Starting phenix.real_space_refine (version: dev) on Wed Feb 22 21:08:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/02_2023/8f3d_28846_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/02_2023/8f3d_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_2023/8f3d_28846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/02_2023/8f3d_28846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/02_2023/8f3d_28846_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/02_2023/8f3d_28846_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 23.13, per 1000 atoms: 0.40 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: 19.83 Conformation dependent library (CDL) restraints added in 6.4 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: 5.30 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: 17.45 Time building geometry restraints manager: 21.44 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: 31852 16.05 - 32.09: 2873 32.09 - 48.14: 603 48.14 - 64.19: 144 64.19 - 80.23: 24 Dihedral angle restraints: 35496 sinusoidal: 14232 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 35493 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 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. 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: 2.340 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: 0.040 Extract box with map and model: 14.870 Check model and map are aligned: 0.630 Process input model: 109.950 Find NCS groups from input model: 3.070 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Set scattering table: 0.390 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 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 : 13.027 80.234 21900 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 % 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 *********************** 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 : 4.932 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 outliers start: 24 outliers final: 2 residues processed: 1532 average time/residue: 0.6434 time to fit residues: 1566.0790 Evaluate side-chains 693 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 691 time to evaluate : 5.418 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3991 time to fit residues: 8.5581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 310 optimal weight: 0.9990 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: 8.9990 chunk 670 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 300 HIS ** 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 306 GLN I 466 HIS ** I 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 HIS ** J 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 306 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 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 306 GLN ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 642 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.102 59010 Z= 0.331 Angle : 0.764 12.318 79776 Z= 0.398 Chirality : 0.050 0.278 8826 Planarity : 0.007 0.078 10464 Dihedral : 5.530 44.792 8202 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer Outliers : 3.33 % 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: -1.22 (0.09), residues: 7440 helix: 0.30 (0.11), residues: 2178 sheet: 0.62 (0.16), residues: 966 loop : -1.84 (0.09), residues: 4296 *********************** 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 927 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 723 time to evaluate : 5.109 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 outliers start: 204 outliers final: 131 residues processed: 876 average time/residue: 0.5949 time to fit residues: 878.8817 Evaluate side-chains 662 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 531 time to evaluate : 5.010 Switching outliers to nearest non-outliers outliers start: 131 outliers final: 0 residues processed: 131 average time/residue: 0.4230 time to fit residues: 112.8745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 372 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 557 optimal weight: 5.9990 chunk 456 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 671 optimal weight: 5.9990 chunk 725 optimal weight: 8.9990 chunk 597 optimal weight: 0.0970 chunk 665 optimal weight: 0.7980 chunk 228 optimal weight: 0.3980 chunk 538 optimal weight: 9.9990 overall best weight: 2.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** 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 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 69 ASN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 HIS ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 469 GLN ** K 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 596 GLN ** 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 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 59010 Z= 0.219 Angle : 0.632 12.051 79776 Z= 0.327 Chirality : 0.045 0.206 8826 Planarity : 0.005 0.063 10464 Dihedral : 5.036 50.585 8202 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer Outliers : 1.98 % 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: -0.91 (0.10), residues: 7440 helix: 0.77 (0.11), residues: 2136 sheet: 0.70 (0.16), residues: 1008 loop : -1.74 (0.09), residues: 4296 *********************** 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 740 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 619 time to evaluate : 4.999 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 outliers start: 121 outliers final: 66 residues processed: 719 average time/residue: 0.5472 time to fit residues: 665.4634 Evaluate side-chains 575 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 509 time to evaluate : 4.973 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.3977 time to fit residues: 57.4022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0970 chunk 348 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 320 optimal weight: 1.9990 chunk 450 optimal weight: 9.9990 chunk 673 optimal weight: 8.9990 chunk 713 optimal weight: 9.9990 chunk 352 optimal weight: 8.9990 chunk 638 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 HIS B 283 ASN B 539 HIS C 283 ASN C 526 GLN C 539 HIS D 283 ASN ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 HIS E 165 GLN F 165 GLN ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 223 GLN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 219 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 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 329 GLN ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 59010 Z= 0.308 Angle : 0.721 12.894 79776 Z= 0.374 Chirality : 0.049 0.283 8826 Planarity : 0.006 0.072 10464 Dihedral : 5.604 59.985 8202 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer Outliers : 3.43 % 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: -1.28 (0.09), residues: 7440 helix: 0.36 (0.11), residues: 2196 sheet: 0.79 (0.16), residues: 966 loop : -2.01 (0.09), residues: 4278 *********************** 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 798 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 588 time to evaluate : 5.140 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 outliers start: 210 outliers final: 114 residues processed: 749 average time/residue: 0.5609 time to fit residues: 710.4245 Evaluate side-chains 618 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 504 time to evaluate : 4.978 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 0 residues processed: 114 average time/residue: 0.4065 time to fit residues: 95.7574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 594 optimal weight: 0.8980 chunk 404 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 531 optimal weight: 8.9990 chunk 294 optimal weight: 5.9990 chunk 608 optimal weight: 20.0000 chunk 493 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 364 optimal weight: 20.0000 chunk 640 optimal weight: 0.0030 chunk 180 optimal weight: 10.0000 overall best weight: 2.7796 ------------------------------------------------------------------------------- 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 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN B 310 ASN C 283 ASN 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** F 539 HIS ** F 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 272 GLN H 495 ASN ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 469 GLN ** 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 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 469 GLN K 495 ASN ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 HIS ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 59010 Z= 0.226 Angle : 0.632 9.581 79776 Z= 0.328 Chirality : 0.046 0.266 8826 Planarity : 0.005 0.065 10464 Dihedral : 5.222 63.087 8202 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer Outliers : 2.01 % 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: -1.10 (0.10), residues: 7440 helix: 0.57 (0.11), residues: 2190 sheet: 0.86 (0.16), residues: 1008 loop : -1.95 (0.09), residues: 4242 *********************** 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 694 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 571 time to evaluate : 5.138 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 outliers start: 123 outliers final: 63 residues processed: 672 average time/residue: 0.5707 time to fit residues: 647.3138 Evaluate side-chains 558 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 495 time to evaluate : 5.009 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.4184 time to fit residues: 56.9786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 240 optimal weight: 0.9990 chunk 642 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 418 optimal weight: 0.1980 chunk 176 optimal weight: 10.0000 chunk 714 optimal weight: 7.9990 chunk 592 optimal weight: 9.9990 chunk 330 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 374 optimal weight: 9.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** 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** C 574 ASN D 283 ASN ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 HIS ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 272 GLN H 329 GLN ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 660 GLN ** 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 495 ASN ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 HIS M 495 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 59010 Z= 0.260 Angle : 0.668 10.141 79776 Z= 0.346 Chirality : 0.047 0.217 8826 Planarity : 0.005 0.070 10464 Dihedral : 5.378 61.985 8202 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer Outliers : 2.19 % 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: -1.26 (0.09), residues: 7440 helix: 0.41 (0.11), residues: 2226 sheet: 0.84 (0.16), residues: 996 loop : -2.07 (0.09), residues: 4218 *********************** 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 688 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 554 time to evaluate : 6.275 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 outliers start: 134 outliers final: 85 residues processed: 649 average time/residue: 0.5661 time to fit residues: 631.2930 Evaluate side-chains 587 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 502 time to evaluate : 4.984 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 0 residues processed: 85 average time/residue: 0.4282 time to fit residues: 76.9972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 688 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 406 optimal weight: 8.9990 chunk 521 optimal weight: 9.9990 chunk 404 optimal weight: 0.0870 chunk 601 optimal weight: 9.9990 chunk 398 optimal weight: 0.8980 chunk 711 optimal weight: 9.9990 chunk 445 optimal weight: 9.9990 chunk 433 optimal weight: 0.9980 chunk 328 optimal weight: 1.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- 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 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 165 GLN C 283 ASN ** C 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN D 324 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** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 630 GLN ** 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 469 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 660 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 59010 Z= 0.181 Angle : 0.598 8.467 79776 Z= 0.310 Chirality : 0.044 0.201 8826 Planarity : 0.004 0.061 10464 Dihedral : 4.974 65.758 8202 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.93 (0.10), residues: 7440 helix: 0.95 (0.12), residues: 2124 sheet: 0.82 (0.16), residues: 1068 loop : -1.95 (0.09), residues: 4248 *********************** 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 619 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 565 time to evaluate : 5.013 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 outliers start: 54 outliers final: 25 residues processed: 608 average time/residue: 0.5523 time to fit residues: 570.6683 Evaluate side-chains 534 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 509 time to evaluate : 4.944 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.4192 time to fit residues: 26.6415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 440 optimal weight: 20.0000 chunk 284 optimal weight: 0.9990 chunk 424 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 chunk 139 optimal weight: 0.0870 chunk 137 optimal weight: 7.9990 chunk 452 optimal weight: 10.0000 chunk 484 optimal weight: 8.9990 chunk 351 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 559 optimal weight: 4.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 283 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN 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 310 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** F 137 HIS F 324 ASN ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 630 GLN ** 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 469 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 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 59010 Z= 0.237 Angle : 0.643 8.537 79776 Z= 0.334 Chirality : 0.046 0.191 8826 Planarity : 0.005 0.081 10464 Dihedral : 5.157 62.428 8202 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer Outliers : 1.42 % 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: -1.08 (0.10), residues: 7440 helix: 0.77 (0.11), residues: 2154 sheet: 0.74 (0.16), residues: 1062 loop : -2.03 (0.09), residues: 4224 *********************** 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 633 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 546 time to evaluate : 5.456 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 outliers start: 87 outliers final: 45 residues processed: 605 average time/residue: 0.5880 time to fit residues: 604.6818 Evaluate side-chains 556 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 511 time to evaluate : 5.109 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.4148 time to fit residues: 43.2070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 647 optimal weight: 3.9990 chunk 681 optimal weight: 3.9990 chunk 621 optimal weight: 7.9990 chunk 662 optimal weight: 10.0000 chunk 398 optimal weight: 20.0000 chunk 288 optimal weight: 8.9990 chunk 520 optimal weight: 10.0000 chunk 203 optimal weight: 8.9990 chunk 598 optimal weight: 20.0000 chunk 626 optimal weight: 20.0000 chunk 660 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** B 138 HIS B 283 ASN B 413 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** E 310 ASN ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 ASN ** F 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 257 HIS H 272 GLN ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 342 GLN ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 GLN ** I 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 257 HIS ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 342 GLN ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 59010 Z= 0.406 Angle : 0.822 13.687 79776 Z= 0.429 Chirality : 0.052 0.314 8826 Planarity : 0.007 0.090 10464 Dihedral : 6.217 63.318 8202 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.99 % Favored : 88.99 % Rotamer Outliers : 1.06 % 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: -1.89 (0.09), residues: 7440 helix: -0.11 (0.11), residues: 2178 sheet: 0.37 (0.16), residues: 1080 loop : -2.46 (0.09), residues: 4182 *********************** 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 626 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 561 time to evaluate : 5.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 40 residues processed: 600 average time/residue: 0.5731 time to fit residues: 583.4121 Evaluate side-chains 540 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 500 time to evaluate : 5.495 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.4182 time to fit residues: 39.4475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 435 optimal weight: 0.8980 chunk 700 optimal weight: 3.9990 chunk 427 optimal weight: 0.0570 chunk 332 optimal weight: 1.9990 chunk 487 optimal weight: 7.9990 chunk 735 optimal weight: 9.9990 chunk 676 optimal weight: 0.4980 chunk 585 optimal weight: 10.0000 chunk 60 optimal weight: 0.0770 chunk 452 optimal weight: 0.9990 chunk 358 optimal weight: 9.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN B 283 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN C 413 HIS D 186 GLN D 283 ASN ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN E 383 ASN ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 ASN ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 272 GLN ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 ASN I 219 HIS ** I 469 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** ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 257 HIS ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 HIS ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 HIS M 69 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 59010 Z= 0.171 Angle : 0.621 14.087 79776 Z= 0.322 Chirality : 0.044 0.242 8826 Planarity : 0.005 0.071 10464 Dihedral : 5.106 71.211 8202 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.10), residues: 7440 helix: 0.76 (0.11), residues: 2118 sheet: 0.72 (0.16), residues: 1068 loop : -2.01 (0.09), residues: 4254 ********************** 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 612 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 597 time to evaluate : 5.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 608 average time/residue: 0.5730 time to fit residues: 587.9415 Evaluate side-chains 535 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 531 time to evaluate : 4.977 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4607 time to fit residues: 10.2310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 465 optimal weight: 0.3980 chunk 623 optimal weight: 8.9990 chunk 179 optimal weight: 7.9990 chunk 539 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 586 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 chunk 602 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN C 283 ASN 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 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 427 GLN ** I 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 257 HIS ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 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 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.148214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.120302 restraints weight = 123967.335| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.45 r_work: 0.3516 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 59010 Z= 0.311 Angle : 0.722 12.308 79776 Z= 0.376 Chirality : 0.048 0.242 8826 Planarity : 0.006 0.080 10464 Dihedral : 5.556 61.835 8202 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer Outliers : 0.47 % 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: -1.38 (0.09), residues: 7440 helix: 0.48 (0.11), residues: 2130 sheet: 0.64 (0.16), residues: 1062 loop : -2.19 (0.09), residues: 4248 =============================================================================== Job complete usr+sys time: 12618.17 seconds wall clock time: 222 minutes 48.69 seconds (13368.69 seconds total)