Starting phenix.real_space_refine (version: dev) on Wed Feb 22 21:22:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f41_28849/02_2023/8f41_28849_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f41_28849/02_2023/8f41_28849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f41_28849/02_2023/8f41_28849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f41_28849/02_2023/8f41_28849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f41_28849/02_2023/8f41_28849_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f41_28849/02_2023/8f41_28849_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "B ARG 183": "NH1" <-> "NH2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "F ARG 183": "NH1" <-> "NH2" Residue "F GLU 259": "OE1" <-> "OE2" Residue "F GLU 335": "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 "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 "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" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "E ARG 183": "NH1" <-> "NH2" Residue "E GLU 259": "OE1" <-> "OE2" Residue "E 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 "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 "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" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 57846 Number of models: 1 Model: "" Number of chains: 18 Chain: "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: "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: "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: "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: "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: "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: 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: "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: "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: "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: "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: "B" 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: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} 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: "C" 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} Time building chain proxies: 23.43, per 1000 atoms: 0.41 Number of scatterers: 57846 At special positions: 0 Unit cell: (160.6, 160.6, 243.1, 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: 18.72 Conformation dependent library (CDL) restraints added in 6.8 seconds 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13596 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 228 helices and 60 sheets defined 28.7% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.48 Creating SS restraints... 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: 4.090A pdb=" N SER B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.585A 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: 3.582A 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 '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: 4.334A 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 '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: 3.618A 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: 3.584A 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: 3.956A 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 '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: 3.579A pdb=" N ARG I 33 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 3.840A 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: 4.462A 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: 3.613A pdb=" N LEU I 489 " --> pdb=" O ALA I 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: 3.581A 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: 4.462A 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: 3.715A 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 'M' and resid 23 through 34 removed outlier: 3.630A 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: 4.461A 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: 4.086A pdb=" N HIS M 466 " --> pdb=" O PHE M 462 " (cutoff:3.500A) removed outlier: 3.713A 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: 3.613A pdb=" N LEU M 489 " --> pdb=" O ALA M 485 " (cutoff:3.500A) 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: 4.333A 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: 3.958A 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 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: 3.930A 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: 3.585A 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: 4.192A 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 '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: 3.618A 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: 3.587A 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: 3.957A 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: 3.994A 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 696 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: 3.586A pdb=" N CYS H 32 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 3.582A 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 '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: 4.086A 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 '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: 4.460A 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: 3.714A 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 sheet with id= A, 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: 5.982A 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: 7.905A 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: 6.371A 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: 6.336A pdb=" N ILE B 378 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N HIS B 422 " --> pdb=" O ILE B 379 " (cutoff:3.500A) Processing sheet with id= B, 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: 6.478A pdb=" N LEU B 552 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 8.136A 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: 8.528A pdb=" N LEU B 593 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE B 616 " --> pdb=" O LEU B 593 " (cutoff:3.500A) Processing sheet with id= C, 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: 7.512A 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: 7.903A 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: 7.700A 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= D, 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: 7.795A pdb=" N ILE D 523 " --> pdb=" O PRO D 550 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU D 552 " --> pdb=" O ILE D 523 " (cutoff:3.500A) removed outlier: 8.136A 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: 6.591A 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= E, first strand: chain 'F' and resid 266 through 273 removed outlier: 7.756A 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: 6.563A pdb=" N VAL F 358 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU F 376 " --> pdb=" O ALA F 357 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL F 359 " --> pdb=" O GLU F 376 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE F 378 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N HIS F 422 " --> pdb=" O ILE F 379 " (cutoff:3.500A) Processing sheet with id= F, 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: 6.477A 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= G, 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= G Processing sheet with id= H, first strand: chain 'I' and resid 41 through 43 Processing sheet with id= I, 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= J, 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: 3.622A pdb=" N VAL I 249 " --> pdb=" O VAL I 242 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL I 242 " --> pdb=" O VAL I 249 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'I' and resid 507 through 514 Processing sheet with id= L, first strand: chain 'I' and resid 532 through 537 removed outlier: 4.244A 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= M, first strand: chain 'I' and resid 585 through 590 Processing sheet with id= N, first strand: chain 'I' and resid 664 through 666 Processing sheet with id= O, 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= O Processing sheet with id= P, first strand: chain 'K' and resid 41 through 43 Processing sheet with id= Q, 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: 5.244A pdb=" N PHE K 298 " --> pdb=" O ILE K 288 " (cutoff:3.500A) Processing sheet with id= R, 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: 6.629A 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= S, first strand: chain 'K' and resid 507 through 514 Processing sheet with id= T, 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: 3.631A pdb=" N ASN K 563 " --> pdb=" O ALA K 579 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 585 through 590 Processing sheet with id= V, first strand: chain 'K' and resid 664 through 666 Processing sheet with id= W, 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= W Processing sheet with id= X, first strand: chain 'M' and resid 41 through 43 Processing sheet with id= Y, first strand: chain 'M' and resid 218 through 226 removed outlier: 3.534A 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: 5.697A 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= Z, 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: 3.624A pdb=" N VAL M 249 " --> pdb=" O VAL M 242 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL M 242 " --> pdb=" O VAL M 249 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 507 through 514 Processing sheet with id= AB, 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= AC, first strand: chain 'M' and resid 585 through 590 Processing sheet with id= AD, first strand: chain 'M' and resid 664 through 666 Processing sheet with id= AE, 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: 5.983A pdb=" N ILE A 315 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 7.513A 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: 7.905A 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: 6.368A 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: 6.339A 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= AF, 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: 8.138A pdb=" N ASN A 525 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 7.700A 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: 7.711A pdb=" N PHE A 616 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 266 through 273 removed outlier: 7.757A 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= AH, first strand: chain 'C' and resid 508 through 514 removed outlier: 3.537A pdb=" N GLY C 511 " --> pdb=" O ILE C 522 " (cutoff:3.500A) removed outlier: 7.797A 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: 6.589A 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: 7.711A pdb=" N PHE C 616 " --> pdb=" O LEU C 593 " (cutoff:3.500A) Processing sheet with id= AI, 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: 5.985A 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: 6.370A pdb=" N GLU E 376 " --> pdb=" O ALA E 357 " (cutoff:3.500A) removed outlier: 7.700A 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= AJ, first strand: chain 'E' and resid 508 through 514 removed outlier: 3.535A pdb=" N GLY E 511 " --> pdb=" O ILE E 522 " (cutoff:3.500A) removed outlier: 7.796A 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: 8.528A 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= AK, first strand: chain 'H' and resid 16 through 18 removed outlier: 6.630A pdb=" N ALA H 88 " --> pdb=" O LEU H 17 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'H' and resid 41 through 43 Processing sheet with id= AM, 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: 3.527A 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= AN, 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: 6.629A 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: 8.111A pdb=" N VAL H 242 " --> pdb=" O VAL H 249 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'H' and resid 507 through 514 Processing sheet with id= AP, 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: 3.630A pdb=" N ASN H 563 " --> pdb=" O ALA H 579 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 585 through 590 Processing sheet with id= AR, first strand: chain 'H' and resid 664 through 666 Processing sheet with id= AS, 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= AS Processing sheet with id= AT, first strand: chain 'J' and resid 41 through 43 Processing sheet with id= AU, 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: 5.242A pdb=" N PHE J 298 " --> pdb=" O ILE J 288 " (cutoff:3.500A) Processing sheet with id= AV, 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= AW, first strand: chain 'J' and resid 507 through 514 Processing sheet with id= AX, first strand: chain 'J' and resid 532 through 537 removed outlier: 4.244A pdb=" N ILE J 561 " --> pdb=" O ALA J 581 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN J 563 " --> pdb=" O ALA J 579 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'J' and resid 585 through 590 Processing sheet with id= AZ, first strand: chain 'J' and resid 664 through 666 Processing sheet with id= BA, 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= BA Processing sheet with id= BB, first strand: chain 'L' and resid 41 through 43 Processing sheet with id= BC, 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: 3.525A pdb=" N GLU L 300 " --> pdb=" O GLU L 286 " (cutoff:3.500A) removed outlier: 5.695A 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= BD, 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= BE, first strand: chain 'L' and resid 507 through 514 Processing sheet with id= BF, 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= BG, first strand: chain 'L' and resid 585 through 590 Processing sheet with id= BH, first strand: chain 'L' and resid 664 through 666 1641 hydrogen bonds defined for protein. 4527 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.62 Time building geometry restraints manager: 20.45 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: 18882 1.34 - 1.46: 9112 1.46 - 1.58: 30530 1.58 - 1.70: 0 1.70 - 1.82: 486 Bond restraints: 59010 Sorted by residual: bond pdb=" CA LEU F 178 " pdb=" C LEU F 178 " ideal model delta sigma weight residual 1.524 1.479 0.046 1.24e-02 6.50e+03 1.36e+01 bond pdb=" CA LEU B 178 " pdb=" C LEU B 178 " ideal model delta sigma weight residual 1.524 1.479 0.046 1.24e-02 6.50e+03 1.35e+01 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 1.34e+01 bond pdb=" CA GLU A 143 " pdb=" C GLU A 143 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.34e-02 5.57e+03 1.32e+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 1.30e+01 ... (remaining 59005 not shown) Histogram of bond angle deviations from ideal: 94.75 - 102.62: 244 102.62 - 110.48: 15110 110.48 - 118.34: 30351 118.34 - 126.20: 33345 126.20 - 134.07: 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 97.88 13.83 1.15e+00 7.56e-01 1.45e+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 97.93 13.78 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 97.94 13.77 1.15e+00 7.56e-01 1.43e+02 angle pdb=" N ARG A 144 " pdb=" CA ARG A 144 " pdb=" C ARG A 144 " ideal model delta sigma weight residual 111.71 97.95 13.76 1.15e+00 7.56e-01 1.43e+02 ... (remaining 79771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 31861 16.06 - 32.11: 2864 32.11 - 48.17: 604 48.17 - 64.23: 143 64.23 - 80.28: 24 Dihedral angle restraints: 35496 sinusoidal: 14232 harmonic: 21264 Sorted by residual: dihedral pdb=" CA GLU C 499 " pdb=" C GLU C 499 " pdb=" N PHE C 500 " pdb=" CA PHE C 500 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 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 180.00 156.27 23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA GLU D 499 " pdb=" C GLU D 499 " pdb=" N PHE D 500 " pdb=" CA PHE D 500 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 35493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 6484 0.048 - 0.096: 1708 0.096 - 0.145: 555 0.145 - 0.193: 60 0.193 - 0.241: 19 Chirality restraints: 8826 Sorted by residual: 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 1.45e+00 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 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 1.43e+00 ... (remaining 8823 not shown) Planarity restraints: 10464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTI D 801 " -0.014 2.00e-02 2.50e+03 3.66e-02 2.01e+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 F 801 " 0.014 2.00e-02 2.50e+03 3.61e-02 1.95e+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 " 0.053 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 delta sigma weight rms_deltas residual plane pdb=" C3 BTI B 801 " 0.015 2.00e-02 2.50e+03 3.58e-02 1.92e+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 ... (remaining 10461 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 39 2.13 - 2.82: 18431 2.82 - 3.51: 82601 3.51 - 4.21: 131160 4.21 - 4.90: 223290 Nonbonded interactions: 455521 Sorted by model distance: nonbonded pdb=" ND1 HIS M 257 " pdb=" OE1 GLU L 261 " model vdw 1.432 2.520 nonbonded pdb=" OE1 GLU I 261 " pdb=" ND1 HIS H 257 " model vdw 1.446 2.520 nonbonded pdb=" OE1 GLU K 261 " pdb=" ND1 HIS J 257 " model vdw 1.618 2.520 nonbonded pdb=" ND1 HIS I 257 " pdb=" OE1 GLU H 261 " model vdw 1.664 2.520 nonbonded pdb=" ND1 HIS K 257 " pdb=" OE1 GLU J 261 " model vdw 1.682 2.520 ... (remaining 455516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 306 5.16 5 C 36504 2.51 5 N 10254 2.21 5 O 10782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.030 Check model and map are aligned: 0.630 Process input model: 109.950 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Set scattering table: 0.390 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5523 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= 0.351 Angle : 0.930 13.850 79776 Z= 0.587 Chirality : 0.049 0.241 8826 Planarity : 0.005 0.091 10464 Dihedral : 13.027 80.285 21900 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.10), residues: 7440 helix: 0.03 (0.11), residues: 2256 sheet: 0.89 (0.17), residues: 1008 loop : -1.89 (0.09), residues: 4176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1798 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1774 time to evaluate : 5.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 1787 average time/residue: 0.6448 time to fit residues: 1825.2651 Evaluate side-chains 716 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 715 time to evaluate : 5.109 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4506 time to fit residues: 7.8719 ------------------------------------------------------------------------------- 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: 9.9990 chunk 559 optimal weight: 5.9990 chunk 310 optimal weight: 0.0050 chunk 191 optimal weight: 9.9990 chunk 377 optimal weight: 2.9990 chunk 298 optimal weight: 0.0870 chunk 578 optimal weight: 0.7980 chunk 223 optimal weight: 7.9990 chunk 351 optimal weight: 6.9990 chunk 430 optimal weight: 6.9990 chunk 670 optimal weight: 20.0000 overall best weight: 1.9776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 HIS B 186 GLN B 216 HIS B 446 HIS B 526 GLN ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 HIS D 151 ASN D 186 GLN D 447 ASN F 186 GLN ** F 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 HIS I 219 HIS I 306 GLN ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 540 HIS K 36 HIS ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 495 ASN K 540 HIS M 36 HIS ** M 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 403 HIS ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 540 HIS A 138 HIS A 151 ASN A 186 GLN A 300 HIS A 526 GLN C 138 HIS C 186 GLN E 138 HIS E 186 GLN E 447 ASN H 36 HIS H 219 HIS H 466 HIS ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 540 HIS J 36 HIS ** J 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 329 GLN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 540 HIS L 36 HIS ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 495 ASN L 540 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5930 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 59010 Z= 0.229 Angle : 0.675 13.863 79776 Z= 0.344 Chirality : 0.046 0.252 8826 Planarity : 0.005 0.072 10464 Dihedral : 4.879 44.758 8202 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.10), residues: 7440 helix: 0.43 (0.11), residues: 2274 sheet: 0.97 (0.15), residues: 1074 loop : -1.79 (0.09), residues: 4092 *********************** 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 873 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 738 time to evaluate : 5.255 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: 135 outliers final: 90 residues processed: 844 average time/residue: 0.5631 time to fit residues: 794.5658 Evaluate side-chains 619 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 529 time to evaluate : 5.151 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 0 residues processed: 90 average time/residue: 0.4160 time to fit residues: 77.3348 ------------------------------------------------------------------------------- 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: 10.0000 chunk 207 optimal weight: 7.9990 chunk 557 optimal weight: 7.9990 chunk 456 optimal weight: 0.0870 chunk 184 optimal weight: 20.0000 chunk 671 optimal weight: 10.0000 chunk 725 optimal weight: 0.8980 chunk 597 optimal weight: 6.9990 chunk 665 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 538 optimal weight: 4.9990 overall best weight: 3.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN B 186 GLN B 442 ASN ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN D 309 GLN D 442 ASN F 442 ASN F 447 ASN ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 495 ASN I 503 ASN ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 491 ASN M 219 HIS ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN A 151 ASN A 300 HIS A 304 GLN A 442 ASN C 442 ASN E 151 ASN E 186 GLN E 309 GLN E 355 GLN E 442 ASN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 495 ASN ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 495 ASN J 503 ASN J 540 HIS L 52 HIS ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 306 GLN L 503 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.123 59010 Z= 0.305 Angle : 0.711 12.519 79776 Z= 0.366 Chirality : 0.048 0.245 8826 Planarity : 0.006 0.084 10464 Dihedral : 5.101 50.747 8202 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.09), residues: 7440 helix: 0.34 (0.11), residues: 2214 sheet: 1.21 (0.16), residues: 1020 loop : -1.84 (0.09), residues: 4206 *********************** 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 716 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 583 time to evaluate : 5.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 69 residues processed: 699 average time/residue: 0.5504 time to fit residues: 652.3952 Evaluate side-chains 502 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 433 time to evaluate : 5.203 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 0 residues processed: 69 average time/residue: 0.4079 time to fit residues: 60.8438 ------------------------------------------------------------------------------- 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: 6.9990 chunk 504 optimal weight: 10.0000 chunk 348 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 320 optimal weight: 1.9990 chunk 450 optimal weight: 0.9990 chunk 673 optimal weight: 9.9990 chunk 713 optimal weight: 10.0000 chunk 352 optimal weight: 4.9990 chunk 638 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN B 506 ASN ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN D 186 GLN F 300 HIS ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN ** F 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN E 304 GLN H 306 GLN ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN J 219 HIS ** J 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 540 HIS ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 563 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.6027 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= 0.219 Angle : 0.605 11.427 79776 Z= 0.310 Chirality : 0.044 0.242 8826 Planarity : 0.005 0.060 10464 Dihedral : 4.817 49.014 8202 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.10), residues: 7440 helix: 0.58 (0.11), residues: 2214 sheet: 0.95 (0.15), residues: 1152 loop : -1.79 (0.09), residues: 4074 *********************** 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 623 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 502 time to evaluate : 5.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 66 residues processed: 591 average time/residue: 0.5402 time to fit residues: 547.4341 Evaluate side-chains 505 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 439 time to evaluate : 5.165 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.4296 time to fit residues: 60.8617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 594 optimal weight: 0.4980 chunk 404 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 531 optimal weight: 20.0000 chunk 294 optimal weight: 0.9980 chunk 608 optimal weight: 4.9990 chunk 493 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 364 optimal weight: 0.0670 chunk 640 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 GLN ** F 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 595 HIS ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 563 ASN ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 503 ASN ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 302 ASN ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 59010 Z= 0.149 Angle : 0.565 14.432 79776 Z= 0.284 Chirality : 0.043 0.162 8826 Planarity : 0.004 0.056 10464 Dihedral : 4.429 42.411 8202 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.10), residues: 7440 helix: 0.90 (0.11), residues: 2220 sheet: 1.08 (0.15), residues: 1188 loop : -1.70 (0.10), residues: 4032 *********************** 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 591 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 532 time to evaluate : 5.170 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: 59 outliers final: 24 residues processed: 572 average time/residue: 0.5397 time to fit residues: 527.4908 Evaluate side-chains 464 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 440 time to evaluate : 5.096 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4185 time to fit residues: 26.0213 ------------------------------------------------------------------------------- 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: 7.9990 chunk 642 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 418 optimal weight: 20.0000 chunk 176 optimal weight: 2.9990 chunk 714 optimal weight: 10.0000 chunk 592 optimal weight: 7.9990 chunk 330 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 chunk 236 optimal weight: 2.9990 chunk 374 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 380 GLN ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 660 GLN K 99 ASN ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 660 GLN A 300 HIS C 304 GLN ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 380 GLN ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 59010 Z= 0.314 Angle : 0.693 12.444 79776 Z= 0.354 Chirality : 0.046 0.166 8826 Planarity : 0.006 0.065 10464 Dihedral : 5.126 57.785 8202 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.10), residues: 7440 helix: 0.61 (0.11), residues: 2178 sheet: 0.84 (0.15), residues: 1194 loop : -1.85 (0.09), residues: 4068 *********************** 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 565 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 460 time to evaluate : 5.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 52 residues processed: 540 average time/residue: 0.5266 time to fit residues: 491.9570 Evaluate side-chains 458 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 406 time to evaluate : 5.442 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 52 outliers final: 1 residues processed: 52 average time/residue: 0.4407 time to fit residues: 49.6243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 688 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 406 optimal weight: 0.9990 chunk 521 optimal weight: 10.0000 chunk 404 optimal weight: 5.9990 chunk 601 optimal weight: 3.9990 chunk 398 optimal weight: 10.0000 chunk 711 optimal weight: 2.9990 chunk 445 optimal weight: 2.9990 chunk 433 optimal weight: 0.8980 chunk 328 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 525 ASN ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 59010 Z= 0.205 Angle : 0.604 12.310 79776 Z= 0.306 Chirality : 0.044 0.244 8826 Planarity : 0.005 0.062 10464 Dihedral : 4.793 48.192 8202 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.10), residues: 7440 helix: 0.82 (0.11), residues: 2202 sheet: 0.98 (0.15), residues: 1158 loop : -1.77 (0.09), residues: 4080 *********************** 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 553 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 487 time to evaluate : 5.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 30 residues processed: 542 average time/residue: 0.5276 time to fit residues: 493.5181 Evaluate side-chains 465 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 435 time to evaluate : 5.135 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4122 time to fit residues: 30.5227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 440 optimal weight: 20.0000 chunk 284 optimal weight: 10.0000 chunk 424 optimal weight: 7.9990 chunk 214 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 452 optimal weight: 5.9990 chunk 484 optimal weight: 20.0000 chunk 351 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 559 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 GLN ** F 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 ASN ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 306 GLN ** K 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 466 HIS ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 525 ASN ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 660 GLN L 99 ASN ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.7736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 59010 Z= 0.337 Angle : 0.722 12.472 79776 Z= 0.370 Chirality : 0.046 0.180 8826 Planarity : 0.006 0.062 10464 Dihedral : 5.451 59.015 8202 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.09), residues: 7440 helix: 0.31 (0.11), residues: 2244 sheet: 0.32 (0.14), residues: 1290 loop : -1.99 (0.09), residues: 3906 *********************** 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 527 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 436 time to evaluate : 5.179 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 46 residues processed: 506 average time/residue: 0.5578 time to fit residues: 487.0114 Evaluate side-chains 427 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 381 time to evaluate : 5.150 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.4370 time to fit residues: 44.4289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 647 optimal weight: 2.9990 chunk 681 optimal weight: 0.6980 chunk 621 optimal weight: 3.9990 chunk 662 optimal weight: 10.0000 chunk 398 optimal weight: 3.9990 chunk 288 optimal weight: 10.0000 chunk 520 optimal weight: 20.0000 chunk 203 optimal weight: 7.9990 chunk 598 optimal weight: 30.0000 chunk 626 optimal weight: 8.9990 chunk 660 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 272 GLN ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN J 660 GLN L 99 ASN ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 563 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.7809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 59010 Z= 0.218 Angle : 0.633 18.446 79776 Z= 0.322 Chirality : 0.044 0.171 8826 Planarity : 0.005 0.061 10464 Dihedral : 5.043 58.610 8202 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.10), residues: 7440 helix: 0.64 (0.11), residues: 2214 sheet: 0.43 (0.14), residues: 1260 loop : -1.84 (0.10), residues: 3966 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 438 time to evaluate : 5.237 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: 39 outliers final: 12 residues processed: 467 average time/residue: 0.5593 time to fit residues: 447.7387 Evaluate side-chains 411 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 399 time to evaluate : 5.153 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4108 time to fit residues: 16.4475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 435 optimal weight: 3.9990 chunk 700 optimal weight: 7.9990 chunk 427 optimal weight: 0.0370 chunk 332 optimal weight: 0.9980 chunk 487 optimal weight: 8.9990 chunk 735 optimal weight: 3.9990 chunk 676 optimal weight: 0.9980 chunk 585 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 452 optimal weight: 30.0000 chunk 358 optimal weight: 4.9990 overall best weight: 2.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 595 HIS M 99 ASN ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN L 99 ASN ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.7906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 59010 Z= 0.199 Angle : 0.625 16.708 79776 Z= 0.316 Chirality : 0.044 0.158 8826 Planarity : 0.005 0.057 10464 Dihedral : 4.813 49.404 8202 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.10), residues: 7440 helix: 0.74 (0.11), residues: 2238 sheet: 0.50 (0.15), residues: 1224 loop : -1.76 (0.10), residues: 3978 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 431 time to evaluate : 5.318 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: 13 outliers final: 6 residues processed: 438 average time/residue: 0.5442 time to fit residues: 413.3679 Evaluate side-chains 408 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 402 time to evaluate : 5.122 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4446 time to fit residues: 11.9606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 465 optimal weight: 4.9990 chunk 623 optimal weight: 0.6980 chunk 179 optimal weight: 10.0000 chunk 539 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 586 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 602 optimal weight: 4.9990 chunk 74 optimal weight: 0.0980 chunk 108 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 ASN ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.124185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101455 restraints weight = 148821.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.100612 restraints weight = 118373.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.100837 restraints weight = 100359.180| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.8015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 59010 Z= 0.208 Angle : 0.622 15.221 79776 Z= 0.316 Chirality : 0.044 0.170 8826 Planarity : 0.005 0.057 10464 Dihedral : 4.772 42.292 8202 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.10), residues: 7440 helix: 0.79 (0.11), residues: 2232 sheet: 0.53 (0.15), residues: 1182 loop : -1.70 (0.10), residues: 4026 =============================================================================== Job complete usr+sys time: 10779.73 seconds wall clock time: 191 minutes 32.40 seconds (11492.40 seconds total)