -0.052 2.00e-02 2.50e+03 pdb=" N3 BTI B 801 " -0.031 2.00e-02 2.50e+03 pdb=" O3 BTI B 801 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI F 801 " 0.014 2.00e-02 2.50e+03 3.59e-02 1.94e+01 pdb=" C4 BTI F 801 " -0.043 2.00e-02 2.50e+03 pdb=" C5 BTI F 801 " -0.011 2.00e-02 2.50e+03 pdb=" N2 BTI F 801 " 0.052 2.00e-02 2.50e+03 pdb=" N3 BTI F 801 " 0.031 2.00e-02 2.50e+03 pdb=" O3 BTI F 801 " -0.044 2.00e-02 2.50e+03 ... (remaining 10461 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 144 2.41 - 3.03: 37758 3.03 - 3.65: 86804 3.65 - 4.28: 128217 4.28 - 4.90: 205726 Nonbonded interactions: 458649 Sorted by model distance: nonbonded pdb=" CE MET M 650 " pdb=" CD LYS M 651 " model vdw 1.784 3.860 nonbonded pdb=" CE MET L 650 " pdb=" CD LYS L 651 " model vdw 1.784 3.860 nonbonded pdb=" CE MET H 650 " pdb=" CD LYS H 651 " model vdw 1.784 3.860 nonbonded pdb=" CE MET J 650 " pdb=" CD LYS J 651 " model vdw 1.785 3.860 nonbonded pdb=" CE MET K 650 " pdb=" CD LYS K 651 " model vdw 1.785 3.860 ... (remaining 458644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 13.660 Check model and map are aligned: 0.630 Set scattering table: 0.410 Process input model: 114.560 Find NCS groups from input model: 3.790 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 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 : 0.005 0.064 59010 Z= 0.349 Angle : 0.930 13.854 79776 Z= 0.586 Chirality : 0.049 0.241 8826 Planarity : 0.005 0.091 10464 Dihedral : 13.028 80.234 21990 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.39 % Allowed : 2.60 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.10), residues: 7440 helix: 0.03 (0.11), residues: 2256 sheet: 0.89 (0.17), residues: 1008 loop : -1.89 (0.09), residues: 4176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 488 HIS 0.012 0.002 HIS F 311 PHE 0.022 0.002 PHE C 500 TYR 0.037 0.002 TYR D 504 ARG 0.006 0.001 ARG F 608 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1544 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1520 time to evaluate : 4.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ILE cc_start: 0.8151 (mt) cc_final: 0.7828 (mt) REVERT: A 557 ILE cc_start: 0.5210 (pt) cc_final: 0.4988 (pt) REVERT: A 626 MET cc_start: 0.5473 (ttp) cc_final: 0.5115 (ttp) REVERT: A 655 ASP cc_start: 0.5949 (t70) cc_final: 0.5260 (m-30) REVERT: B 171 MET cc_start: 0.6208 (tpp) cc_final: 0.5835 (mmm) REVERT: B 222 MET cc_start: 0.5605 (mtp) cc_final: 0.5330 (mtm) REVERT: B 298 LYS cc_start: 0.7593 (ttmt) cc_final: 0.7252 (tttt) REVERT: B 360 MET cc_start: 0.6838 (mtp) cc_final: 0.6610 (mtt) REVERT: B 433 LEU cc_start: 0.7744 (mt) cc_final: 0.7506 (mt) REVERT: B 541 ILE cc_start: 0.7965 (mt) cc_final: 0.7732 (mt) REVERT: C 142 TYR cc_start: 0.6376 (m-10) cc_final: 0.6077 (m-10) REVERT: C 153 LEU cc_start: 0.7262 (pp) cc_final: 0.6696 (mp) REVERT: C 222 MET cc_start: 0.5770 (mtp) cc_final: 0.5230 (mtm) REVERT: C 392 PRO cc_start: 0.7880 (Cg_endo) cc_final: 0.7675 (Cg_exo) REVERT: C 541 ILE cc_start: 0.7987 (mt) cc_final: 0.7748 (mt) REVERT: D 376 GLU cc_start: 0.6704 (mm-30) cc_final: 0.6439 (mt-10) REVERT: D 514 ARG cc_start: 0.7196 (mmm160) cc_final: 0.6853 (mtp85) REVERT: D 626 MET cc_start: 0.4940 (ttp) cc_final: 0.4641 (ttp) REVERT: D 655 ASP cc_start: 0.6080 (t70) cc_final: 0.5308 (m-30) REVERT: E 168 MET cc_start: 0.6483 (tpp) cc_final: 0.5911 (tpp) REVERT: E 198 LYS cc_start: 0.6292 (tptp) cc_final: 0.6002 (ptpt) REVERT: E 514 ARG cc_start: 0.7427 (mmm160) cc_final: 0.7064 (mtp85) REVERT: E 655 ASP cc_start: 0.5697 (t70) cc_final: 0.5220 (m-30) REVERT: F 198 LYS cc_start: 0.6345 (tptp) cc_final: 0.5842 (ptpt) REVERT: F 305 LYS cc_start: 0.7594 (tptt) cc_final: 0.7370 (ttpt) REVERT: F 376 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6709 (mt-10) REVERT: F 514 ARG cc_start: 0.7529 (mmm160) cc_final: 0.7179 (mtp85) REVERT: F 655 ASP cc_start: 0.5674 (t70) cc_final: 0.5268 (m-30) REVERT: H 134 MET cc_start: 0.5209 (mpp) cc_final: 0.4960 (mmp) REVERT: H 228 LYS cc_start: 0.6026 (mtmm) cc_final: 0.5781 (ttmm) REVERT: H 412 ILE cc_start: 0.6627 (mp) cc_final: 0.5940 (mp) REVERT: H 483 MET cc_start: 0.5404 (mpp) cc_final: 0.4986 (mtm) REVERT: H 588 VAL cc_start: 0.7493 (m) cc_final: 0.7197 (p) REVERT: I 11 ARG cc_start: 0.4880 (mmm160) cc_final: 0.4197 (ptm160) REVERT: I 134 MET cc_start: 0.5521 (mpp) cc_final: 0.5302 (mmp) REVERT: I 191 MET cc_start: 0.3213 (ppp) cc_final: 0.2579 (tmm) REVERT: I 296 PHE cc_start: 0.5011 (p90) cc_final: 0.4344 (p90) REVERT: I 342 GLN cc_start: 0.5930 (tm-30) cc_final: 0.5727 (tp40) REVERT: I 407 MET cc_start: 0.4699 (tpt) cc_final: 0.4383 (tpt) REVERT: I 412 ILE cc_start: 0.6535 (mp) cc_final: 0.5715 (mp) REVERT: I 483 MET cc_start: 0.5585 (mpp) cc_final: 0.4339 (mtt) REVERT: I 533 ILE cc_start: 0.7550 (mt) cc_final: 0.7258 (tt) REVERT: I 609 SER cc_start: 0.4674 (m) cc_final: 0.4436 (p) REVERT: I 648 GLU cc_start: 0.5788 (mp0) cc_final: 0.5229 (mm-30) REVERT: J 11 ARG cc_start: 0.4855 (mmm160) cc_final: 0.4373 (ptm160) REVERT: J 124 MET cc_start: 0.5441 (mmm) cc_final: 0.4244 (ttm) REVERT: J 134 MET cc_start: 0.5467 (mpp) cc_final: 0.5069 (mmp) REVERT: J 191 MET cc_start: 0.3150 (ppp) cc_final: 0.2774 (tmm) REVERT: J 342 GLN cc_start: 0.6030 (tm-30) cc_final: 0.5728 (tp40) REVERT: J 407 MET cc_start: 0.5110 (tpt) cc_final: 0.4806 (tpt) REVERT: J 483 MET cc_start: 0.5349 (mpp) cc_final: 0.3993 (mtt) REVERT: K 47 GLU cc_start: 0.4176 (mm-30) cc_final: 0.3811 (mt-10) REVERT: K 52 HIS cc_start: 0.5000 (p-80) cc_final: 0.4557 (p90) REVERT: K 191 MET cc_start: 0.3153 (ppp) cc_final: 0.2786 (ppp) REVERT: K 296 PHE cc_start: 0.5172 (p90) cc_final: 0.4854 (p90) REVERT: K 331 LYS cc_start: 0.7013 (mttt) cc_final: 0.6611 (mmtp) REVERT: K 407 MET cc_start: 0.5565 (tpt) cc_final: 0.4526 (tmm) REVERT: K 412 ILE cc_start: 0.6424 (mp) cc_final: 0.5800 (mp) REVERT: K 444 LEU cc_start: 0.7226 (mm) cc_final: 0.7010 (mp) REVERT: K 483 MET cc_start: 0.5440 (mpp) cc_final: 0.4830 (mtm) REVERT: L 134 MET cc_start: 0.5603 (mpp) cc_final: 0.5283 (mmp) REVERT: L 179 MET cc_start: 0.2906 (mtm) cc_final: 0.2467 (tmm) REVERT: L 192 LEU cc_start: 0.4998 (pp) cc_final: 0.4651 (mt) REVERT: L 290 ASP cc_start: 0.4622 (t0) cc_final: 0.3752 (m-30) REVERT: L 295 GLU cc_start: 0.4352 (pt0) cc_final: 0.3212 (mm-30) REVERT: L 376 ARG cc_start: 0.4681 (mmm160) cc_final: 0.4277 (mmm-85) REVERT: L 483 MET cc_start: 0.5995 (mpp) cc_final: 0.4942 (mtt) REVERT: L 596 GLN cc_start: 0.6144 (pp30) cc_final: 0.5832 (pp30) REVERT: L 633 LYS cc_start: 0.3188 (tptp) cc_final: 0.2978 (mmmt) REVERT: M 52 HIS cc_start: 0.5197 (p-80) cc_final: 0.4883 (p90) REVERT: M 133 ILE cc_start: 0.6282 (mm) cc_final: 0.5561 (mm) REVERT: M 192 LEU cc_start: 0.5174 (pp) cc_final: 0.4847 (mt) REVERT: M 376 ARG cc_start: 0.4862 (mmm160) cc_final: 0.4469 (mmm-85) REVERT: M 412 ILE cc_start: 0.6605 (mp) cc_final: 0.6075 (mp) REVERT: M 470 LEU cc_start: 0.7746 (mt) cc_final: 0.7345 (mt) REVERT: M 483 MET cc_start: 0.5985 (mpp) cc_final: 0.4752 (mtt) REVERT: M 513 TYR cc_start: 0.4760 (t80) cc_final: 0.4550 (t80) REVERT: M 609 SER cc_start: 0.5385 (m) cc_final: 0.4946 (p) outliers start: 24 outliers final: 2 residues processed: 1532 average time/residue: 0.6271 time to fit residues: 1529.0738 Evaluate side-chains 714 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 712 time to evaluate : 4.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain M residue 233 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 623 optimal weight: 4.9990 chunk 559 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 377 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 578 optimal weight: 10.0000 chunk 223 optimal weight: 3.9990 chunk 351 optimal weight: 6.9990 chunk 430 optimal weight: 10.0000 chunk 670 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 HIS A 442 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN B 186 GLN B 300 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN C 186 GLN C 300 HIS D 186 GLN D 300 HIS D 442 ASN D 446 HIS D 525 ASN D 574 ASN E 186 GLN E 300 HIS ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 574 ASN F 186 GLN F 300 HIS F 383 ASN ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 574 ASN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS H 306 GLN H 466 HIS ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 HIS I 223 GLN I 306 GLN I 466 HIS ** I 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 HIS J 69 ASN ** J 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 223 GLN J 306 GLN J 427 GLN J 466 HIS ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 306 GLN K 469 GLN ** K 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 517 HIS ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 HIS L 52 HIS ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 219 HIS L 306 GLN ** L 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 HIS M 306 GLN ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 642 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 59010 Z= 0.351 Angle : 0.771 11.873 79776 Z= 0.401 Chirality : 0.050 0.300 8826 Planarity : 0.007 0.071 10464 Dihedral : 5.562 37.776 8294 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 3.32 % Allowed : 11.85 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.09), residues: 7440 helix: 0.16 (0.11), residues: 2214 sheet: 0.57 (0.16), residues: 960 loop : -1.84 (0.09), residues: 4266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 538 HIS 0.017 0.002 HIS A 216 PHE 0.031 0.003 PHE B 500 TYR 0.038 0.003 TYR D 504 ARG 0.019 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 718 time to evaluate : 4.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ILE cc_start: 0.7967 (mt) cc_final: 0.7756 (mt) REVERT: A 655 ASP cc_start: 0.5719 (t70) cc_final: 0.5102 (m-30) REVERT: B 168 MET cc_start: 0.6255 (tmm) cc_final: 0.5831 (tmm) REVERT: B 608 ARG cc_start: 0.7646 (tpp80) cc_final: 0.7432 (tpp80) REVERT: D 373 MET cc_start: 0.5199 (mtm) cc_final: 0.4943 (mtm) REVERT: D 655 ASP cc_start: 0.6008 (t70) cc_final: 0.5264 (m-30) REVERT: E 258 TYR cc_start: 0.4196 (m-10) cc_final: 0.3769 (m-80) REVERT: E 442 ASN cc_start: 0.7785 (m110) cc_final: 0.7512 (m110) REVERT: E 668 TYR cc_start: 0.4738 (m-80) cc_final: 0.4464 (m-10) REVERT: H 52 HIS cc_start: 0.5131 (p-80) cc_final: 0.4885 (p90) REVERT: H 249 VAL cc_start: 0.5211 (t) cc_final: 0.4950 (t) REVERT: H 286 GLU cc_start: 0.5596 (tp30) cc_final: 0.5132 (tp30) REVERT: H 298 PHE cc_start: 0.5268 (t80) cc_final: 0.5055 (t80) REVERT: H 323 LEU cc_start: 0.5656 (tt) cc_final: 0.5449 (tt) REVERT: H 407 MET cc_start: 0.4876 (tpt) cc_final: 0.4442 (tpt) REVERT: H 483 MET cc_start: 0.6543 (mpp) cc_final: 0.5535 (mtt) REVERT: I 249 VAL cc_start: 0.5656 (t) cc_final: 0.5339 (t) REVERT: I 407 MET cc_start: 0.5008 (tpt) cc_final: 0.4370 (tpt) REVERT: I 429 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7684 (mm) REVERT: I 483 MET cc_start: 0.6478 (mpp) cc_final: 0.5371 (mtt) REVERT: I 648 GLU cc_start: 0.6280 (mp0) cc_final: 0.5926 (mm-30) REVERT: I 685 GLU cc_start: 0.2790 (tp30) cc_final: 0.2532 (tm-30) REVERT: J 124 MET cc_start: 0.5830 (mmm) cc_final: 0.5625 (mmm) REVERT: J 191 MET cc_start: 0.3423 (ppp) cc_final: 0.3091 (tmm) REVERT: J 249 VAL cc_start: 0.5247 (t) cc_final: 0.5032 (t) REVERT: J 301 MET cc_start: 0.4526 (ttt) cc_final: 0.4307 (ttt) REVERT: J 407 MET cc_start: 0.5042 (tpt) cc_final: 0.4750 (tpt) REVERT: J 483 MET cc_start: 0.6460 (mpp) cc_final: 0.5496 (mtt) REVERT: J 513 TYR cc_start: 0.4164 (t80) cc_final: 0.3870 (t80) REVERT: J 609 SER cc_start: 0.5146 (m) cc_final: 0.4710 (p) REVERT: J 652 MET cc_start: 0.5559 (tpp) cc_final: 0.4627 (tpp) REVERT: J 661 ASP cc_start: 0.6072 (m-30) cc_final: 0.5581 (p0) REVERT: K 52 HIS cc_start: 0.5297 (p-80) cc_final: 0.4952 (p90) REVERT: K 249 VAL cc_start: 0.5161 (t) cc_final: 0.4907 (t) REVERT: K 272 GLN cc_start: 0.6826 (mt0) cc_final: 0.6527 (tm-30) REVERT: K 296 PHE cc_start: 0.4962 (p90) cc_final: 0.4705 (p90) REVERT: K 299 MET cc_start: 0.6508 (tmm) cc_final: 0.6162 (ttp) REVERT: K 334 MET cc_start: 0.6216 (mmm) cc_final: 0.5937 (mmm) REVERT: K 407 MET cc_start: 0.5164 (tpt) cc_final: 0.4127 (tmm) REVERT: K 483 MET cc_start: 0.6494 (mpp) cc_final: 0.5806 (mpp) REVERT: K 515 ASP cc_start: 0.5170 (m-30) cc_final: 0.4902 (t0) REVERT: K 540 HIS cc_start: 0.5833 (OUTLIER) cc_final: 0.5325 (t-90) REVERT: K 652 MET cc_start: 0.5156 (tpp) cc_final: 0.4894 (tpp) REVERT: K 677 ASP cc_start: 0.5501 (m-30) cc_final: 0.4967 (t70) REVERT: L 179 MET cc_start: 0.2994 (mtm) cc_final: 0.2396 (tmm) REVERT: L 192 LEU cc_start: 0.5246 (pp) cc_final: 0.4887 (mt) REVERT: L 290 ASP cc_start: 0.5236 (t0) cc_final: 0.4384 (m-30) REVERT: L 295 GLU cc_start: 0.4653 (pt0) cc_final: 0.4368 (tm-30) REVERT: L 298 PHE cc_start: 0.6258 (t80) cc_final: 0.5232 (t80) REVERT: L 322 PRO cc_start: 0.5985 (Cg_exo) cc_final: 0.5776 (Cg_endo) REVERT: L 376 ARG cc_start: 0.4649 (mmm160) cc_final: 0.4142 (tpp-160) REVERT: L 407 MET cc_start: 0.5067 (tpt) cc_final: 0.4372 (tpt) REVERT: L 483 MET cc_start: 0.6536 (mpp) cc_final: 0.5670 (mtt) REVERT: L 609 SER cc_start: 0.5528 (m) cc_final: 0.5076 (p) REVERT: L 643 VAL cc_start: 0.4716 (p) cc_final: 0.4383 (t) REVERT: M 52 HIS cc_start: 0.4991 (p-80) cc_final: 0.4595 (p90) REVERT: M 134 MET cc_start: 0.5175 (mmp) cc_final: 0.4896 (mmm) REVERT: M 192 LEU cc_start: 0.5142 (pp) cc_final: 0.4809 (mt) REVERT: M 260 MET cc_start: 0.6380 (tpt) cc_final: 0.5816 (mmm) REVERT: M 334 MET cc_start: 0.6329 (mmm) cc_final: 0.5924 (mmm) REVERT: M 376 ARG cc_start: 0.4953 (mmm160) cc_final: 0.4690 (mmm-85) REVERT: M 407 MET cc_start: 0.4710 (tpt) cc_final: 0.4141 (tpt) REVERT: M 483 MET cc_start: 0.6629 (mpp) cc_final: 0.6126 (mpp) REVERT: M 642 GLN cc_start: 0.5358 (OUTLIER) cc_final: 0.4555 (tm-30) REVERT: M 652 MET cc_start: 0.5087 (tpp) cc_final: 0.4770 (tpp) REVERT: M 677 ASP cc_start: 0.5291 (m-30) cc_final: 0.4655 (t70) outliers start: 203 outliers final: 132 residues processed: 871 average time/residue: 0.5578 time to fit residues: 811.1253 Evaluate side-chains 699 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 564 time to evaluate : 4.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 ASN Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain H residue 345 VAL Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 411 VAL Chi-restraints excluded: chain H residue 494 ASP Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 674 VAL Chi-restraints excluded: chain H residue 679 VAL Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 429 LEU Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 602 LEU Chi-restraints excluded: chain I residue 665 SER Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 564 ASP Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain J residue 679 VAL Chi-restraints excluded: chain K residue 194 SER Chi-restraints excluded: chain K residue 219 HIS Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 494 ASP Chi-restraints excluded: chain K residue 540 HIS Chi-restraints excluded: chain K residue 578 LEU Chi-restraints excluded: chain K residue 588 VAL Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 219 HIS Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain L residue 365 PHE Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 564 ASP Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 604 ASP Chi-restraints excluded: chain L residue 679 VAL Chi-restraints excluded: chain M residue 219 HIS Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 269 VAL Chi-restraints excluded: chain M residue 284 THR Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain M residue 564 ASP Chi-restraints excluded: chain M residue 573 MET Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 642 GLN Chi-restraints excluded: chain M residue 674 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 372 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 557 optimal weight: 5.9990 chunk 456 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 671 optimal weight: 10.0000 chunk 725 optimal weight: 0.0770 chunk 597 optimal weight: 0.0270 chunk 665 optimal weight: 0.0030 chunk 228 optimal weight: 5.9990 chunk 538 optimal weight: 7.9990 overall best weight: 2.0210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 HIS ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 511 HIS ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 HIS ** K 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 219 HIS ** L 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 642 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 59010 Z= 0.203 Angle : 0.621 11.415 79776 Z= 0.321 Chirality : 0.045 0.209 8826 Planarity : 0.005 0.059 10464 Dihedral : 5.006 32.654 8292 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.14 % Allowed : 15.20 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.10), residues: 7440 helix: 0.65 (0.11), residues: 2196 sheet: 0.81 (0.16), residues: 996 loop : -1.80 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 538 HIS 0.019 0.001 HIS L 219 PHE 0.020 0.001 PHE M 298 TYR 0.027 0.002 TYR D 504 ARG 0.010 0.000 ARG F 465 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 645 time to evaluate : 4.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6530 (tp) REVERT: A 168 MET cc_start: 0.6674 (tpp) cc_final: 0.6237 (tpp) REVERT: A 305 LYS cc_start: 0.7544 (tptt) cc_final: 0.7337 (ttmt) REVERT: A 423 TYR cc_start: 0.5502 (m-80) cc_final: 0.5109 (m-80) REVERT: A 655 ASP cc_start: 0.5651 (t70) cc_final: 0.5051 (m-30) REVERT: B 608 ARG cc_start: 0.7536 (tpp80) cc_final: 0.7305 (tpp80) REVERT: C 168 MET cc_start: 0.6316 (tpp) cc_final: 0.6054 (tpp) REVERT: D 168 MET cc_start: 0.6261 (tpp) cc_final: 0.5914 (tpt) REVERT: D 171 MET cc_start: 0.5643 (tpp) cc_final: 0.5216 (mmm) REVERT: D 334 ASP cc_start: 0.5869 (t0) cc_final: 0.5007 (t0) REVERT: D 655 ASP cc_start: 0.6017 (t70) cc_final: 0.5286 (m-30) REVERT: E 140 ILE cc_start: 0.7443 (tp) cc_final: 0.7186 (tp) REVERT: E 168 MET cc_start: 0.5785 (tpp) cc_final: 0.5368 (tpp) REVERT: H 124 MET cc_start: 0.6505 (mmm) cc_final: 0.6270 (tpp) REVERT: H 179 MET cc_start: 0.2787 (mtp) cc_final: 0.1936 (tmm) REVERT: H 249 VAL cc_start: 0.5112 (t) cc_final: 0.4883 (t) REVERT: H 299 MET cc_start: 0.6449 (ttp) cc_final: 0.5953 (ttp) REVERT: H 334 MET cc_start: 0.6650 (mmm) cc_final: 0.6277 (mmm) REVERT: H 407 MET cc_start: 0.4813 (tpt) cc_final: 0.4363 (tpt) REVERT: H 483 MET cc_start: 0.6372 (mpp) cc_final: 0.5600 (mtt) REVERT: H 513 TYR cc_start: 0.4749 (t80) cc_final: 0.4455 (t80) REVERT: H 643 VAL cc_start: 0.4414 (OUTLIER) cc_final: 0.4202 (t) REVERT: I 407 MET cc_start: 0.5080 (tpt) cc_final: 0.4486 (tpt) REVERT: I 483 MET cc_start: 0.6489 (mpp) cc_final: 0.5475 (mtt) REVERT: I 505 ASP cc_start: 0.6380 (p0) cc_final: 0.6170 (p0) REVERT: I 513 TYR cc_start: 0.4474 (t80) cc_final: 0.4257 (t80) REVERT: I 648 GLU cc_start: 0.6337 (mp0) cc_final: 0.5838 (mm-30) REVERT: I 685 GLU cc_start: 0.2938 (tp30) cc_final: 0.2556 (tm-30) REVERT: J 123 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6882 (tt) REVERT: J 124 MET cc_start: 0.5760 (mmm) cc_final: 0.4939 (ttm) REVERT: J 191 MET cc_start: 0.2915 (ppp) cc_final: 0.2599 (tmm) REVERT: J 221 GLU cc_start: 0.4217 (OUTLIER) cc_final: 0.3308 (pm20) REVERT: J 249 VAL cc_start: 0.5503 (t) cc_final: 0.5241 (t) REVERT: J 334 MET cc_start: 0.6690 (mmm) cc_final: 0.6262 (mmm) REVERT: J 407 MET cc_start: 0.4957 (tpt) cc_final: 0.4720 (tpt) REVERT: J 483 MET cc_start: 0.6551 (mpp) cc_final: 0.5782 (mtt) REVERT: J 513 TYR cc_start: 0.4583 (t80) cc_final: 0.4288 (t80) REVERT: J 661 ASP cc_start: 0.6552 (m-30) cc_final: 0.6043 (p0) REVERT: J 685 GLU cc_start: 0.2962 (tp30) cc_final: 0.2351 (tm-30) REVERT: K 52 HIS cc_start: 0.5260 (p-80) cc_final: 0.4987 (p90) REVERT: K 286 GLU cc_start: 0.5708 (tp30) cc_final: 0.5297 (tp30) REVERT: K 296 PHE cc_start: 0.4880 (p90) cc_final: 0.4531 (p90) REVERT: K 299 MET cc_start: 0.6555 (tmm) cc_final: 0.6046 (ttp) REVERT: K 407 MET cc_start: 0.4860 (tpt) cc_final: 0.4414 (tpt) REVERT: K 483 MET cc_start: 0.6585 (mpp) cc_final: 0.5666 (mtt) REVERT: K 513 TYR cc_start: 0.4360 (t80) cc_final: 0.3988 (t80) REVERT: K 540 HIS cc_start: 0.5947 (OUTLIER) cc_final: 0.5472 (t-90) REVERT: K 652 MET cc_start: 0.5141 (tpp) cc_final: 0.4883 (tpp) REVERT: K 677 ASP cc_start: 0.5447 (m-30) cc_final: 0.4968 (t70) REVERT: L 179 MET cc_start: 0.2704 (mtm) cc_final: 0.1960 (tmm) REVERT: L 192 LEU cc_start: 0.5332 (pp) cc_final: 0.4991 (mt) REVERT: L 290 ASP cc_start: 0.5127 (t0) cc_final: 0.4240 (m-30) REVERT: L 295 GLU cc_start: 0.4602 (pt0) cc_final: 0.4328 (tm-30) REVERT: L 322 PRO cc_start: 0.6111 (Cg_exo) cc_final: 0.5883 (Cg_endo) REVERT: L 407 MET cc_start: 0.4986 (tpt) cc_final: 0.4444 (tpt) REVERT: L 483 MET cc_start: 0.6678 (mpp) cc_final: 0.6011 (mtt) REVERT: L 631 LEU cc_start: 0.3582 (OUTLIER) cc_final: 0.3208 (tp) REVERT: L 643 VAL cc_start: 0.4616 (p) cc_final: 0.4158 (t) REVERT: L 652 MET cc_start: 0.5270 (tpp) cc_final: 0.4917 (tpp) REVERT: M 52 HIS cc_start: 0.5147 (p-80) cc_final: 0.4926 (p-80) REVERT: M 192 LEU cc_start: 0.5079 (pp) cc_final: 0.4747 (mt) REVERT: M 260 MET cc_start: 0.6861 (tpt) cc_final: 0.5951 (mmm) REVERT: M 290 ASP cc_start: 0.5231 (t0) cc_final: 0.4165 (m-30) REVERT: M 298 PHE cc_start: 0.6024 (t80) cc_final: 0.4901 (t80) REVERT: M 301 MET cc_start: 0.4523 (ttt) cc_final: 0.4235 (ttt) REVERT: M 407 MET cc_start: 0.4432 (tpt) cc_final: 0.3936 (tpt) REVERT: M 631 LEU cc_start: 0.2576 (OUTLIER) cc_final: 0.2051 (tp) REVERT: M 642 GLN cc_start: 0.5669 (OUTLIER) cc_final: 0.4626 (tm-30) REVERT: M 677 ASP cc_start: 0.4966 (m-30) cc_final: 0.4600 (t70) outliers start: 192 outliers final: 137 residues processed: 792 average time/residue: 0.5411 time to fit residues: 726.1985 Evaluate side-chains 675 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 530 time to evaluate : 4.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 ASN Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 598 TYR Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 591 THR Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 219 HIS Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 345 VAL Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 562 VAL Chi-restraints excluded: chain H residue 643 VAL Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 661 ASP Chi-restraints excluded: chain H residue 667 LEU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 609 SER Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 221 GLU Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 194 SER Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 540 HIS Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 661 ASP Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 218 ARG Chi-restraints excluded: chain L residue 219 HIS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain L residue 365 PHE Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 564 ASP Chi-restraints excluded: chain L residue 602 LEU Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain M residue 32 CYS Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 494 ASP Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 564 ASP Chi-restraints excluded: chain M residue 588 VAL Chi-restraints excluded: chain M residue 604 ASP Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 642 GLN Chi-restraints excluded: chain M residue 661 ASP Chi-restraints excluded: chain M residue 674 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 663 optimal weight: 10.0000 chunk 504 optimal weight: 20.0000 chunk 348 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 320 optimal weight: 7.9990 chunk 450 optimal weight: 9.9990 chunk 673 optimal weight: 1.9990 chunk 713 optimal weight: 10.0000 chunk 352 optimal weight: 4.9990 chunk 638 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 HIS B 283 ASN B 539 HIS C 310 ASN ** C 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 HIS C 574 ASN D 283 ASN ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 HIS ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 ASN F 539 HIS ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 HIS ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 223 GLN K 466 HIS ** K 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 329 GLN ** L 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 329 GLN ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 642 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 59010 Z= 0.401 Angle : 0.812 13.228 79776 Z= 0.423 Chirality : 0.052 0.273 8826 Planarity : 0.007 0.092 10464 Dihedral : 6.087 44.268 8292 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.48 % Favored : 90.51 % Rotamer: Outliers : 5.72 % Allowed : 16.32 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.09), residues: 7440 helix: -0.03 (0.11), residues: 2184 sheet: 0.57 (0.16), residues: 996 loop : -2.11 (0.09), residues: 4260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 251 HIS 0.042 0.002 HIS H 219 PHE 0.048 0.003 PHE C 500 TYR 0.031 0.003 TYR A 669 ARG 0.017 0.001 ARG D 465 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 595 time to evaluate : 4.862 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: B 474 MET cc_start: 0.3284 (OUTLIER) cc_final: 0.2589 (mtp) REVERT: B 674 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6023 (mp) REVERT: C 239 LEU cc_start: 0.7920 (tp) cc_final: 0.7650 (tt) REVERT: C 674 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.5927 (mp) REVERT: E 674 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6049 (mp) REVERT: F 674 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.5950 (mp) REVERT: H 124 MET cc_start: 0.6112 (mmm) cc_final: 0.5274 (tpp) REVERT: H 179 MET cc_start: 0.2740 (mtp) cc_final: 0.2085 (tmm) REVERT: H 260 MET cc_start: 0.6658 (mmp) cc_final: 0.6415 (mmm) REVERT: H 334 MET cc_start: 0.6544 (mmm) cc_final: 0.5898 (mmm) REVERT: H 483 MET cc_start: 0.6623 (mpp) cc_final: 0.5861 (mtt) REVERT: H 677 ASP cc_start: 0.5292 (m-30) cc_final: 0.4922 (t70) REVERT: H 685 GLU cc_start: 0.3689 (OUTLIER) cc_final: 0.2841 (tm-30) REVERT: I 58 GLU cc_start: 0.6075 (OUTLIER) cc_final: 0.5860 (pm20) REVERT: I 407 MET cc_start: 0.4763 (tpt) cc_final: 0.4175 (tpt) REVERT: I 450 THR cc_start: 0.5543 (m) cc_final: 0.5217 (p) REVERT: I 483 MET cc_start: 0.6814 (mpp) cc_final: 0.5875 (mtt) REVERT: I 623 MET cc_start: 0.4390 (ptt) cc_final: 0.3880 (tpp) REVERT: I 648 GLU cc_start: 0.6456 (mp0) cc_final: 0.6157 (mm-30) REVERT: I 650 MET cc_start: 0.5651 (OUTLIER) cc_final: 0.5397 (tpp) REVERT: I 685 GLU cc_start: 0.3091 (OUTLIER) cc_final: 0.2571 (tm-30) REVERT: J 58 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5812 (pm20) REVERT: J 322 PRO cc_start: 0.6015 (Cg_exo) cc_final: 0.5735 (Cg_endo) REVERT: J 407 MET cc_start: 0.4815 (tpt) cc_final: 0.4195 (tpt) REVERT: J 483 MET cc_start: 0.6868 (mpp) cc_final: 0.5913 (mtt) REVERT: J 513 TYR cc_start: 0.4299 (t80) cc_final: 0.4069 (t80) REVERT: J 685 GLU cc_start: 0.3244 (OUTLIER) cc_final: 0.2566 (tm-30) REVERT: K 52 HIS cc_start: 0.5194 (p-80) cc_final: 0.4944 (p-80) REVERT: K 260 MET cc_start: 0.6721 (mmp) cc_final: 0.6411 (mmm) REVERT: K 286 GLU cc_start: 0.5869 (tp30) cc_final: 0.5574 (tp30) REVERT: K 296 PHE cc_start: 0.4839 (p90) cc_final: 0.4410 (p90) REVERT: K 407 MET cc_start: 0.4394 (tpt) cc_final: 0.3916 (tpt) REVERT: K 483 MET cc_start: 0.6687 (mpp) cc_final: 0.5901 (mtt) REVERT: K 513 TYR cc_start: 0.4443 (t80) cc_final: 0.4162 (t80) REVERT: K 652 MET cc_start: 0.5728 (tpp) cc_final: 0.5510 (tpp) REVERT: K 677 ASP cc_start: 0.5378 (m-30) cc_final: 0.4823 (t70) REVERT: L 165 PRO cc_start: 0.1588 (Cg_exo) cc_final: 0.1277 (Cg_endo) REVERT: L 179 MET cc_start: 0.2706 (mtm) cc_final: 0.1982 (tmm) REVERT: L 192 LEU cc_start: 0.5057 (pp) cc_final: 0.4721 (mt) REVERT: L 298 PHE cc_start: 0.6123 (t80) cc_final: 0.5263 (t80) REVERT: L 322 PRO cc_start: 0.5895 (Cg_exo) cc_final: 0.5594 (Cg_endo) REVERT: L 407 MET cc_start: 0.4926 (tpt) cc_final: 0.4313 (tpt) REVERT: L 643 VAL cc_start: 0.4317 (p) cc_final: 0.4096 (t) REVERT: L 685 GLU cc_start: 0.3622 (OUTLIER) cc_final: 0.2728 (tm-30) REVERT: M 35 MET cc_start: 0.5934 (ttp) cc_final: 0.5713 (ttp) REVERT: M 165 PRO cc_start: 0.1574 (Cg_exo) cc_final: 0.1260 (Cg_endo) REVERT: M 192 LEU cc_start: 0.5043 (pp) cc_final: 0.4701 (mt) REVERT: M 260 MET cc_start: 0.6638 (tpt) cc_final: 0.5935 (mmp) REVERT: M 301 MET cc_start: 0.4666 (ttt) cc_final: 0.4362 (ttt) REVERT: M 407 MET cc_start: 0.4095 (tpt) cc_final: 0.3524 (tpt) REVERT: M 469 GLN cc_start: 0.5561 (tm-30) cc_final: 0.5017 (pt0) REVERT: M 677 ASP cc_start: 0.5005 (m-30) cc_final: 0.4718 (t70) REVERT: M 685 GLU cc_start: 0.3819 (OUTLIER) cc_final: 0.2875 (tm-30) outliers start: 350 outliers final: 244 residues processed: 877 average time/residue: 0.5235 time to fit residues: 786.3026 Evaluate side-chains 768 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 511 time to evaluate : 4.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 ASN Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 591 THR Chi-restraints excluded: chain D residue 598 TYR Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 617 MET Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 655 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 591 THR Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 587 VAL Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 301 MET Chi-restraints excluded: chain H residue 345 VAL Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 562 VAL Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 594 LEU Chi-restraints excluded: chain H residue 604 ASP Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 661 ASP Chi-restraints excluded: chain H residue 673 VAL Chi-restraints excluded: chain H residue 685 GLU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 519 VAL Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 589 ILE Chi-restraints excluded: chain I residue 602 LEU Chi-restraints excluded: chain I residue 604 ASP Chi-restraints excluded: chain I residue 650 MET Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 685 GLU Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 596 GLN Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 604 ASP Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain J residue 685 GLU Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 194 SER Chi-restraints excluded: chain K residue 219 HIS Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 398 ASP Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 444 LEU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 578 LEU Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 588 VAL Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain K residue 604 ASP Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 656 VAL Chi-restraints excluded: chain K residue 673 VAL Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 218 ARG Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 301 MET Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain L residue 365 PHE Chi-restraints excluded: chain L residue 398 ASP Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 562 VAL Chi-restraints excluded: chain L residue 564 ASP Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 604 ASP Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain L residue 685 GLU Chi-restraints excluded: chain M residue 32 CYS Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 219 HIS Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 269 VAL Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain M residue 325 LEU Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 422 LEU Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 486 THR Chi-restraints excluded: chain M residue 521 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 562 VAL Chi-restraints excluded: chain M residue 564 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 588 VAL Chi-restraints excluded: chain M residue 604 ASP Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 674 VAL Chi-restraints excluded: chain M residue 685 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 594 optimal weight: 0.0270 chunk 404 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 531 optimal weight: 0.7980 chunk 294 optimal weight: 9.9990 chunk 608 optimal weight: 0.0570 chunk 493 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 364 optimal weight: 3.9990 chunk 640 optimal weight: 0.5980 chunk 180 optimal weight: 10.0000 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN A 300 HIS ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN B 630 GLN C 283 ASN ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN D 300 HIS ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 495 ASN ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 495 ASN ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 495 ASN ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 329 GLN M 495 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 59010 Z= 0.162 Angle : 0.591 9.508 79776 Z= 0.305 Chirality : 0.044 0.228 8826 Planarity : 0.004 0.056 10464 Dihedral : 4.914 31.115 8292 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.35 % Allowed : 19.48 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.10), residues: 7440 helix: 0.79 (0.11), residues: 2166 sheet: 0.88 (0.16), residues: 1068 loop : -1.81 (0.09), residues: 4206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 251 HIS 0.010 0.001 HIS M 52 PHE 0.022 0.001 PHE M 298 TYR 0.016 0.001 TYR M 146 ARG 0.011 0.000 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 615 time to evaluate : 4.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.1871 (mptt) cc_final: 0.1551 (mppt) REVERT: A 423 TYR cc_start: 0.5563 (m-80) cc_final: 0.5214 (m-80) REVERT: A 655 ASP cc_start: 0.5538 (OUTLIER) cc_final: 0.4957 (m-30) REVERT: B 272 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5965 (tp) REVERT: B 288 LYS cc_start: 0.2202 (mptt) cc_final: 0.1228 (mmtm) REVERT: B 474 MET cc_start: 0.3127 (OUTLIER) cc_final: 0.2434 (mtp) REVERT: C 272 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.6022 (tp) REVERT: D 288 LYS cc_start: 0.1811 (mptt) cc_final: 0.1543 (mppt) REVERT: D 373 MET cc_start: 0.5243 (mtm) cc_final: 0.4932 (ttp) REVERT: D 414 CYS cc_start: 0.2871 (t) cc_final: 0.2642 (t) REVERT: D 655 ASP cc_start: 0.5692 (t70) cc_final: 0.5041 (m-30) REVERT: E 288 LYS cc_start: 0.2386 (mptt) cc_final: 0.1873 (mppt) REVERT: E 373 MET cc_start: 0.5070 (mtm) cc_final: 0.4748 (ttp) REVERT: E 674 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6184 (mp) REVERT: F 288 LYS cc_start: 0.1839 (mptt) cc_final: 0.1440 (mppt) REVERT: F 674 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6180 (mp) REVERT: H 124 MET cc_start: 0.6373 (mmm) cc_final: 0.5675 (tpp) REVERT: H 179 MET cc_start: 0.2668 (mtp) cc_final: 0.2116 (tmm) REVERT: H 220 ILE cc_start: 0.7162 (mt) cc_final: 0.6651 (tp) REVERT: H 260 MET cc_start: 0.6708 (mmp) cc_final: 0.6422 (mmm) REVERT: H 407 MET cc_start: 0.4453 (tpt) cc_final: 0.3752 (tpt) REVERT: H 483 MET cc_start: 0.6360 (mpp) cc_final: 0.5746 (mtt) REVERT: H 602 LEU cc_start: 0.4839 (OUTLIER) cc_final: 0.4472 (mt) REVERT: H 642 GLN cc_start: 0.4781 (OUTLIER) cc_final: 0.4134 (tm-30) REVERT: H 677 ASP cc_start: 0.5106 (m-30) cc_final: 0.4884 (t70) REVERT: H 685 GLU cc_start: 0.3583 (tp30) cc_final: 0.3019 (tm-30) REVERT: I 250 LEU cc_start: 0.6317 (tt) cc_final: 0.6114 (tp) REVERT: I 334 MET cc_start: 0.6539 (mmm) cc_final: 0.6038 (mmm) REVERT: I 407 MET cc_start: 0.4803 (tpt) cc_final: 0.4243 (tpt) REVERT: I 483 MET cc_start: 0.6651 (mpp) cc_final: 0.6011 (mtt) REVERT: I 623 MET cc_start: 0.4346 (ptt) cc_final: 0.3894 (tpp) REVERT: I 648 GLU cc_start: 0.6155 (mp0) cc_final: 0.5951 (mm-30) REVERT: I 652 MET cc_start: 0.5770 (tpp) cc_final: 0.5368 (tpp) REVERT: J 191 MET cc_start: 0.4395 (ppp) cc_final: 0.3968 (tmm) REVERT: J 322 PRO cc_start: 0.5894 (Cg_exo) cc_final: 0.5600 (Cg_endo) REVERT: J 334 MET cc_start: 0.6497 (mmm) cc_final: 0.6178 (mmm) REVERT: J 407 MET cc_start: 0.4600 (tpt) cc_final: 0.4300 (tpt) REVERT: J 450 THR cc_start: 0.5238 (m) cc_final: 0.4953 (p) REVERT: J 483 MET cc_start: 0.6551 (mpp) cc_final: 0.6034 (mtt) REVERT: J 513 TYR cc_start: 0.4314 (t80) cc_final: 0.4111 (t80) REVERT: J 665 SER cc_start: 0.3419 (OUTLIER) cc_final: 0.3111 (t) REVERT: J 685 GLU cc_start: 0.3322 (tp30) cc_final: 0.2652 (tm-30) REVERT: K 260 MET cc_start: 0.6642 (mmp) cc_final: 0.6282 (mmm) REVERT: K 296 PHE cc_start: 0.4728 (p90) cc_final: 0.4402 (p90) REVERT: K 407 MET cc_start: 0.4200 (tpt) cc_final: 0.3831 (tpt) REVERT: K 483 MET cc_start: 0.6438 (mpp) cc_final: 0.5856 (mtt) REVERT: K 513 TYR cc_start: 0.4747 (t80) cc_final: 0.4269 (t80) REVERT: K 652 MET cc_start: 0.5560 (tpp) cc_final: 0.5310 (tpp) REVERT: L 179 MET cc_start: 0.2767 (mtm) cc_final: 0.2033 (tmm) REVERT: L 192 LEU cc_start: 0.5228 (pp) cc_final: 0.4923 (mt) REVERT: L 298 PHE cc_start: 0.6200 (t80) cc_final: 0.5181 (t80) REVERT: L 301 MET cc_start: 0.4490 (OUTLIER) cc_final: 0.4220 (ttt) REVERT: L 322 PRO cc_start: 0.6165 (Cg_exo) cc_final: 0.5894 (Cg_endo) REVERT: L 407 MET cc_start: 0.4653 (tpt) cc_final: 0.4109 (tpt) REVERT: L 483 MET cc_start: 0.6801 (mpp) cc_final: 0.6067 (mtt) REVERT: L 495 ASN cc_start: 0.6082 (m-40) cc_final: 0.5704 (t0) REVERT: M 124 MET cc_start: 0.6261 (mmm) cc_final: 0.6009 (mmm) REVERT: M 192 LEU cc_start: 0.5156 (pp) cc_final: 0.4819 (mt) REVERT: M 260 MET cc_start: 0.6814 (tpt) cc_final: 0.6020 (mmp) REVERT: M 407 MET cc_start: 0.4097 (tpt) cc_final: 0.3626 (tpt) REVERT: M 469 GLN cc_start: 0.5287 (tm-30) cc_final: 0.5009 (pt0) REVERT: M 483 MET cc_start: 0.6804 (mpp) cc_final: 0.6021 (mtt) REVERT: M 677 ASP cc_start: 0.4986 (m-30) cc_final: 0.4757 (t70) REVERT: M 685 GLU cc_start: 0.4093 (tp30) cc_final: 0.2904 (tm-30) outliers start: 144 outliers final: 92 residues processed: 727 average time/residue: 0.5442 time to fit residues: 671.1726 Evaluate side-chains 639 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 537 time to evaluate : 4.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 383 ASN Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 219 HIS Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 602 LEU Chi-restraints excluded: chain H residue 642 GLN Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 661 ASP Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 486 THR Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 219 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 486 THR Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 661 ASP Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 219 HIS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 271 LEU Chi-restraints excluded: chain L residue 301 MET Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 564 ASP Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 422 LEU Chi-restraints excluded: chain M residue 521 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain M residue 564 ASP Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 674 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 240 optimal weight: 9.9990 chunk 642 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 418 optimal weight: 0.8980 chunk 176 optimal weight: 10.0000 chunk 714 optimal weight: 6.9990 chunk 592 optimal weight: 20.0000 chunk 330 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 chunk 374 optimal weight: 8.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN ** C 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS D 151 ASN ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 ASN ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 GLN ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 342 GLN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 469 GLN ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 329 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 59010 Z= 0.297 Angle : 0.701 12.036 79776 Z= 0.363 Chirality : 0.048 0.231 8826 Planarity : 0.006 0.068 10464 Dihedral : 5.480 34.840 8292 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 4.75 % Allowed : 18.14 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.09), residues: 7440 helix: 0.38 (0.11), residues: 2232 sheet: 0.86 (0.16), residues: 1002 loop : -2.03 (0.09), residues: 4206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 251 HIS 0.013 0.002 HIS E 137 PHE 0.024 0.002 PHE M 298 TYR 0.019 0.002 TYR F 669 ARG 0.009 0.001 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 573 time to evaluate : 4.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.5625 (m-80) cc_final: 0.5224 (m-80) REVERT: A 497 PHE cc_start: 0.5843 (OUTLIER) cc_final: 0.5334 (t80) REVERT: B 272 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6238 (tp) REVERT: B 474 MET cc_start: 0.3342 (OUTLIER) cc_final: 0.2589 (mtp) REVERT: C 239 LEU cc_start: 0.7928 (tp) cc_final: 0.7663 (tt) REVERT: C 272 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6304 (tp) REVERT: C 474 MET cc_start: 0.3056 (OUTLIER) cc_final: 0.2345 (mtp) REVERT: D 288 LYS cc_start: 0.2442 (mptt) cc_final: 0.1885 (mppt) REVERT: E 166 GLU cc_start: 0.6332 (mm-30) cc_final: 0.6068 (mm-30) REVERT: E 288 LYS cc_start: 0.3083 (mptt) cc_final: 0.2426 (ttmt) REVERT: E 483 ASP cc_start: 0.5205 (OUTLIER) cc_final: 0.4922 (m-30) REVERT: E 674 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6195 (mp) REVERT: F 288 LYS cc_start: 0.3087 (mptt) cc_final: 0.2364 (ttmt) REVERT: F 674 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6175 (mp) REVERT: H 55 GLU cc_start: 0.5780 (mt-10) cc_final: 0.5379 (mm-30) REVERT: H 124 MET cc_start: 0.6381 (mmm) cc_final: 0.5335 (tpp) REVERT: H 220 ILE cc_start: 0.7630 (mt) cc_final: 0.7125 (tp) REVERT: H 249 VAL cc_start: 0.5664 (m) cc_final: 0.5435 (t) REVERT: H 251 GLU cc_start: 0.1456 (mp0) cc_final: 0.1167 (mp0) REVERT: H 260 MET cc_start: 0.6711 (mmp) cc_final: 0.6440 (mmm) REVERT: H 334 MET cc_start: 0.6513 (mmm) cc_final: 0.6216 (mtp) REVERT: H 407 MET cc_start: 0.4494 (tpt) cc_final: 0.3805 (tpt) REVERT: H 483 MET cc_start: 0.6488 (mpp) cc_final: 0.5787 (mtt) REVERT: H 642 GLN cc_start: 0.4888 (OUTLIER) cc_final: 0.4389 (tm-30) REVERT: H 685 GLU cc_start: 0.3830 (OUTLIER) cc_final: 0.3120 (tm-30) REVERT: I 342 GLN cc_start: 0.6909 (tm-30) cc_final: 0.6593 (tp-100) REVERT: I 363 ARG cc_start: 0.4156 (mmt180) cc_final: 0.3923 (ttp-110) REVERT: I 407 MET cc_start: 0.4584 (tpt) cc_final: 0.3979 (tpt) REVERT: I 483 MET cc_start: 0.6812 (mpp) cc_final: 0.6231 (mtt) REVERT: I 623 MET cc_start: 0.4516 (ptt) cc_final: 0.3920 (tpp) REVERT: I 685 GLU cc_start: 0.3095 (OUTLIER) cc_final: 0.2598 (tm-30) REVERT: J 58 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.6061 (pm20) REVERT: J 322 PRO cc_start: 0.5900 (Cg_exo) cc_final: 0.5572 (Cg_endo) REVERT: J 407 MET cc_start: 0.4532 (tpt) cc_final: 0.4193 (tpt) REVERT: J 483 MET cc_start: 0.6785 (mpp) cc_final: 0.5959 (mtt) REVERT: J 642 GLN cc_start: 0.4819 (OUTLIER) cc_final: 0.4199 (tm-30) REVERT: J 665 SER cc_start: 0.3477 (OUTLIER) cc_final: 0.3239 (t) REVERT: J 685 GLU cc_start: 0.3428 (OUTLIER) cc_final: 0.2588 (tm-30) REVERT: K 260 MET cc_start: 0.6653 (mmp) cc_final: 0.6320 (mmm) REVERT: K 296 PHE cc_start: 0.4779 (p90) cc_final: 0.4413 (p90) REVERT: K 407 MET cc_start: 0.4224 (tpt) cc_final: 0.3765 (tpt) REVERT: K 483 MET cc_start: 0.6648 (mpp) cc_final: 0.5927 (mtt) REVERT: K 513 TYR cc_start: 0.4719 (t80) cc_final: 0.4502 (t80) REVERT: K 619 ILE cc_start: 0.4924 (OUTLIER) cc_final: 0.4604 (pt) REVERT: K 642 GLN cc_start: 0.5179 (OUTLIER) cc_final: 0.4268 (tm-30) REVERT: K 652 MET cc_start: 0.5841 (tpp) cc_final: 0.5558 (tpp) REVERT: L 134 MET cc_start: 0.5265 (ptp) cc_final: 0.5053 (ptt) REVERT: L 165 PRO cc_start: 0.1734 (Cg_exo) cc_final: 0.1399 (Cg_endo) REVERT: L 179 MET cc_start: 0.2779 (mtm) cc_final: 0.1986 (tmm) REVERT: L 298 PHE cc_start: 0.6066 (t80) cc_final: 0.5255 (t80) REVERT: L 322 PRO cc_start: 0.6038 (Cg_exo) cc_final: 0.5791 (Cg_endo) REVERT: L 407 MET cc_start: 0.4647 (tpt) cc_final: 0.4044 (tpt) REVERT: M 165 PRO cc_start: 0.2173 (Cg_exo) cc_final: 0.1839 (Cg_endo) REVERT: M 192 LEU cc_start: 0.5217 (pp) cc_final: 0.4876 (mt) REVERT: M 260 MET cc_start: 0.6728 (tpt) cc_final: 0.5969 (mmm) REVERT: M 299 MET cc_start: 0.6595 (tmm) cc_final: 0.6325 (ttp) REVERT: M 407 MET cc_start: 0.4109 (tpt) cc_final: 0.3426 (tpt) REVERT: M 469 GLN cc_start: 0.5434 (tm-30) cc_final: 0.4941 (pt0) REVERT: M 685 GLU cc_start: 0.4263 (tp30) cc_final: 0.3010 (tm-30) outliers start: 291 outliers final: 214 residues processed: 796 average time/residue: 0.5227 time to fit residues: 711.8463 Evaluate side-chains 760 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 529 time to evaluate : 4.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 383 ASN Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 598 TYR Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 625 VAL Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 587 VAL Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 629 THR Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 219 HIS Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 301 MET Chi-restraints excluded: chain H residue 314 GLU Chi-restraints excluded: chain H residue 353 GLU Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 562 VAL Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 604 ASP Chi-restraints excluded: chain H residue 642 GLN Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 661 ASP Chi-restraints excluded: chain H residue 667 LEU Chi-restraints excluded: chain H residue 685 GLU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 52 HIS Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 562 VAL Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 602 LEU Chi-restraints excluded: chain I residue 604 ASP Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 685 GLU Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 301 MET Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 486 THR Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 519 VAL Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 562 VAL Chi-restraints excluded: chain J residue 578 LEU Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 589 ILE Chi-restraints excluded: chain J residue 596 GLN Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 604 ASP Chi-restraints excluded: chain J residue 642 GLN Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain J residue 685 GLU Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 219 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 486 THR Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 578 LEU Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 604 ASP Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 642 GLN Chi-restraints excluded: chain K residue 661 ASP Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 219 HIS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 271 LEU Chi-restraints excluded: chain L residue 301 MET Chi-restraints excluded: chain L residue 345 VAL Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 562 VAL Chi-restraints excluded: chain L residue 564 ASP Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 604 ASP Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain M residue 32 CYS Chi-restraints excluded: chain M residue 52 HIS Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 422 LEU Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 483 MET Chi-restraints excluded: chain M residue 486 THR Chi-restraints excluded: chain M residue 521 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 564 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 588 VAL Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 604 ASP Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 674 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 688 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 406 optimal weight: 6.9990 chunk 521 optimal weight: 0.5980 chunk 404 optimal weight: 10.0000 chunk 601 optimal weight: 4.9990 chunk 398 optimal weight: 0.9990 chunk 711 optimal weight: 7.9990 chunk 445 optimal weight: 5.9990 chunk 433 optimal weight: 0.0980 chunk 328 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN A 324 ASN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN C 165 GLN C 283 ASN ** C 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS D 283 ASN ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 ASN E 383 ASN ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 59010 Z= 0.160 Angle : 0.584 11.072 79776 Z= 0.302 Chirality : 0.044 0.202 8826 Planarity : 0.004 0.057 10464 Dihedral : 4.746 28.792 8292 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.06 % Allowed : 20.05 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.10), residues: 7440 helix: 0.95 (0.12), residues: 2172 sheet: 0.97 (0.16), residues: 1068 loop : -1.83 (0.09), residues: 4200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 251 HIS 0.013 0.001 HIS D 137 PHE 0.025 0.001 PHE M 298 TYR 0.015 0.001 TYR H 146 ARG 0.016 0.000 ARG C 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 578 time to evaluate : 5.042 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: A 288 LYS cc_start: 0.2364 (mptt) cc_final: 0.1958 (mppt) REVERT: A 423 TYR cc_start: 0.5560 (m-80) cc_final: 0.5315 (m-80) REVERT: A 655 ASP cc_start: 0.5536 (OUTLIER) cc_final: 0.5011 (m-30) REVERT: B 272 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5964 (tp) REVERT: B 288 LYS cc_start: 0.2370 (mptt) cc_final: 0.1383 (mmtm) REVERT: B 474 MET cc_start: 0.2853 (OUTLIER) cc_final: 0.2050 (mtp) REVERT: C 239 LEU cc_start: 0.7879 (tp) cc_final: 0.7611 (tt) REVERT: C 272 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.6017 (tp) REVERT: C 474 MET cc_start: 0.2968 (OUTLIER) cc_final: 0.2228 (mtp) REVERT: D 227 ARG cc_start: 0.6858 (mtt90) cc_final: 0.6649 (mtt180) REVERT: D 414 CYS cc_start: 0.3212 (t) cc_final: 0.3008 (t) REVERT: D 655 ASP cc_start: 0.5752 (OUTLIER) cc_final: 0.5057 (m-30) REVERT: E 288 LYS cc_start: 0.2389 (mptt) cc_final: 0.2103 (ttmt) REVERT: E 474 MET cc_start: 0.3568 (OUTLIER) cc_final: 0.2986 (mtp) REVERT: E 483 ASP cc_start: 0.5049 (OUTLIER) cc_final: 0.4731 (m-30) REVERT: E 674 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6361 (mp) REVERT: F 288 LYS cc_start: 0.2268 (mptt) cc_final: 0.1860 (ttmt) REVERT: F 674 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.6084 (mp) REVERT: H 179 MET cc_start: 0.2697 (mtp) cc_final: 0.1848 (tmm) REVERT: H 209 ILE cc_start: 0.2794 (mm) cc_final: 0.2426 (mm) REVERT: H 249 VAL cc_start: 0.5476 (m) cc_final: 0.5168 (t) REVERT: H 251 GLU cc_start: 0.1439 (mp0) cc_final: 0.1165 (mp0) REVERT: H 260 MET cc_start: 0.6705 (mmp) cc_final: 0.6408 (mmm) REVERT: H 407 MET cc_start: 0.4517 (tpt) cc_final: 0.4002 (tpt) REVERT: H 483 MET cc_start: 0.6239 (mpp) cc_final: 0.5601 (mtt) REVERT: H 642 GLN cc_start: 0.4901 (OUTLIER) cc_final: 0.4421 (tm-30) REVERT: H 685 GLU cc_start: 0.3626 (tp30) cc_final: 0.2971 (tm-30) REVERT: I 53 VAL cc_start: 0.5057 (m) cc_final: 0.4855 (p) REVERT: I 342 GLN cc_start: 0.7025 (tm-30) cc_final: 0.6736 (tp-100) REVERT: I 407 MET cc_start: 0.4620 (tpt) cc_final: 0.4060 (tpt) REVERT: I 483 MET cc_start: 0.6482 (mpp) cc_final: 0.6002 (mtt) REVERT: I 623 MET cc_start: 0.4276 (ptt) cc_final: 0.3702 (tpp) REVERT: I 642 GLN cc_start: 0.4486 (OUTLIER) cc_final: 0.3986 (tm-30) REVERT: I 652 MET cc_start: 0.5857 (tpp) cc_final: 0.5453 (tpp) REVERT: J 322 PRO cc_start: 0.5811 (Cg_exo) cc_final: 0.5466 (Cg_endo) REVERT: J 407 MET cc_start: 0.4590 (tpt) cc_final: 0.4278 (tpt) REVERT: J 483 MET cc_start: 0.6556 (mpp) cc_final: 0.6089 (mtt) REVERT: J 515 ASP cc_start: 0.4536 (m-30) cc_final: 0.4293 (t0) REVERT: J 623 MET cc_start: 0.5106 (tpp) cc_final: 0.4839 (ptm) REVERT: J 642 GLN cc_start: 0.4654 (OUTLIER) cc_final: 0.4063 (tm-30) REVERT: J 665 SER cc_start: 0.3323 (OUTLIER) cc_final: 0.2992 (t) REVERT: J 685 GLU cc_start: 0.3680 (tp30) cc_final: 0.2593 (tm-30) REVERT: K 260 MET cc_start: 0.6678 (mmp) cc_final: 0.6318 (mmm) REVERT: K 296 PHE cc_start: 0.4806 (p90) cc_final: 0.4382 (p90) REVERT: K 299 MET cc_start: 0.6601 (ttp) cc_final: 0.6225 (ptm) REVERT: K 407 MET cc_start: 0.4172 (tpt) cc_final: 0.3744 (tpt) REVERT: K 483 MET cc_start: 0.6316 (mpp) cc_final: 0.5743 (mtt) REVERT: K 513 TYR cc_start: 0.4460 (t80) cc_final: 0.4201 (t80) REVERT: K 619 ILE cc_start: 0.4728 (OUTLIER) cc_final: 0.4442 (pt) REVERT: K 642 GLN cc_start: 0.5076 (OUTLIER) cc_final: 0.4200 (tm-30) REVERT: K 652 MET cc_start: 0.5805 (tpp) cc_final: 0.5461 (tpp) REVERT: L 134 MET cc_start: 0.5298 (ptp) cc_final: 0.5076 (ptt) REVERT: L 179 MET cc_start: 0.2783 (mtm) cc_final: 0.2047 (tmm) REVERT: L 301 MET cc_start: 0.4528 (OUTLIER) cc_final: 0.4304 (ttt) REVERT: L 322 PRO cc_start: 0.6062 (Cg_exo) cc_final: 0.5779 (Cg_endo) REVERT: L 407 MET cc_start: 0.4469 (tpt) cc_final: 0.3920 (tpt) REVERT: L 483 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6136 (mtt) REVERT: L 685 GLU cc_start: 0.3730 (tp30) cc_final: 0.2721 (tm-30) REVERT: M 165 PRO cc_start: 0.2063 (Cg_exo) cc_final: 0.1757 (Cg_endo) REVERT: M 192 LEU cc_start: 0.5141 (pp) cc_final: 0.4819 (mt) REVERT: M 260 MET cc_start: 0.6726 (tpt) cc_final: 0.6008 (mmp) REVERT: M 299 MET cc_start: 0.6668 (tmm) cc_final: 0.6287 (ttp) REVERT: M 407 MET cc_start: 0.4140 (tpt) cc_final: 0.3539 (tpt) REVERT: M 469 GLN cc_start: 0.5246 (tm-30) cc_final: 0.4925 (pt0) REVERT: M 685 GLU cc_start: 0.4301 (tp30) cc_final: 0.3013 (tm-30) outliers start: 187 outliers final: 127 residues processed: 725 average time/residue: 0.5294 time to fit residues: 658.3279 Evaluate side-chains 667 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 522 time to evaluate : 4.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 383 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 617 MET Chi-restraints excluded: chain D residue 655 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 625 VAL Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 219 HIS Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 642 GLN Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 661 ASP Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 573 MET Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 642 GLN Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 301 MET Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 486 THR Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 642 GLN Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 194 SER Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 486 THR Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 602 LEU Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 642 GLN Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 271 LEU Chi-restraints excluded: chain L residue 301 MET Chi-restraints excluded: chain L residue 408 LEU Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 564 ASP Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain M residue 52 HIS Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain M residue 301 MET Chi-restraints excluded: chain M residue 408 LEU Chi-restraints excluded: chain M residue 422 LEU Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 483 MET Chi-restraints excluded: chain M residue 521 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 564 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 617 THR Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 674 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 440 optimal weight: 10.0000 chunk 284 optimal weight: 0.6980 chunk 424 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 452 optimal weight: 10.0000 chunk 484 optimal weight: 30.0000 chunk 351 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 559 optimal weight: 9.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN C 137 HIS C 283 ASN ** C 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 HIS ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 69 ASN ** K 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 59010 Z= 0.213 Angle : 0.614 11.027 79776 Z= 0.317 Chirality : 0.045 0.189 8826 Planarity : 0.005 0.071 10464 Dihedral : 4.864 28.085 8292 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 3.69 % Allowed : 19.80 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.10), residues: 7440 helix: 0.99 (0.12), residues: 2124 sheet: 0.96 (0.16), residues: 1068 loop : -1.87 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 251 HIS 0.010 0.001 HIS M 52 PHE 0.025 0.001 PHE M 298 TYR 0.023 0.001 TYR E 603 ARG 0.007 0.000 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 542 time to evaluate : 4.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.6840 (mtt90) cc_final: 0.6543 (mtt180) REVERT: A 288 LYS cc_start: 0.2220 (mptt) cc_final: 0.1648 (mppt) REVERT: A 423 TYR cc_start: 0.5583 (m-80) cc_final: 0.5356 (m-80) REVERT: A 655 ASP cc_start: 0.5330 (OUTLIER) cc_final: 0.4806 (m-30) REVERT: B 272 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.6047 (tp) REVERT: B 288 LYS cc_start: 0.2142 (mptt) cc_final: 0.1826 (mppt) REVERT: B 474 MET cc_start: 0.3243 (OUTLIER) cc_final: 0.2472 (mtp) REVERT: C 272 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.6111 (tp) REVERT: C 474 MET cc_start: 0.3133 (OUTLIER) cc_final: 0.2392 (mtp) REVERT: E 288 LYS cc_start: 0.2768 (mptt) cc_final: 0.2196 (ttmt) REVERT: E 474 MET cc_start: 0.3645 (OUTLIER) cc_final: 0.2953 (mtp) REVERT: E 483 ASP cc_start: 0.5117 (OUTLIER) cc_final: 0.4863 (m-30) REVERT: E 674 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6196 (mp) REVERT: F 288 LYS cc_start: 0.2192 (mptt) cc_final: 0.1752 (ttmt) REVERT: F 674 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6134 (mp) REVERT: H 55 GLU cc_start: 0.5792 (mt-10) cc_final: 0.5368 (mm-30) REVERT: H 179 MET cc_start: 0.2664 (mtp) cc_final: 0.1845 (tmm) REVERT: H 209 ILE cc_start: 0.2723 (mm) cc_final: 0.2397 (mm) REVERT: H 249 VAL cc_start: 0.5591 (m) cc_final: 0.5283 (t) REVERT: H 251 GLU cc_start: 0.1655 (mp0) cc_final: 0.1294 (mp0) REVERT: H 260 MET cc_start: 0.6703 (mmp) cc_final: 0.6410 (mmm) REVERT: H 407 MET cc_start: 0.4517 (tpt) cc_final: 0.3959 (tpt) REVERT: H 483 MET cc_start: 0.6455 (mpp) cc_final: 0.5870 (mtt) REVERT: H 642 GLN cc_start: 0.4908 (OUTLIER) cc_final: 0.4393 (tm-30) REVERT: H 685 GLU cc_start: 0.3870 (tp30) cc_final: 0.3131 (tm-30) REVERT: I 342 GLN cc_start: 0.6852 (tm-30) cc_final: 0.6584 (tp-100) REVERT: I 407 MET cc_start: 0.4539 (tpt) cc_final: 0.3969 (tpt) REVERT: I 483 MET cc_start: 0.6607 (mpp) cc_final: 0.6106 (mtt) REVERT: I 642 GLN cc_start: 0.4608 (OUTLIER) cc_final: 0.4042 (tm-30) REVERT: J 249 VAL cc_start: 0.5414 (m) cc_final: 0.5197 (t) REVERT: J 322 PRO cc_start: 0.5919 (Cg_exo) cc_final: 0.5557 (Cg_endo) REVERT: J 334 MET cc_start: 0.6502 (mmm) cc_final: 0.6073 (mmm) REVERT: J 407 MET cc_start: 0.4550 (tpt) cc_final: 0.4156 (tpt) REVERT: J 483 MET cc_start: 0.6631 (mpp) cc_final: 0.5853 (mtt) REVERT: J 642 GLN cc_start: 0.4873 (OUTLIER) cc_final: 0.4257 (tm-30) REVERT: J 665 SER cc_start: 0.3318 (OUTLIER) cc_final: 0.2978 (t) REVERT: J 685 GLU cc_start: 0.3544 (OUTLIER) cc_final: 0.2544 (tm-30) REVERT: K 260 MET cc_start: 0.6679 (mmp) cc_final: 0.6305 (mmm) REVERT: K 296 PHE cc_start: 0.4845 (p90) cc_final: 0.4373 (p90) REVERT: K 299 MET cc_start: 0.6350 (ttp) cc_final: 0.5987 (ptm) REVERT: K 407 MET cc_start: 0.4175 (tpt) cc_final: 0.3725 (tpt) REVERT: K 483 MET cc_start: 0.6444 (mpp) cc_final: 0.5821 (mtt) REVERT: K 513 TYR cc_start: 0.4552 (t80) cc_final: 0.4309 (t80) REVERT: K 619 ILE cc_start: 0.4788 (OUTLIER) cc_final: 0.4552 (pt) REVERT: K 642 GLN cc_start: 0.5142 (OUTLIER) cc_final: 0.4271 (tm-30) REVERT: K 652 MET cc_start: 0.5997 (tpp) cc_final: 0.5617 (tpp) REVERT: L 134 MET cc_start: 0.5425 (ptp) cc_final: 0.5221 (ptt) REVERT: L 179 MET cc_start: 0.2939 (mtm) cc_final: 0.2170 (tmm) REVERT: L 322 PRO cc_start: 0.5973 (Cg_exo) cc_final: 0.5726 (Cg_endo) REVERT: L 407 MET cc_start: 0.4581 (tpt) cc_final: 0.3997 (tpt) REVERT: L 483 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6164 (mtt) REVERT: L 685 GLU cc_start: 0.3543 (tp30) cc_final: 0.2508 (tm-30) REVERT: M 165 PRO cc_start: 0.1951 (Cg_exo) cc_final: 0.1633 (Cg_endo) REVERT: M 192 LEU cc_start: 0.5214 (pp) cc_final: 0.4888 (mt) REVERT: M 260 MET cc_start: 0.6621 (tpt) cc_final: 0.5974 (mmp) REVERT: M 299 MET cc_start: 0.6643 (tmm) cc_final: 0.6313 (ttp) REVERT: M 407 MET cc_start: 0.4059 (tpt) cc_final: 0.3379 (tpt) REVERT: M 469 GLN cc_start: 0.5368 (tm-30) cc_final: 0.4909 (pt0) REVERT: M 685 GLU cc_start: 0.4339 (OUTLIER) cc_final: 0.2996 (tm-30) outliers start: 226 outliers final: 171 residues processed: 702 average time/residue: 0.5269 time to fit residues: 638.0995 Evaluate side-chains 711 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 522 time to evaluate : 4.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 383 ASN Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 617 MET Chi-restraints excluded: chain D residue 655 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 625 VAL Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 219 HIS Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 353 GLU Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 642 GLN Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 661 ASP Chi-restraints excluded: chain H residue 667 LEU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 642 GLN Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 301 MET Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 486 THR Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 578 LEU Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 642 GLN Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain J residue 685 GLU Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 194 SER Chi-restraints excluded: chain K residue 219 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 486 THR Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 578 LEU Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain K residue 602 LEU Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 642 GLN Chi-restraints excluded: chain K residue 661 ASP Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 219 HIS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 271 LEU Chi-restraints excluded: chain L residue 301 MET Chi-restraints excluded: chain L residue 408 LEU Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 564 ASP Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain M residue 32 CYS Chi-restraints excluded: chain M residue 52 HIS Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain M residue 301 MET Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 408 LEU Chi-restraints excluded: chain M residue 422 LEU Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 483 MET Chi-restraints excluded: chain M residue 521 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 564 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 617 THR Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 674 VAL Chi-restraints excluded: chain M residue 685 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 647 optimal weight: 10.0000 chunk 681 optimal weight: 1.9990 chunk 621 optimal weight: 10.0000 chunk 662 optimal weight: 7.9990 chunk 398 optimal weight: 0.0970 chunk 288 optimal weight: 6.9990 chunk 520 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 598 optimal weight: 8.9990 chunk 626 optimal weight: 5.9990 chunk 660 optimal weight: 3.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN ** C 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 59010 Z= 0.263 Angle : 0.674 11.015 79776 Z= 0.348 Chirality : 0.047 0.204 8826 Planarity : 0.005 0.061 10464 Dihedral : 5.289 31.507 8292 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 4.36 % Allowed : 19.56 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.10), residues: 7440 helix: 0.66 (0.11), residues: 2148 sheet: 0.77 (0.16), residues: 1062 loop : -2.04 (0.09), residues: 4230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 251 HIS 0.010 0.001 HIS M 52 PHE 0.026 0.002 PHE M 298 TYR 0.022 0.002 TYR E 603 ARG 0.007 0.001 ARG K 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 560 time to evaluate : 4.863 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: A 168 MET cc_start: 0.5899 (tpt) cc_final: 0.5678 (tpp) REVERT: B 142 TYR cc_start: 0.6045 (m-10) cc_final: 0.5730 (m-10) REVERT: B 272 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.6056 (tp) REVERT: B 373 MET cc_start: 0.5429 (mtm) cc_final: 0.5156 (mtm) REVERT: B 474 MET cc_start: 0.3332 (OUTLIER) cc_final: 0.2583 (mtp) REVERT: C 272 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6168 (tp) REVERT: C 474 MET cc_start: 0.3190 (OUTLIER) cc_final: 0.2482 (mtp) REVERT: D 474 MET cc_start: 0.3594 (OUTLIER) cc_final: 0.3317 (mtt) REVERT: E 288 LYS cc_start: 0.2795 (mptt) cc_final: 0.2254 (ttmt) REVERT: E 436 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7072 (mmm160) REVERT: E 483 ASP cc_start: 0.4899 (OUTLIER) cc_final: 0.4614 (m-30) REVERT: E 674 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6129 (mp) REVERT: F 288 LYS cc_start: 0.2674 (mptt) cc_final: 0.1995 (ttmt) REVERT: F 674 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6042 (mp) REVERT: H 55 GLU cc_start: 0.5829 (mt-10) cc_final: 0.5377 (mm-30) REVERT: H 179 MET cc_start: 0.3115 (mtp) cc_final: 0.1930 (tmm) REVERT: H 209 ILE cc_start: 0.2749 (mm) cc_final: 0.2393 (mm) REVERT: H 249 VAL cc_start: 0.5687 (m) cc_final: 0.5471 (t) REVERT: H 260 MET cc_start: 0.6666 (mmp) cc_final: 0.6405 (mmm) REVERT: H 334 MET cc_start: 0.6548 (mmm) cc_final: 0.6257 (mtp) REVERT: H 407 MET cc_start: 0.4439 (tpt) cc_final: 0.3854 (tpt) REVERT: H 483 MET cc_start: 0.6424 (mpp) cc_final: 0.5740 (mtt) REVERT: H 642 GLN cc_start: 0.4997 (OUTLIER) cc_final: 0.4180 (tm-30) REVERT: H 685 GLU cc_start: 0.3922 (tp30) cc_final: 0.3057 (tm-30) REVERT: I 334 MET cc_start: 0.6505 (mmm) cc_final: 0.6060 (mmm) REVERT: I 407 MET cc_start: 0.4492 (tpt) cc_final: 0.3911 (tpt) REVERT: I 483 MET cc_start: 0.6795 (mpp) cc_final: 0.6263 (mtt) REVERT: I 623 MET cc_start: 0.4474 (ptt) cc_final: 0.4026 (tpp) REVERT: I 642 GLN cc_start: 0.4782 (OUTLIER) cc_final: 0.4183 (tm-30) REVERT: J 192 LEU cc_start: 0.5718 (pp) cc_final: 0.5468 (mt) REVERT: J 298 PHE cc_start: 0.5861 (t80) cc_final: 0.5472 (t80) REVERT: J 322 PRO cc_start: 0.5898 (Cg_exo) cc_final: 0.5526 (Cg_endo) REVERT: J 334 MET cc_start: 0.6538 (mmm) cc_final: 0.6088 (mmm) REVERT: J 407 MET cc_start: 0.4521 (tpt) cc_final: 0.4113 (tpt) REVERT: J 483 MET cc_start: 0.6789 (mpp) cc_final: 0.6007 (mtt) REVERT: J 623 MET cc_start: 0.4498 (ptm) cc_final: 0.4056 (tpp) REVERT: J 642 GLN cc_start: 0.4795 (OUTLIER) cc_final: 0.4184 (tm-30) REVERT: J 665 SER cc_start: 0.3149 (OUTLIER) cc_final: 0.2874 (t) REVERT: J 685 GLU cc_start: 0.3591 (OUTLIER) cc_final: 0.2485 (tm-30) REVERT: K 146 TYR cc_start: 0.5434 (t80) cc_final: 0.5019 (t80) REVERT: K 260 MET cc_start: 0.6652 (mmp) cc_final: 0.6287 (mmm) REVERT: K 296 PHE cc_start: 0.4673 (p90) cc_final: 0.4142 (p90) REVERT: K 299 MET cc_start: 0.6538 (ttp) cc_final: 0.6239 (ptm) REVERT: K 407 MET cc_start: 0.4143 (tpt) cc_final: 0.3675 (tpt) REVERT: K 483 MET cc_start: 0.6617 (mpp) cc_final: 0.5918 (mtt) REVERT: K 619 ILE cc_start: 0.4759 (OUTLIER) cc_final: 0.4507 (pt) REVERT: K 642 GLN cc_start: 0.5323 (OUTLIER) cc_final: 0.4445 (tm-30) REVERT: K 652 MET cc_start: 0.5852 (tpp) cc_final: 0.5461 (tpp) REVERT: L 134 MET cc_start: 0.5459 (ptp) cc_final: 0.5240 (ptt) REVERT: L 165 PRO cc_start: 0.2095 (Cg_exo) cc_final: 0.1788 (Cg_endo) REVERT: L 179 MET cc_start: 0.2861 (mtm) cc_final: 0.2046 (tmm) REVERT: L 322 PRO cc_start: 0.6066 (Cg_exo) cc_final: 0.5812 (Cg_endo) REVERT: L 342 GLN cc_start: 0.6519 (tp40) cc_final: 0.6240 (tp-100) REVERT: L 407 MET cc_start: 0.4456 (tpt) cc_final: 0.3907 (tpt) REVERT: L 422 LEU cc_start: 0.6386 (tt) cc_final: 0.6019 (mt) REVERT: L 623 MET cc_start: 0.5158 (ptm) cc_final: 0.4546 (tpp) REVERT: L 642 GLN cc_start: 0.4811 (OUTLIER) cc_final: 0.4446 (tm-30) REVERT: L 685 GLU cc_start: 0.3452 (tp30) cc_final: 0.2375 (tm-30) REVERT: M 71 TYR cc_start: 0.6386 (m-80) cc_final: 0.5783 (m-80) REVERT: M 124 MET cc_start: 0.6148 (mmm) cc_final: 0.5857 (tpp) REVERT: M 165 PRO cc_start: 0.2032 (Cg_exo) cc_final: 0.1684 (Cg_endo) REVERT: M 192 LEU cc_start: 0.5405 (pp) cc_final: 0.5069 (mt) REVERT: M 260 MET cc_start: 0.6585 (tpt) cc_final: 0.5905 (mmp) REVERT: M 407 MET cc_start: 0.4044 (tpt) cc_final: 0.3368 (tpt) REVERT: M 469 GLN cc_start: 0.5388 (tm-30) cc_final: 0.4930 (pt0) REVERT: M 685 GLU cc_start: 0.4255 (OUTLIER) cc_final: 0.2913 (tm-30) outliers start: 267 outliers final: 218 residues processed: 758 average time/residue: 0.5159 time to fit residues: 672.7797 Evaluate side-chains 765 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 529 time to evaluate : 4.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 383 ASN Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 591 THR Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 655 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 436 ARG Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 219 HIS Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain H residue 353 GLU Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 594 LEU Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 642 GLN Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 661 ASP Chi-restraints excluded: chain H residue 667 LEU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 398 ASP Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 578 LEU Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 596 GLN Chi-restraints excluded: chain I residue 642 GLN Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 301 MET Chi-restraints excluded: chain J residue 398 ASP Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 486 THR Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 519 VAL Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 562 VAL Chi-restraints excluded: chain J residue 578 LEU Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 589 ILE Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 642 GLN Chi-restraints excluded: chain J residue 661 ASP Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain J residue 685 GLU Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 194 SER Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 219 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 486 THR Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 578 LEU Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain K residue 602 LEU Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 642 GLN Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 219 HIS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 271 LEU Chi-restraints excluded: chain L residue 301 MET Chi-restraints excluded: chain L residue 408 LEU Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 564 ASP Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 589 ILE Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 616 SER Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 642 GLN Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain M residue 32 CYS Chi-restraints excluded: chain M residue 52 HIS Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 250 LEU Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain M residue 301 MET Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 422 LEU Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 483 MET Chi-restraints excluded: chain M residue 486 THR Chi-restraints excluded: chain M residue 521 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 564 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 589 ILE Chi-restraints excluded: chain M residue 594 LEU Chi-restraints excluded: chain M residue 617 THR Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 674 VAL Chi-restraints excluded: chain M residue 685 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 435 optimal weight: 0.1980 chunk 700 optimal weight: 9.9990 chunk 427 optimal weight: 0.9990 chunk 332 optimal weight: 0.9980 chunk 487 optimal weight: 4.9990 chunk 735 optimal weight: 5.9990 chunk 676 optimal weight: 5.9990 chunk 585 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 452 optimal weight: 10.0000 chunk 358 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 283 ASN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN ** C 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 495 ASN ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** M 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 59010 Z= 0.188 Angle : 0.612 10.687 79776 Z= 0.315 Chirality : 0.045 0.206 8826 Planarity : 0.005 0.059 10464 Dihedral : 4.927 28.177 8292 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.51 % Allowed : 20.51 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.10), residues: 7440 helix: 0.95 (0.12), residues: 2124 sheet: 0.82 (0.16), residues: 1074 loop : -1.94 (0.09), residues: 4242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 251 HIS 0.010 0.001 HIS M 52 PHE 0.025 0.001 PHE M 298 TYR 0.016 0.001 TYR J 146 ARG 0.020 0.000 ARG C 465 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 565 time to evaluate : 4.870 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: A 168 MET cc_start: 0.5832 (tpt) cc_final: 0.5529 (tpp) REVERT: A 288 LYS cc_start: 0.2230 (mptt) cc_final: 0.1651 (mppt) REVERT: A 655 ASP cc_start: 0.5263 (OUTLIER) cc_final: 0.4716 (m-30) REVERT: B 142 TYR cc_start: 0.6019 (m-10) cc_final: 0.5706 (m-10) REVERT: B 272 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.6052 (tp) REVERT: B 288 LYS cc_start: 0.2594 (mptt) cc_final: 0.2327 (mppt) REVERT: B 373 MET cc_start: 0.5262 (mtm) cc_final: 0.4980 (mtm) REVERT: B 474 MET cc_start: 0.3395 (OUTLIER) cc_final: 0.2608 (mtp) REVERT: C 272 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.6162 (tp) REVERT: C 288 LYS cc_start: 0.2200 (mptt) cc_final: 0.1877 (mppt) REVERT: C 474 MET cc_start: 0.3130 (OUTLIER) cc_final: 0.2383 (mtp) REVERT: D 474 MET cc_start: 0.3275 (OUTLIER) cc_final: 0.3032 (mtt) REVERT: E 288 LYS cc_start: 0.2456 (mptt) cc_final: 0.2054 (ttmt) REVERT: E 483 ASP cc_start: 0.4984 (OUTLIER) cc_final: 0.4723 (m-30) REVERT: E 674 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6248 (mp) REVERT: F 288 LYS cc_start: 0.2317 (mptt) cc_final: 0.1812 (ttmt) REVERT: F 436 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6987 (mmm160) REVERT: F 674 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.6145 (mp) REVERT: H 55 GLU cc_start: 0.5639 (mt-10) cc_final: 0.5231 (mm-30) REVERT: H 179 MET cc_start: 0.2706 (mtp) cc_final: 0.1829 (tmm) REVERT: H 209 ILE cc_start: 0.3040 (mm) cc_final: 0.2755 (mm) REVERT: H 260 MET cc_start: 0.6699 (mmp) cc_final: 0.6403 (mmm) REVERT: H 407 MET cc_start: 0.4416 (tpt) cc_final: 0.3822 (tpt) REVERT: H 483 MET cc_start: 0.6547 (mpp) cc_final: 0.5927 (mtt) REVERT: H 642 GLN cc_start: 0.5132 (OUTLIER) cc_final: 0.4251 (tm-30) REVERT: H 685 GLU cc_start: 0.3939 (tp30) cc_final: 0.3080 (tm-30) REVERT: I 134 MET cc_start: 0.6141 (ptp) cc_final: 0.5804 (ptt) REVERT: I 407 MET cc_start: 0.4579 (tpt) cc_final: 0.3893 (tpt) REVERT: I 483 MET cc_start: 0.6653 (mpp) cc_final: 0.6131 (mtt) REVERT: I 515 ASP cc_start: 0.5085 (m-30) cc_final: 0.4677 (t0) REVERT: I 623 MET cc_start: 0.4392 (ptt) cc_final: 0.3881 (tpp) REVERT: I 642 GLN cc_start: 0.4901 (OUTLIER) cc_final: 0.4286 (tm-30) REVERT: J 179 MET cc_start: 0.3445 (mtp) cc_final: 0.1944 (tmm) REVERT: J 192 LEU cc_start: 0.5826 (pp) cc_final: 0.5588 (mt) REVERT: J 322 PRO cc_start: 0.5875 (Cg_exo) cc_final: 0.5497 (Cg_endo) REVERT: J 334 MET cc_start: 0.6515 (mmm) cc_final: 0.6103 (mmm) REVERT: J 407 MET cc_start: 0.4685 (tpt) cc_final: 0.4378 (tpt) REVERT: J 483 MET cc_start: 0.6693 (mpp) cc_final: 0.5885 (mtt) REVERT: J 623 MET cc_start: 0.4378 (ptm) cc_final: 0.3758 (tpp) REVERT: J 642 GLN cc_start: 0.4709 (OUTLIER) cc_final: 0.4133 (tm-30) REVERT: J 665 SER cc_start: 0.3177 (OUTLIER) cc_final: 0.2870 (t) REVERT: K 146 TYR cc_start: 0.5460 (t80) cc_final: 0.5054 (t80) REVERT: K 260 MET cc_start: 0.6647 (mmp) cc_final: 0.6267 (mmm) REVERT: K 296 PHE cc_start: 0.4708 (p90) cc_final: 0.4213 (p90) REVERT: K 299 MET cc_start: 0.6668 (ttp) cc_final: 0.6243 (ptm) REVERT: K 407 MET cc_start: 0.4129 (tpt) cc_final: 0.3697 (tpt) REVERT: K 483 MET cc_start: 0.6491 (mpp) cc_final: 0.5861 (mtt) REVERT: K 619 ILE cc_start: 0.4776 (OUTLIER) cc_final: 0.4425 (pt) REVERT: K 642 GLN cc_start: 0.5230 (OUTLIER) cc_final: 0.4358 (tm-30) REVERT: K 650 MET cc_start: 0.3816 (tpt) cc_final: 0.3348 (tpt) REVERT: K 652 MET cc_start: 0.5953 (tpp) cc_final: 0.5619 (tpp) REVERT: K 680 LEU cc_start: 0.3977 (mp) cc_final: 0.3459 (mt) REVERT: L 134 MET cc_start: 0.5431 (ptp) cc_final: 0.5229 (ptt) REVERT: L 165 PRO cc_start: 0.2076 (Cg_exo) cc_final: 0.1764 (Cg_endo) REVERT: L 179 MET cc_start: 0.2800 (mtm) cc_final: 0.2035 (tmm) REVERT: L 322 PRO cc_start: 0.6060 (Cg_exo) cc_final: 0.5800 (Cg_endo) REVERT: L 342 GLN cc_start: 0.6529 (tp40) cc_final: 0.6283 (tp-100) REVERT: L 407 MET cc_start: 0.4436 (tpt) cc_final: 0.3908 (tpt) REVERT: L 623 MET cc_start: 0.5259 (ptm) cc_final: 0.4599 (tpp) REVERT: L 685 GLU cc_start: 0.3541 (tp30) cc_final: 0.2491 (tm-30) REVERT: M 165 PRO cc_start: 0.2073 (Cg_exo) cc_final: 0.1758 (Cg_endo) REVERT: M 192 LEU cc_start: 0.5270 (pp) cc_final: 0.4966 (mt) REVERT: M 260 MET cc_start: 0.6647 (tpt) cc_final: 0.5969 (mmp) REVERT: M 407 MET cc_start: 0.4034 (tpt) cc_final: 0.3359 (tpt) REVERT: M 469 GLN cc_start: 0.5381 (tm-30) cc_final: 0.4982 (pt0) REVERT: M 685 GLU cc_start: 0.4252 (tp30) cc_final: 0.2914 (tm-30) outliers start: 215 outliers final: 184 residues processed: 726 average time/residue: 0.5189 time to fit residues: 648.5457 Evaluate side-chains 735 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 535 time to evaluate : 4.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 383 ASN Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 655 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 591 THR Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 655 ASP Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 314 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 436 ARG Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 655 ASP Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 219 HIS Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 353 GLU Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 578 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 642 GLN Chi-restraints excluded: chain H residue 650 MET Chi-restraints excluded: chain H residue 661 ASP Chi-restraints excluded: chain H residue 667 LEU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 398 ASP Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 578 LEU Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 596 GLN Chi-restraints excluded: chain I residue 642 GLN Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 301 MET Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 486 THR Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 519 VAL Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 578 LEU Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 589 ILE Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 642 GLN Chi-restraints excluded: chain J residue 661 ASP Chi-restraints excluded: chain J residue 665 SER Chi-restraints excluded: chain J residue 674 VAL Chi-restraints excluded: chain K residue 32 CYS Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 194 SER Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 486 THR Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 562 VAL Chi-restraints excluded: chain K residue 578 LEU Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain K residue 602 LEU Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 631 LEU Chi-restraints excluded: chain K residue 642 GLN Chi-restraints excluded: chain K residue 661 ASP Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain L residue 32 CYS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 271 LEU Chi-restraints excluded: chain L residue 301 MET Chi-restraints excluded: chain L residue 408 LEU Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain L residue 483 MET Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 562 VAL Chi-restraints excluded: chain L residue 564 ASP Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 631 LEU Chi-restraints excluded: chain L residue 674 VAL Chi-restraints excluded: chain M residue 32 CYS Chi-restraints excluded: chain M residue 52 HIS Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain M residue 301 MET Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 398 ASP Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 483 MET Chi-restraints excluded: chain M residue 486 THR Chi-restraints excluded: chain M residue 521 VAL Chi-restraints excluded: chain M residue 533 ILE Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 564 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 589 ILE Chi-restraints excluded: chain M residue 617 THR Chi-restraints excluded: chain M residue 631 LEU Chi-restraints excluded: chain M residue 674 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 465 optimal weight: 0.1980 chunk 623 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 539 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 586 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 602 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN A 311 HIS ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN B 413 HIS ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN ** C 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 HIS I 342 GLN ** I 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 HIS L 149 ASN ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.149454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.120872 restraints weight = 124249.033| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.38 r_work: 0.3537 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 59010 Z= 0.237 Angle : 0.651 10.734 79776 Z= 0.337 Chirality : 0.046 0.207 8826 Planarity : 0.005 0.058 10464 Dihedral : 5.164 29.662 8292 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 3.91 % Allowed : 20.20 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.10), residues: 7440 helix: 0.76 (0.11), residues: 2148 sheet: 0.74 (0.16), residues: 1062 loop : -2.02 (0.09), residues: 4230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 251 HIS 0.010 0.001 HIS M 52 PHE 0.025 0.002 PHE M 298 TYR 0.020 0.002 TYR A 504 ARG 0.007 0.001 ARG L 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13611.73 seconds wall clock time: 239 minutes 31.26 seconds (14371.26 seconds total)