Starting phenix.real_space_refine on Fri Dec 8 13:50:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/12_2023/8f3d_28846_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/12_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_28846/12_2023/8f3d_28846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/12_2023/8f3d_28846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/12_2023/8f3d_28846_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f3d_28846/12_2023/8f3d_28846_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 306 5.16 5 C 36504 2.51 5 N 10254 2.21 5 O 10782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 183": "NH1" <-> "NH2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "E ARG 183": "NH1" <-> "NH2" Residue "E GLU 259": "OE1" <-> "OE2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "F ARG 183": "NH1" <-> "NH2" Residue "F GLU 259": "OE1" <-> "OE2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H GLU 261": "OE1" <-> "OE2" Residue "H GLU 308": "OE1" <-> "OE2" Residue "H GLU 314": "OE1" <-> "OE2" Residue "H GLU 545": "OE1" <-> "OE2" Residue "H GLU 648": "OE1" <-> "OE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "I GLU 261": "OE1" <-> "OE2" Residue "I GLU 308": "OE1" <-> "OE2" Residue "I GLU 314": "OE1" <-> "OE2" Residue "I GLU 545": "OE1" <-> "OE2" Residue "I GLU 648": "OE1" <-> "OE2" Residue "J GLU 34": "OE1" <-> "OE2" Residue "J GLU 261": "OE1" <-> "OE2" Residue "J GLU 308": "OE1" <-> "OE2" Residue "J GLU 314": "OE1" <-> "OE2" Residue "J GLU 545": "OE1" <-> "OE2" Residue "J GLU 648": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 261": "OE1" <-> "OE2" Residue "K GLU 308": "OE1" <-> "OE2" Residue "K GLU 314": "OE1" <-> "OE2" Residue "K GLU 545": "OE1" <-> "OE2" Residue "K GLU 648": "OE1" <-> "OE2" Residue "L GLU 34": "OE1" <-> "OE2" Residue "L GLU 261": "OE1" <-> "OE2" Residue "L GLU 308": "OE1" <-> "OE2" Residue "L GLU 314": "OE1" <-> "OE2" Residue "L GLU 545": "OE1" <-> "OE2" Residue "L GLU 648": "OE1" <-> "OE2" Residue "M GLU 34": "OE1" <-> "OE2" Residue "M GLU 261": "OE1" <-> "OE2" Residue "M GLU 308": "OE1" <-> "OE2" Residue "M GLU 314": "OE1" <-> "OE2" Residue "M GLU 545": "OE1" <-> "OE2" Residue "M GLU 648": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 57846 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "B" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "C" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "D" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "E" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "F" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4350 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "H" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "I" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "J" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "K" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "L" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "M" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5276 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.50, per 1000 atoms: 0.37 Number of scatterers: 57846 At special positions: 0 Unit cell: (155.1, 166.1, 232.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 306 16.00 O 10782 8.00 N 10254 7.00 C 36504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.88 Conformation dependent library (CDL) restraints added in 7.6 seconds 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13596 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 228 helices and 60 sheets defined 28.7% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.11 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: 18.67 Time building geometry restraints manager: 18.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18910 1.34 - 1.46: 9055 1.46 - 1.58: 30559 1.58 - 1.70: 0 1.70 - 1.82: 486 Bond restraints: 59010 Sorted by residual: bond pdb=" CA LEU E 178 " pdb=" C LEU E 178 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.33e+01 bond pdb=" CA LEU A 178 " pdb=" C LEU A 178 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.33e+01 bond pdb=" CA LEU B 178 " pdb=" C LEU B 178 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.32e+01 bond pdb=" CA LEU D 178 " pdb=" C LEU D 178 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.31e+01 bond pdb=" CA GLU A 143 " pdb=" C GLU A 143 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.34e-02 5.57e+03 1.30e+01 ... (remaining 59005 not shown) Histogram of bond angle deviations from ideal: 94.77 - 102.62: 245 102.62 - 110.47: 15015 110.47 - 118.33: 30384 118.33 - 126.18: 33406 126.18 - 134.03: 726 Bond angle restraints: 79776 Sorted by residual: angle pdb=" N ARG D 144 " pdb=" CA ARG D 144 " pdb=" C ARG D 144 " ideal model delta sigma weight residual 111.71 97.86 13.85 1.15e+00 7.56e-01 1.45e+02 angle pdb=" N ARG C 144 " pdb=" CA ARG C 144 " pdb=" C ARG C 144 " ideal model delta sigma weight residual 111.71 97.91 13.80 1.15e+00 7.56e-01 1.44e+02 angle pdb=" N ARG F 144 " pdb=" CA ARG F 144 " pdb=" C ARG F 144 " ideal model delta sigma weight residual 111.71 97.92 13.79 1.15e+00 7.56e-01 1.44e+02 angle pdb=" N ARG B 144 " pdb=" CA ARG B 144 " pdb=" C ARG B 144 " ideal model delta sigma weight residual 111.71 97.92 13.79 1.15e+00 7.56e-01 1.44e+02 angle pdb=" N ARG E 144 " pdb=" CA ARG E 144 " pdb=" C ARG E 144 " ideal model delta sigma weight residual 111.71 97.92 13.79 1.15e+00 7.56e-01 1.44e+02 ... (remaining 79771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 31910 16.05 - 32.09: 2905 32.09 - 48.14: 603 48.14 - 64.19: 144 64.19 - 80.23: 24 Dihedral angle restraints: 35586 sinusoidal: 14322 harmonic: 21264 Sorted by residual: dihedral pdb=" CA GLU C 499 " pdb=" C GLU C 499 " pdb=" N PHE C 500 " pdb=" CA PHE C 500 " ideal model delta harmonic sigma weight residual 180.00 156.21 23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLU F 499 " pdb=" C GLU F 499 " pdb=" N PHE F 500 " pdb=" CA PHE F 500 " ideal model delta harmonic sigma weight residual 180.00 156.26 23.74 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLU D 499 " pdb=" C GLU D 499 " pdb=" N PHE D 500 " pdb=" CA PHE D 500 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 35583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 6485 0.048 - 0.096: 1710 0.096 - 0.145: 558 0.145 - 0.193: 54 0.193 - 0.241: 19 Chirality restraints: 8826 Sorted by residual: chirality pdb=" CA GLU M 362 " pdb=" N GLU M 362 " pdb=" C GLU M 362 " pdb=" CB GLU M 362 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA GLU I 362 " pdb=" N GLU I 362 " pdb=" C GLU I 362 " pdb=" CB GLU I 362 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA GLU H 362 " pdb=" N GLU H 362 " pdb=" C GLU H 362 " pdb=" CB GLU H 362 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 8823 not shown) Planarity restraints: 10464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTI D 801 " 0.015 2.00e-02 2.50e+03 3.64e-02 1.99e+01 pdb=" C4 BTI D 801 " -0.043 2.00e-02 2.50e+03 pdb=" C5 BTI D 801 " -0.011 2.00e-02 2.50e+03 pdb=" N2 BTI D 801 " 0.053 2.00e-02 2.50e+03 pdb=" N3 BTI D 801 " 0.031 2.00e-02 2.50e+03 pdb=" O3 BTI D 801 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI B 801 " -0.015 2.00e-02 2.50e+03 3.60e-02 1.95e+01 pdb=" C4 BTI B 801 " 0.042 2.00e-02 2.50e+03 pdb=" C5 BTI B 801 " 0.011 2.00e-02 2.50e+03 pdb=" N2 BTI B 801 " -0.052 2.00e-02 2.50e+03 pdb=" N3 BTI B 801 " -0.031 2.00e-02 2.50e+03 pdb=" O3 BTI B 801 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI F 801 " 0.014 2.00e-02 2.50e+03 3.59e-02 1.94e+01 pdb=" C4 BTI F 801 " -0.043 2.00e-02 2.50e+03 pdb=" C5 BTI F 801 " -0.011 2.00e-02 2.50e+03 pdb=" N2 BTI F 801 " 0.052 2.00e-02 2.50e+03 pdb=" N3 BTI F 801 " 0.031 2.00e-02 2.50e+03 pdb=" O3 BTI F 801 " -0.044 2.00e-02 2.50e+03 ... (remaining 10461 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 144 2.41 - 3.03: 37758 3.03 - 3.65: 86804 3.65 - 4.28: 128217 4.28 - 4.90: 205726 Nonbonded interactions: 458649 Sorted by model distance: nonbonded pdb=" CE MET M 650 " pdb=" CD LYS M 651 " model vdw 1.784 3.860 nonbonded pdb=" CE MET L 650 " pdb=" CD LYS L 651 " model vdw 1.784 3.860 nonbonded pdb=" CE MET H 650 " pdb=" CD LYS H 651 " model vdw 1.784 3.860 nonbonded pdb=" CE MET J 650 " pdb=" CD LYS J 651 " model vdw 1.785 3.860 nonbonded pdb=" CE MET K 650 " pdb=" CD LYS K 651 " model vdw 1.785 3.860 ... (remaining 458644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 13.380 Check model and map are aligned: 0.640 Set scattering table: 0.420 Process input model: 112.800 Find NCS groups from input model: 2.920 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 59010 Z= 0.349 Angle : 0.930 13.854 79776 Z= 0.586 Chirality : 0.049 0.241 8826 Planarity : 0.005 0.091 10464 Dihedral : 13.028 80.234 21990 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.39 % Allowed : 2.60 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.10), residues: 7440 helix: 0.03 (0.11), residues: 2256 sheet: 0.89 (0.17), residues: 1008 loop : -1.89 (0.09), residues: 4176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 488 HIS 0.012 0.002 HIS F 311 PHE 0.022 0.002 PHE C 500 TYR 0.037 0.002 TYR D 504 ARG 0.006 0.001 ARG F 608 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1544 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1520 time to evaluate : 4.875 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: 0.6291 time to fit residues: 1529.1107 Evaluate side-chains 693 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 691 time to evaluate : 4.822 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3872 time to fit residues: 8.0992 ------------------------------------------------------------------------------- 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 442 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN B 186 GLN B 300 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN C 186 GLN C 300 HIS D 186 GLN D 300 HIS D 442 ASN D 446 HIS D 525 ASN D 574 ASN E 186 GLN E 300 HIS ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 574 ASN F 186 GLN F 300 HIS F 383 ASN ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 574 ASN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS H 306 GLN H 466 HIS ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 HIS I 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 223 GLN J 306 GLN J 427 GLN J 466 HIS ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.3638 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= 0.336 Angle : 0.761 12.219 79776 Z= 0.396 Chirality : 0.050 0.293 8826 Planarity : 0.007 0.078 10464 Dihedral : 5.527 38.496 8292 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.32 % Allowed : 11.85 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.21 (0.09), residues: 7440 helix: 0.31 (0.11), residues: 2178 sheet: 0.63 (0.16), residues: 966 loop : -1.84 (0.09), residues: 4296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 496 HIS 0.014 0.002 HIS A 216 PHE 0.029 0.002 PHE B 500 TYR 0.036 0.003 TYR B 164 ARG 0.016 0.001 ARG E 465 *********************** 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 919 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 716 time to evaluate : 5.078 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 outliers start: 203 outliers final: 132 residues processed: 868 average time/residue: 0.5704 time to fit residues: 831.0754 Evaluate side-chains 664 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 532 time to evaluate : 4.856 Switching outliers to nearest non-outliers outliers start: 132 outliers final: 0 residues processed: 132 average time/residue: 0.4159 time to fit residues: 111.1668 ------------------------------------------------------------------------------- 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: 7.9990 chunk 207 optimal weight: 5.9990 chunk 557 optimal weight: 2.9990 chunk 456 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 671 optimal weight: 4.9990 chunk 725 optimal weight: 2.9990 chunk 597 optimal weight: 20.0000 chunk 665 optimal weight: 0.0020 chunk 228 optimal weight: 8.9990 chunk 538 optimal weight: 10.0000 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 469 GLN ** K 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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** M 642 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 59010 Z= 0.232 Angle : 0.643 10.261 79776 Z= 0.334 Chirality : 0.046 0.212 8826 Planarity : 0.005 0.062 10464 Dihedral : 5.155 32.954 8292 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.25 % Allowed : 15.57 % Favored : 82.17 % 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: -0.99 (0.10), residues: 7440 helix: 0.66 (0.11), residues: 2160 sheet: 0.70 (0.16), residues: 1008 loop : -1.80 (0.09), residues: 4272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 251 HIS 0.013 0.001 HIS M 52 PHE 0.021 0.002 PHE E 500 TYR 0.027 0.002 TYR D 504 ARG 0.006 0.001 ARG E 260 *********************** 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 772 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 634 time to evaluate : 4.925 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 outliers start: 138 outliers final: 73 residues processed: 748 average time/residue: 0.5823 time to fit residues: 739.6354 Evaluate side-chains 594 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 521 time to evaluate : 4.820 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.4296 time to fit residues: 67.1741 ------------------------------------------------------------------------------- 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: 8.9990 chunk 504 optimal weight: 0.0370 chunk 348 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 320 optimal weight: 1.9990 chunk 450 optimal weight: 10.0000 chunk 673 optimal weight: 8.9990 chunk 713 optimal weight: 10.0000 chunk 352 optimal weight: 5.9990 chunk 638 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 overall best weight: 3.2064 ------------------------------------------------------------------------------- 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 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 ASN ** 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 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 329 GLN ** L 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 642 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 59010 Z= 0.255 Angle : 0.656 9.876 79776 Z= 0.340 Chirality : 0.046 0.270 8826 Planarity : 0.005 0.075 10464 Dihedral : 5.251 36.409 8292 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.66 % Allowed : 17.70 % Favored : 79.64 % 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: -1.01 (0.10), residues: 7440 helix: 0.60 (0.11), residues: 2184 sheet: 0.91 (0.16), residues: 978 loop : -1.85 (0.09), residues: 4278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.010 0.001 HIS L 52 PHE 0.026 0.002 PHE C 500 TYR 0.029 0.002 TYR D 504 ARG 0.023 0.001 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 584 time to evaluate : 4.935 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 outliers start: 163 outliers final: 89 residues processed: 704 average time/residue: 0.5544 time to fit residues: 660.8506 Evaluate side-chains 590 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 501 time to evaluate : 4.820 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 0 residues processed: 89 average time/residue: 0.4031 time to fit residues: 75.2149 ------------------------------------------------------------------------------- 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: 5.9990 chunk 404 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 531 optimal weight: 0.1980 chunk 294 optimal weight: 1.9990 chunk 608 optimal weight: 0.0020 chunk 493 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 364 optimal weight: 20.0000 chunk 640 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 overall best weight: 3.2394 ------------------------------------------------------------------------------- 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** A 539 HIS B 283 ASN B 539 HIS ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN ** C 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 HIS D 283 ASN D 300 HIS ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 HIS E 442 ASN ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 HIS 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 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 219 HIS ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 59010 Z= 0.250 Angle : 0.650 10.501 79776 Z= 0.337 Chirality : 0.046 0.267 8826 Planarity : 0.005 0.067 10464 Dihedral : 5.234 33.030 8292 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.24 % Allowed : 18.68 % Favored : 79.08 % 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: -1.07 (0.09), residues: 7440 helix: 0.59 (0.11), residues: 2184 sheet: 0.99 (0.16), residues: 978 loop : -1.93 (0.09), residues: 4278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 251 HIS 0.008 0.001 HIS L 52 PHE 0.023 0.002 PHE E 500 TYR 0.021 0.002 TYR B 142 ARG 0.006 0.001 ARG M 21 *********************** 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 707 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 570 time to evaluate : 4.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 137 outliers final: 73 residues processed: 679 average time/residue: 0.5542 time to fit residues: 639.4888 Evaluate side-chains 587 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 514 time to evaluate : 4.877 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.4109 time to fit residues: 63.6740 ------------------------------------------------------------------------------- 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: 1.9990 chunk 642 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 418 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 chunk 714 optimal weight: 9.9990 chunk 592 optimal weight: 10.0000 chunk 330 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 374 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 630 GLN 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 137 HIS ** 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 257 HIS ** 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** K 219 HIS ** 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 495 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 59010 Z= 0.179 Angle : 0.591 8.816 79776 Z= 0.306 Chirality : 0.044 0.189 8826 Planarity : 0.005 0.068 10464 Dihedral : 4.837 30.965 8292 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.84 % Favored : 92.15 % Rotamer: Outliers : 1.41 % Allowed : 19.74 % Favored : 78.86 % 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: -0.84 (0.10), residues: 7440 helix: 0.86 (0.11), residues: 2190 sheet: 1.01 (0.16), residues: 1038 loop : -1.86 (0.09), residues: 4212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 251 HIS 0.015 0.001 HIS E 137 PHE 0.024 0.001 PHE M 298 TYR 0.017 0.001 TYR M 146 ARG 0.005 0.000 ARG L 21 *********************** 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 677 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 591 time to evaluate : 4.946 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: 86 outliers final: 45 residues processed: 656 average time/residue: 0.5752 time to fit residues: 635.9444 Evaluate side-chains 562 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 517 time to evaluate : 4.897 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.4036 time to fit residues: 41.5905 ------------------------------------------------------------------------------- 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: 8.9990 chunk 80 optimal weight: 6.9990 chunk 406 optimal weight: 9.9990 chunk 521 optimal weight: 5.9990 chunk 404 optimal weight: 7.9990 chunk 601 optimal weight: 0.7980 chunk 398 optimal weight: 10.0000 chunk 711 optimal weight: 9.9990 chunk 445 optimal weight: 10.0000 chunk 433 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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** B 138 HIS B 283 ASN B 310 ASN ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS C 283 ASN C 310 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** E 137 HIS ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 HIS ** 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** ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** 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 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 469 GLN ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 660 GLN ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 59010 Z= 0.348 Angle : 0.742 11.443 79776 Z= 0.387 Chirality : 0.049 0.244 8826 Planarity : 0.006 0.078 10464 Dihedral : 5.716 41.710 8292 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 1.90 % Allowed : 20.02 % Favored : 78.09 % 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: -1.37 (0.09), residues: 7440 helix: 0.36 (0.11), residues: 2166 sheet: 0.76 (0.16), residues: 1056 loop : -2.17 (0.09), residues: 4218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 251 HIS 0.014 0.002 HIS E 137 PHE 0.025 0.002 PHE M 298 TYR 0.023 0.002 TYR A 669 ARG 0.010 0.001 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 558 time to evaluate : 5.358 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: 116 outliers final: 66 residues processed: 645 average time/residue: 0.5663 time to fit residues: 620.3934 Evaluate side-chains 579 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 513 time to evaluate : 4.906 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.4202 time to fit residues: 59.4224 ------------------------------------------------------------------------------- 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: 4.9990 chunk 284 optimal weight: 0.9990 chunk 424 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 452 optimal weight: 4.9990 chunk 484 optimal weight: 0.4980 chunk 351 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 559 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 324 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN B 283 ASN C 283 ASN ** C 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN ** D 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS F 324 ASN ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN ** 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** K 257 HIS ** 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 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.6011 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= 0.178 Angle : 0.603 9.197 79776 Z= 0.312 Chirality : 0.044 0.202 8826 Planarity : 0.004 0.071 10464 Dihedral : 4.975 31.812 8292 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.59 % Allowed : 21.03 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.10), residues: 7440 helix: 0.85 (0.11), residues: 2154 sheet: 0.81 (0.16), residues: 1068 loop : -1.94 (0.09), residues: 4218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 251 HIS 0.013 0.001 HIS F 137 PHE 0.026 0.001 PHE M 298 TYR 0.015 0.001 TYR A 504 ARG 0.008 0.000 ARG F 183 *********************** 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 608 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 572 time to evaluate : 5.967 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: 36 outliers final: 23 residues processed: 601 average time/residue: 0.5714 time to fit residues: 584.4894 Evaluate side-chains 535 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 512 time to evaluate : 4.912 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4534 time to fit residues: 26.0730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.5373 > 50: distance: 9 - 13: 34.322 distance: 13 - 14: 11.929 distance: 14 - 15: 35.679 distance: 14 - 17: 52.923 distance: 15 - 16: 41.467 distance: 15 - 21: 21.180 distance: 17 - 18: 25.025 distance: 17 - 19: 41.505 distance: 18 - 20: 52.685 distance: 21 - 22: 25.683 distance: 22 - 23: 51.613 distance: 22 - 25: 42.121 distance: 23 - 24: 47.666 distance: 23 - 28: 42.861 distance: 25 - 26: 68.551 distance: 25 - 27: 56.879 distance: 28 - 29: 33.373 distance: 29 - 30: 42.718 distance: 29 - 32: 58.885 distance: 30 - 31: 51.536 distance: 30 - 34: 34.994 distance: 32 - 33: 3.163 distance: 34 - 35: 17.651 distance: 34 - 40: 32.293 distance: 35 - 36: 43.882 distance: 35 - 38: 29.313 distance: 36 - 37: 31.601 distance: 36 - 41: 42.936 distance: 38 - 39: 22.370 distance: 39 - 40: 48.900 distance: 41 - 42: 35.960 distance: 42 - 43: 55.308 distance: 42 - 45: 25.305 distance: 43 - 44: 35.328 distance: 43 - 49: 58.197 distance: 45 - 46: 27.967 distance: 46 - 47: 31.798 distance: 47 - 48: 16.412 distance: 49 - 50: 33.306 distance: 49 - 55: 52.398 distance: 50 - 51: 48.341 distance: 50 - 53: 32.724 distance: 51 - 52: 55.707 distance: 51 - 56: 47.240 distance: 53 - 54: 56.615 distance: 54 - 55: 59.084 distance: 56 - 57: 50.970 distance: 57 - 58: 39.135 distance: 58 - 59: 50.790 distance: 58 - 60: 38.873 distance: 60 - 61: 22.453 distance: 61 - 62: 36.112 distance: 61 - 64: 15.037 distance: 62 - 63: 38.697 distance: 62 - 69: 43.177 distance: 64 - 65: 31.472 distance: 65 - 66: 11.655 distance: 66 - 67: 28.302 distance: 67 - 68: 35.384 distance: 69 - 70: 27.874 distance: 70 - 71: 42.312 distance: 70 - 73: 18.520 distance: 71 - 72: 47.290 distance: 71 - 76: 31.436 distance: 73 - 74: 25.638 distance: 73 - 75: 38.419 distance: 76 - 77: 14.651 distance: 77 - 78: 17.696 distance: 77 - 80: 17.480 distance: 78 - 79: 26.357 distance: 78 - 82: 21.694 distance: 80 - 81: 4.159