Starting phenix.real_space_refine on Wed Feb 14 02:36:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f41_28849/02_2024/8f41_28849_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f41_28849/02_2024/8f41_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_2024/8f41_28849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f41_28849/02_2024/8f41_28849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f41_28849/02_2024/8f41_28849_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f41_28849/02_2024/8f41_28849_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 306 5.16 5 C 36504 2.51 5 N 10254 2.21 5 O 10782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 57846 Number of models: 1 Model: "" Number of chains: 18 Chain: "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: 21.85, per 1000 atoms: 0.38 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: 17.43 Conformation dependent library (CDL) restraints added in 8.2 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: 8.98 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: 17.78 Time building geometry restraints manager: 19.19 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: 31919 16.06 - 32.11: 2896 32.11 - 48.17: 604 48.17 - 64.23: 143 64.23 - 80.28: 24 Dihedral angle restraints: 35586 sinusoidal: 14322 harmonic: 21264 Sorted by residual: dihedral pdb=" CA GLU C 499 " pdb=" C GLU C 499 " pdb=" N PHE C 500 " pdb=" CA PHE C 500 " ideal model delta harmonic sigma weight residual 180.00 156.23 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 35583 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 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: 0.010 Normalize map: mean=0, sd=1: 2.070 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: 13.550 Check model and map are aligned: 0.620 Set scattering table: 0.420 Process input model: 113.970 Find NCS groups from input model: 3.200 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5495 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 : 13.028 80.285 21990 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 % Allowed : 2.63 % Favored : 96.98 % 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: -1.29 (0.10), residues: 7440 helix: 0.03 (0.11), residues: 2256 sheet: 0.89 (0.17), residues: 1008 loop : -1.89 (0.09), residues: 4176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 488 HIS 0.012 0.002 HIS A 311 PHE 0.022 0.002 PHE C 500 TYR 0.037 0.002 TYR A 504 ARG 0.006 0.001 ARG E 608 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1798 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1774 time to evaluate : 4.968 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 REVERT: B 171 MET cc_start: 0.5980 (tpp) cc_final: 0.5510 (tpp) REVERT: D 135 TYR cc_start: 0.4758 (m-80) cc_final: 0.4171 (t80) REVERT: D 488 ILE cc_start: 0.8332 (pt) cc_final: 0.7953 (mt) REVERT: D 549 VAL cc_start: 0.8054 (t) cc_final: 0.7846 (t) REVERT: F 425 THR cc_start: 0.6098 (p) cc_final: 0.5745 (t) REVERT: F 438 VAL cc_start: 0.6184 (t) cc_final: 0.5858 (t) REVERT: I 34 GLU cc_start: 0.7664 (mm-30) cc_final: 0.6921 (mt-10) REVERT: I 260 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6017 (mmt) REVERT: I 295 GLU cc_start: 0.6582 (pt0) cc_final: 0.6322 (tp30) REVERT: I 327 LYS cc_start: 0.7984 (tttt) cc_final: 0.7774 (ttmt) REVERT: I 342 GLN cc_start: 0.5012 (tm-30) cc_final: 0.4741 (tm-30) REVERT: I 377 GLU cc_start: 0.6955 (tp30) cc_final: 0.6701 (tp30) REVERT: I 506 THR cc_start: 0.6298 (m) cc_final: 0.5407 (p) REVERT: I 652 MET cc_start: 0.6751 (tpt) cc_final: 0.6536 (mmt) REVERT: K 34 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6983 (mt-10) REVERT: K 233 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8512 (t) REVERT: K 244 ARG cc_start: 0.6590 (ttp80) cc_final: 0.6004 (tmm-80) REVERT: K 260 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.6275 (mmt) REVERT: K 506 THR cc_start: 0.6411 (m) cc_final: 0.5920 (m) REVERT: K 604 ASP cc_start: 0.4480 (p0) cc_final: 0.3989 (p0) REVERT: M 215 LYS cc_start: 0.6721 (tttm) cc_final: 0.6481 (tptt) REVERT: M 231 ARG cc_start: 0.6999 (tpt170) cc_final: 0.6675 (mmp-170) REVERT: M 295 GLU cc_start: 0.7155 (pt0) cc_final: 0.6885 (tp30) REVERT: M 296 PHE cc_start: 0.7470 (p90) cc_final: 0.7083 (p90) REVERT: M 342 GLN cc_start: 0.6313 (tm-30) cc_final: 0.6051 (tp40) REVERT: M 352 ILE cc_start: 0.7679 (mt) cc_final: 0.7346 (mt) REVERT: A 216 HIS cc_start: 0.3440 (t-90) cc_final: 0.3019 (t-90) REVERT: A 425 THR cc_start: 0.6393 (p) cc_final: 0.5907 (t) REVERT: A 544 CYS cc_start: 0.7496 (m) cc_final: 0.7039 (m) REVERT: A 626 MET cc_start: 0.2796 (ttp) cc_final: 0.2527 (tpt) REVERT: C 135 TYR cc_start: 0.4637 (m-80) cc_final: 0.4329 (t80) REVERT: C 179 ARG cc_start: 0.6448 (mtp-110) cc_final: 0.5797 (mmm160) REVERT: C 425 THR cc_start: 0.6226 (p) cc_final: 0.5629 (t) REVERT: E 178 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6530 (tt) REVERT: H 34 GLU cc_start: 0.7521 (mm-30) cc_final: 0.6777 (mt-10) REVERT: H 226 PHE cc_start: 0.6520 (m-80) cc_final: 0.6089 (m-80) REVERT: H 231 ARG cc_start: 0.6854 (tpt170) cc_final: 0.6435 (tpp-160) REVERT: H 342 GLN cc_start: 0.4993 (tm-30) cc_final: 0.4729 (tm-30) REVERT: H 377 GLU cc_start: 0.6820 (tp30) cc_final: 0.6619 (tp30) REVERT: H 506 THR cc_start: 0.6059 (m) cc_final: 0.5198 (p) REVERT: J 17 LEU cc_start: 0.7699 (tp) cc_final: 0.7446 (tt) REVERT: J 215 LYS cc_start: 0.6910 (tttm) cc_final: 0.6527 (tptt) REVERT: J 311 VAL cc_start: 0.8023 (t) cc_final: 0.7754 (t) REVERT: J 316 CYS cc_start: 0.6225 (p) cc_final: 0.5950 (p) REVERT: J 506 THR cc_start: 0.6325 (m) cc_final: 0.5893 (p) REVERT: L 20 ASN cc_start: 0.6806 (m-40) cc_final: 0.6574 (t0) REVERT: L 34 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7414 (mt-10) REVERT: L 231 ARG cc_start: 0.6953 (tpt170) cc_final: 0.6182 (tpp-160) REVERT: L 244 ARG cc_start: 0.6658 (ttp80) cc_final: 0.6260 (tmm-80) REVERT: L 260 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.6319 (mmt) REVERT: L 326 VAL cc_start: 0.8124 (t) cc_final: 0.7839 (p) REVERT: L 327 LYS cc_start: 0.7580 (tttt) cc_final: 0.7326 (tttp) REVERT: L 496 TRP cc_start: 0.4302 (m100) cc_final: 0.4038 (m100) REVERT: L 604 ASP cc_start: 0.4724 (p0) cc_final: 0.4287 (p0) outliers start: 24 outliers final: 1 residues processed: 1787 average time/residue: 0.6370 time to fit residues: 1813.9589 Evaluate side-chains 755 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 749 time to evaluate : 4.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 260 MET Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain L residue 260 MET 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: 8.9990 chunk 310 optimal weight: 0.0050 chunk 191 optimal weight: 9.9990 chunk 377 optimal weight: 0.9990 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: 1.7776 ------------------------------------------------------------------------------- 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 I 36 HIS I 219 HIS I 306 GLN ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 495 ASN I 540 HIS K 36 HIS ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 247 GLN K 495 ASN K 540 HIS M 36 HIS ** M 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 329 GLN 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 ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 151 ASN 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 403 HIS J 495 ASN J 540 HIS L 36 HIS ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 GLN L 495 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 59010 Z= 0.223 Angle : 0.679 14.605 79776 Z= 0.346 Chirality : 0.046 0.236 8826 Planarity : 0.005 0.071 10464 Dihedral : 5.061 41.450 8307 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.52 % Allowed : 12.61 % Favored : 84.87 % 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: 0.42 (0.11), residues: 2268 sheet: 1.09 (0.16), residues: 1044 loop : -1.82 (0.09), residues: 4128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 414 HIS 0.009 0.002 HIS B 446 PHE 0.023 0.002 PHE D 500 TYR 0.022 0.002 TYR F 142 ARG 0.023 0.001 ARG B 213 *********************** 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 935 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 781 time to evaluate : 4.949 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: B 215 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6517 (tp) REVERT: B 373 MET cc_start: 0.4981 (mtm) cc_final: 0.4385 (mtp) REVERT: D 143 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.4563 (tt0) REVERT: F 168 MET cc_start: 0.7607 (tmm) cc_final: 0.6981 (ttp) REVERT: F 673 ARG cc_start: 0.5100 (mtt180) cc_final: 0.4355 (mtm180) REVERT: I 23 GLU cc_start: 0.7560 (tp30) cc_final: 0.7325 (mm-30) REVERT: I 34 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7166 (mm-30) REVERT: I 179 MET cc_start: 0.2918 (mmm) cc_final: 0.2624 (ppp) REVERT: I 260 MET cc_start: 0.6516 (OUTLIER) cc_final: 0.5189 (mmt) REVERT: I 268 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6835 (tp30) REVERT: I 272 GLN cc_start: 0.7290 (mt0) cc_final: 0.6139 (tp-100) REVERT: I 301 MET cc_start: 0.5126 (ppp) cc_final: 0.4674 (ppp) REVERT: I 377 GLU cc_start: 0.7016 (tp30) cc_final: 0.6766 (tp30) REVERT: I 483 MET cc_start: 0.6966 (mpp) cc_final: 0.6760 (mmt) REVERT: K 34 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7102 (mm-30) REVERT: K 179 MET cc_start: 0.2529 (mmm) cc_final: 0.2259 (ppp) REVERT: K 215 LYS cc_start: 0.7078 (tttm) cc_final: 0.6741 (tptt) REVERT: K 260 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.5786 (mmt) REVERT: K 272 GLN cc_start: 0.7572 (mt0) cc_final: 0.6810 (mm110) REVERT: K 652 MET cc_start: 0.5112 (mmt) cc_final: 0.4899 (mmm) REVERT: M 34 GLU cc_start: 0.7565 (mm-30) cc_final: 0.6915 (mm-30) REVERT: M 215 LYS cc_start: 0.6590 (tttm) cc_final: 0.6388 (tptt) REVERT: M 231 ARG cc_start: 0.7076 (tpt170) cc_final: 0.6798 (mmp-170) REVERT: M 237 GLU cc_start: 0.7614 (mp0) cc_final: 0.7247 (mp0) REVERT: M 308 GLU cc_start: 0.6481 (mm-30) cc_final: 0.6089 (mm-30) REVERT: M 353 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7428 (tm-30) REVERT: M 519 VAL cc_start: 0.7574 (OUTLIER) cc_final: 0.7335 (m) REVERT: A 143 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.4693 (tt0) REVERT: A 673 ARG cc_start: 0.5322 (mtt180) cc_final: 0.4440 (mtm180) REVERT: C 179 ARG cc_start: 0.6052 (mtp-110) cc_final: 0.5453 (mtp180) REVERT: E 143 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.4839 (tt0) REVERT: E 179 ARG cc_start: 0.5987 (mtp-110) cc_final: 0.5725 (mtp180) REVERT: E 190 VAL cc_start: 0.5919 (t) cc_final: 0.5666 (t) REVERT: H 34 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7124 (mt-10) REVERT: H 231 ARG cc_start: 0.6931 (tpt170) cc_final: 0.6580 (tpp-160) REVERT: H 268 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6502 (tp30) REVERT: H 272 GLN cc_start: 0.6882 (mt0) cc_final: 0.5683 (tp-100) REVERT: H 295 GLU cc_start: 0.7631 (tp30) cc_final: 0.7251 (tp30) REVERT: J 34 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6974 (mm-30) REVERT: J 215 LYS cc_start: 0.6990 (tttm) cc_final: 0.6632 (tptt) REVERT: J 519 VAL cc_start: 0.7747 (OUTLIER) cc_final: 0.7535 (m) REVERT: J 563 ASN cc_start: 0.6552 (OUTLIER) cc_final: 0.5981 (m110) REVERT: L 34 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7221 (mm-30) REVERT: L 215 LYS cc_start: 0.7044 (tttm) cc_final: 0.6754 (tptt) REVERT: L 231 ARG cc_start: 0.6992 (tpt170) cc_final: 0.6571 (mmt-90) REVERT: L 251 GLU cc_start: 0.6499 (mp0) cc_final: 0.5977 (mp0) REVERT: L 260 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.5771 (mmt) REVERT: L 271 LEU cc_start: 0.7241 (mm) cc_final: 0.6869 (mp) REVERT: L 272 GLN cc_start: 0.7597 (mt0) cc_final: 0.6798 (mm110) REVERT: L 488 TRP cc_start: 0.7763 (t60) cc_final: 0.7547 (t60) outliers start: 154 outliers final: 95 residues processed: 900 average time/residue: 0.5456 time to fit residues: 824.5727 Evaluate side-chains 661 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 556 time to evaluate : 4.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 501 LYS Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 506 ASN Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 510 CYS Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 636 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 260 MET Chi-restraints excluded: chain I residue 316 CYS Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 563 ASN Chi-restraints excluded: chain I residue 577 VAL Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 217 SER Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 412 ILE Chi-restraints excluded: chain K residue 447 CYS Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 577 VAL Chi-restraints excluded: chain M residue 445 LYS Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 519 VAL Chi-restraints excluded: chain M residue 563 ASN Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 506 ASN Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 217 SER Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 412 ILE Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 519 VAL Chi-restraints excluded: chain J residue 563 ASN Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 260 MET Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 577 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 372 optimal weight: 20.0000 chunk 207 optimal weight: 3.9990 chunk 557 optimal weight: 9.9990 chunk 456 optimal weight: 0.0050 chunk 184 optimal weight: 2.9990 chunk 671 optimal weight: 6.9990 chunk 725 optimal weight: 20.0000 chunk 597 optimal weight: 10.0000 chunk 665 optimal weight: 0.0040 chunk 228 optimal weight: 7.9990 chunk 538 optimal weight: 8.9990 overall best weight: 2.8012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN B 506 ASN ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN D 309 GLN D 442 ASN ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 GLN ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 HIS ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN A 151 ASN A 304 GLN A 442 ASN ** C 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 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 540 HIS L 20 ASN L 85 ASN ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 306 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 59010 Z= 0.250 Angle : 0.657 12.250 79776 Z= 0.335 Chirality : 0.046 0.253 8826 Planarity : 0.005 0.064 10464 Dihedral : 4.935 36.765 8301 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.97 % Allowed : 15.46 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.10), residues: 7440 helix: 0.54 (0.11), residues: 2244 sheet: 0.82 (0.15), residues: 1164 loop : -1.82 (0.10), residues: 4032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 251 HIS 0.009 0.001 HIS K 654 PHE 0.021 0.002 PHE H 374 TYR 0.023 0.002 TYR L 432 ARG 0.009 0.001 ARG C 237 *********************** 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 802 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 620 time to evaluate : 4.982 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: B 143 GLU cc_start: 0.5296 (OUTLIER) cc_final: 0.4584 (mt-10) REVERT: D 143 GLU cc_start: 0.4607 (OUTLIER) cc_final: 0.3815 (tt0) REVERT: D 625 VAL cc_start: 0.4123 (m) cc_final: 0.3540 (m) REVERT: F 168 MET cc_start: 0.7759 (tmm) cc_final: 0.7327 (ttp) REVERT: F 179 ARG cc_start: 0.6409 (mtp-110) cc_final: 0.5644 (mtt180) REVERT: F 360 MET cc_start: 0.4558 (OUTLIER) cc_final: 0.3787 (mtt) REVERT: F 477 ASP cc_start: 0.3017 (p0) cc_final: 0.2723 (p0) REVERT: F 518 MET cc_start: 0.7379 (mtm) cc_final: 0.7043 (mtm) REVERT: I 260 MET cc_start: 0.6876 (mpt) cc_final: 0.5550 (mmt) REVERT: I 272 GLN cc_start: 0.7763 (mt0) cc_final: 0.7437 (tt0) REVERT: I 286 GLU cc_start: 0.7235 (pt0) cc_final: 0.6951 (pm20) REVERT: I 301 MET cc_start: 0.5729 (ppp) cc_final: 0.5163 (ppp) REVERT: I 377 GLU cc_start: 0.7379 (tp30) cc_final: 0.7077 (tp30) REVERT: I 453 PHE cc_start: 0.6430 (OUTLIER) cc_final: 0.6084 (p90) REVERT: I 483 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6907 (mmt) REVERT: K 34 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6958 (mm-30) REVERT: K 179 MET cc_start: 0.2919 (mmm) cc_final: 0.2310 (ppp) REVERT: K 308 GLU cc_start: 0.6082 (mm-30) cc_final: 0.5302 (mm-30) REVERT: K 453 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.6026 (p90) REVERT: K 652 MET cc_start: 0.5008 (mmt) cc_final: 0.4807 (mmm) REVERT: M 34 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6890 (mt-10) REVERT: M 179 MET cc_start: 0.1969 (mmm) cc_final: 0.1083 (ppp) REVERT: M 231 ARG cc_start: 0.7063 (tpt170) cc_final: 0.6635 (mmp-170) REVERT: M 295 GLU cc_start: 0.7666 (tp30) cc_final: 0.7297 (tp30) REVERT: M 299 MET cc_start: 0.6901 (tpt) cc_final: 0.6691 (tpt) REVERT: M 308 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6238 (mm-30) REVERT: M 353 GLU cc_start: 0.8025 (tm-30) cc_final: 0.6985 (tm-30) REVERT: M 453 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.6111 (p90) REVERT: A 143 GLU cc_start: 0.4708 (OUTLIER) cc_final: 0.3905 (tt0) REVERT: A 369 TYR cc_start: 0.4112 (m-80) cc_final: 0.3792 (m-10) REVERT: A 673 ARG cc_start: 0.5535 (mtt180) cc_final: 0.5032 (mtm180) REVERT: C 168 MET cc_start: 0.7620 (tmm) cc_final: 0.7186 (ttp) REVERT: C 179 ARG cc_start: 0.6520 (mtp-110) cc_final: 0.5996 (mtp180) REVERT: C 580 MET cc_start: 0.6155 (tpp) cc_final: 0.5582 (tpt) REVERT: C 653 PHE cc_start: 0.2411 (m-10) cc_final: 0.2175 (m-10) REVERT: E 143 GLU cc_start: 0.5082 (OUTLIER) cc_final: 0.4531 (tm-30) REVERT: E 179 ARG cc_start: 0.6467 (mtp-110) cc_final: 0.6073 (mtp180) REVERT: E 477 ASP cc_start: 0.4321 (p0) cc_final: 0.4010 (p0) REVERT: H 34 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7203 (mt-10) REVERT: H 231 ARG cc_start: 0.7111 (tpt170) cc_final: 0.6603 (mmp-170) REVERT: H 272 GLN cc_start: 0.7473 (mt0) cc_final: 0.6541 (tp-100) REVERT: H 295 GLU cc_start: 0.7640 (tp30) cc_final: 0.7237 (tp30) REVERT: H 453 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.6148 (p90) REVERT: H 599 LEU cc_start: 0.8153 (tp) cc_final: 0.7905 (mt) REVERT: J 215 LYS cc_start: 0.7022 (tttm) cc_final: 0.6711 (tptt) REVERT: J 295 GLU cc_start: 0.7645 (tp30) cc_final: 0.7326 (tp30) REVERT: J 453 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.6442 (p90) REVERT: J 563 ASN cc_start: 0.7031 (OUTLIER) cc_final: 0.6827 (m110) REVERT: L 231 ARG cc_start: 0.7035 (tpt170) cc_final: 0.6224 (tpp-160) REVERT: L 260 MET cc_start: 0.6714 (mpt) cc_final: 0.5825 (mmt) REVERT: L 268 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6988 (mm-30) REVERT: L 272 GLN cc_start: 0.7736 (mt0) cc_final: 0.7089 (mm110) outliers start: 182 outliers final: 111 residues processed: 769 average time/residue: 0.5360 time to fit residues: 701.9083 Evaluate side-chains 597 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 474 time to evaluate : 4.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 501 LYS Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 158 ASN Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 422 HIS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 483 MET Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 563 ASN Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 217 SER Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 412 ILE Chi-restraints excluded: chain K residue 447 CYS Chi-restraints excluded: chain K residue 453 PHE Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 445 LYS Chi-restraints excluded: chain M residue 453 PHE Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 563 ASN Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 158 ASN Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 421 ASP Chi-restraints excluded: chain E residue 422 HIS Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 636 THR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 577 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 217 SER Chi-restraints excluded: chain J residue 228 LYS Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 540 HIS Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 563 ASN Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 506 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 663 optimal weight: 0.7980 chunk 504 optimal weight: 9.9990 chunk 348 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 320 optimal weight: 5.9990 chunk 450 optimal weight: 0.3980 chunk 673 optimal weight: 9.9990 chunk 713 optimal weight: 10.0000 chunk 352 optimal weight: 1.9990 chunk 638 optimal weight: 0.4980 chunk 192 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN ** D 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 HIS ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 ASN ** 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** A 151 ASN A 300 HIS E 304 GLN H 306 GLN H 380 GLN ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 302 ASN ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 563 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 59010 Z= 0.187 Angle : 0.583 13.368 79776 Z= 0.295 Chirality : 0.043 0.164 8826 Planarity : 0.004 0.060 10464 Dihedral : 4.844 58.535 8292 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.65 % Allowed : 17.97 % Favored : 79.38 % 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: -0.70 (0.10), residues: 7440 helix: 0.78 (0.11), residues: 2214 sheet: 0.98 (0.15), residues: 1140 loop : -1.69 (0.10), residues: 4086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 488 HIS 0.018 0.001 HIS J 540 PHE 0.018 0.001 PHE M 234 TYR 0.016 0.001 TYR E 566 ARG 0.008 0.000 ARG M 244 *********************** 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 721 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 559 time to evaluate : 4.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 454 ASP cc_start: 0.6244 (OUTLIER) cc_final: 0.5843 (p0) REVERT: F 168 MET cc_start: 0.7560 (tmm) cc_final: 0.7294 (ttp) REVERT: F 179 ARG cc_start: 0.6258 (mtp-110) cc_final: 0.5762 (mtp180) REVERT: F 477 ASP cc_start: 0.3086 (p0) cc_final: 0.2791 (p0) REVERT: F 518 MET cc_start: 0.7577 (mtm) cc_final: 0.7232 (mtm) REVERT: I 179 MET cc_start: 0.2303 (mmm) cc_final: 0.1477 (ppp) REVERT: I 260 MET cc_start: 0.6861 (mpt) cc_final: 0.5565 (mmt) REVERT: I 272 GLN cc_start: 0.7760 (mt0) cc_final: 0.7427 (tt0) REVERT: I 483 MET cc_start: 0.7113 (mpp) cc_final: 0.6835 (mmt) REVERT: K 179 MET cc_start: 0.2995 (mmm) cc_final: 0.2575 (ppp) REVERT: K 404 TYR cc_start: 0.3792 (OUTLIER) cc_final: 0.2686 (m-10) REVERT: M 134 MET cc_start: 0.5870 (tpp) cc_final: 0.5491 (tpp) REVERT: M 179 MET cc_start: 0.2222 (mmm) cc_final: 0.1369 (ppp) REVERT: M 231 ARG cc_start: 0.7140 (tpt170) cc_final: 0.6640 (mmp-170) REVERT: M 295 GLU cc_start: 0.7725 (tp30) cc_final: 0.7356 (tp30) REVERT: A 171 MET cc_start: 0.6577 (tpp) cc_final: 0.6165 (tpp) REVERT: A 179 ARG cc_start: 0.6177 (mtp-110) cc_final: 0.5880 (mtm180) REVERT: A 369 TYR cc_start: 0.4350 (m-80) cc_final: 0.3991 (m-10) REVERT: A 454 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6265 (p0) REVERT: A 673 ARG cc_start: 0.5609 (mtt180) cc_final: 0.5312 (mtm180) REVERT: C 179 ARG cc_start: 0.6289 (mtp-110) cc_final: 0.5764 (mtp180) REVERT: E 179 ARG cc_start: 0.6358 (mtp-110) cc_final: 0.6025 (mtp180) REVERT: E 477 ASP cc_start: 0.4352 (p0) cc_final: 0.4073 (p0) REVERT: H 179 MET cc_start: 0.2529 (mmm) cc_final: 0.1653 (ppp) REVERT: H 231 ARG cc_start: 0.7147 (tpt170) cc_final: 0.6658 (mmp-170) REVERT: H 268 GLU cc_start: 0.6827 (mm-30) cc_final: 0.5924 (tt0) REVERT: H 272 GLN cc_start: 0.7478 (mt0) cc_final: 0.6810 (mm110) REVERT: H 295 GLU cc_start: 0.7577 (tp30) cc_final: 0.7239 (tp30) REVERT: J 21 ARG cc_start: 0.6971 (ttp-170) cc_final: 0.6560 (ttp-170) REVERT: J 215 LYS cc_start: 0.6930 (tttm) cc_final: 0.6679 (tptt) REVERT: J 295 GLU cc_start: 0.7611 (tp30) cc_final: 0.7392 (tp30) REVERT: J 299 MET cc_start: 0.6792 (tpt) cc_final: 0.6564 (tpt) REVERT: J 650 MET cc_start: 0.4412 (tmm) cc_final: 0.3709 (ttm) REVERT: L 231 ARG cc_start: 0.6934 (tpt170) cc_final: 0.6605 (mmt-90) REVERT: L 251 GLU cc_start: 0.6613 (mp0) cc_final: 0.6403 (mp0) REVERT: L 260 MET cc_start: 0.6729 (mpt) cc_final: 0.5729 (mmt) REVERT: L 268 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6917 (mm-30) REVERT: L 272 GLN cc_start: 0.7849 (mt0) cc_final: 0.7199 (mm110) REVERT: L 308 GLU cc_start: 0.6381 (mt-10) cc_final: 0.6145 (mt-10) REVERT: L 453 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.6165 (p90) REVERT: L 488 TRP cc_start: 0.7882 (t60) cc_final: 0.7656 (t60) outliers start: 162 outliers final: 111 residues processed: 692 average time/residue: 0.5406 time to fit residues: 640.1389 Evaluate side-chains 587 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 472 time to evaluate : 4.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 501 LYS Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 422 HIS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 316 CYS Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 447 CYS Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 563 ASN Chi-restraints excluded: chain I residue 577 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 TYR Chi-restraints excluded: chain K residue 447 CYS Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 563 ASN Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 369 TYR Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 422 HIS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain E residue 679 VAL Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 396 GLU Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 577 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 217 SER Chi-restraints excluded: chain J residue 228 LYS Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain L residue 447 CYS Chi-restraints excluded: chain L residue 453 PHE Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 547 CYS Chi-restraints excluded: chain L residue 577 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 594 optimal weight: 10.0000 chunk 404 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 531 optimal weight: 20.0000 chunk 294 optimal weight: 4.9990 chunk 608 optimal weight: 1.9990 chunk 493 optimal weight: 9.9990 chunk 0 optimal weight: 10.9990 chunk 364 optimal weight: 0.6980 chunk 640 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 442 ASN ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN D 186 GLN D 546 GLN ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 GLN ** F 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 380 GLN I 491 ASN ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 563 ASN ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 HIS ** C 304 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 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN J 219 HIS 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: 0.6236 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 59010 Z= 0.238 Angle : 0.623 11.651 79776 Z= 0.318 Chirality : 0.044 0.185 8826 Planarity : 0.005 0.063 10464 Dihedral : 4.993 54.342 8292 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.48 % Allowed : 18.42 % Favored : 78.10 % 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: -0.73 (0.10), residues: 7440 helix: 0.70 (0.11), residues: 2220 sheet: 1.20 (0.15), residues: 1122 loop : -1.74 (0.09), residues: 4098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 488 HIS 0.007 0.001 HIS M 654 PHE 0.019 0.002 PHE F 482 TYR 0.018 0.002 TYR L 432 ARG 0.010 0.001 ARG H 207 *********************** 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 711 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 498 time to evaluate : 5.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 668 TYR cc_start: 0.3614 (m-80) cc_final: 0.3400 (m-80) REVERT: D 528 ILE cc_start: 0.5688 (tt) cc_final: 0.5467 (tt) REVERT: F 179 ARG cc_start: 0.6440 (mtp-110) cc_final: 0.6229 (mtm180) REVERT: F 477 ASP cc_start: 0.3478 (p0) cc_final: 0.3194 (p0) REVERT: F 668 TYR cc_start: 0.4074 (m-80) cc_final: 0.3550 (m-80) REVERT: I 179 MET cc_start: 0.2013 (mmm) cc_final: 0.1552 (ppp) REVERT: I 260 MET cc_start: 0.6959 (mpt) cc_final: 0.5720 (mmt) REVERT: I 272 GLN cc_start: 0.7800 (mt0) cc_final: 0.7360 (tt0) REVERT: I 449 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5838 (mt-10) REVERT: I 483 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6872 (mmt) REVERT: I 563 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.6824 (m110) REVERT: K 179 MET cc_start: 0.3388 (mmm) cc_final: 0.2828 (ppp) REVERT: K 404 TYR cc_start: 0.4104 (OUTLIER) cc_final: 0.2826 (m-10) REVERT: K 453 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.6142 (p90) REVERT: K 500 PHE cc_start: 0.6798 (t80) cc_final: 0.6597 (t80) REVERT: M 231 ARG cc_start: 0.7064 (tpt170) cc_final: 0.6632 (mmp-170) REVERT: M 295 GLU cc_start: 0.7656 (tp30) cc_final: 0.7312 (tp30) REVERT: M 308 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6620 (mm-30) REVERT: M 404 TYR cc_start: 0.5371 (OUTLIER) cc_final: 0.4341 (m-80) REVERT: M 407 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7512 (tpt) REVERT: M 453 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.6261 (p90) REVERT: M 563 ASN cc_start: 0.6948 (OUTLIER) cc_final: 0.6654 (m110) REVERT: A 143 GLU cc_start: 0.4231 (OUTLIER) cc_final: 0.3330 (tt0) REVERT: A 171 MET cc_start: 0.6641 (tpp) cc_final: 0.6219 (tpp) REVERT: A 179 ARG cc_start: 0.6412 (mtp-110) cc_final: 0.6065 (mtm180) REVERT: C 144 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.6086 (mmm160) REVERT: C 179 ARG cc_start: 0.6419 (mtp-110) cc_final: 0.6151 (mtm180) REVERT: C 555 GLN cc_start: 0.5976 (OUTLIER) cc_final: 0.5645 (tp40) REVERT: E 143 GLU cc_start: 0.4205 (OUTLIER) cc_final: 0.3690 (tt0) REVERT: E 179 ARG cc_start: 0.6288 (mtp-110) cc_final: 0.5968 (mtp180) REVERT: E 477 ASP cc_start: 0.4536 (p0) cc_final: 0.4210 (p0) REVERT: H 179 MET cc_start: 0.2628 (mmm) cc_final: 0.1833 (ppp) REVERT: H 231 ARG cc_start: 0.7138 (tpt170) cc_final: 0.6603 (mmm160) REVERT: H 272 GLN cc_start: 0.7717 (mt0) cc_final: 0.7079 (mm110) REVERT: H 295 GLU cc_start: 0.7697 (tp30) cc_final: 0.7354 (tp30) REVERT: H 453 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.6223 (p90) REVERT: H 490 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7297 (mm) REVERT: J 21 ARG cc_start: 0.7211 (ttp-170) cc_final: 0.5118 (ttp-170) REVERT: J 179 MET cc_start: 0.1753 (mmm) cc_final: 0.0731 (ppp) REVERT: J 215 LYS cc_start: 0.7094 (tttm) cc_final: 0.6866 (tptt) REVERT: J 299 MET cc_start: 0.6943 (tpt) cc_final: 0.6694 (tpt) REVERT: J 353 GLU cc_start: 0.8557 (tt0) cc_final: 0.7950 (tt0) REVERT: J 404 TYR cc_start: 0.5214 (OUTLIER) cc_final: 0.3791 (m-80) REVERT: J 407 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7506 (tpt) REVERT: J 453 PHE cc_start: 0.6959 (OUTLIER) cc_final: 0.6467 (p90) REVERT: L 231 ARG cc_start: 0.6911 (tpt170) cc_final: 0.6606 (mmm160) REVERT: L 251 GLU cc_start: 0.6477 (mp0) cc_final: 0.6260 (mp0) REVERT: L 260 MET cc_start: 0.6585 (mpt) cc_final: 0.5590 (mmt) REVERT: L 272 GLN cc_start: 0.7905 (mt0) cc_final: 0.7307 (mm110) REVERT: L 353 GLU cc_start: 0.8555 (tm-30) cc_final: 0.7859 (tm-30) REVERT: L 404 TYR cc_start: 0.4275 (OUTLIER) cc_final: 0.2861 (m-80) REVERT: L 453 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6148 (p90) outliers start: 213 outliers final: 140 residues processed: 677 average time/residue: 0.5299 time to fit residues: 620.0926 Evaluate side-chains 587 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 427 time to evaluate : 4.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain D residue 158 ASN Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 422 HIS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 525 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 636 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 447 CYS Chi-restraints excluded: chain I residue 449 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 483 MET Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 563 ASN Chi-restraints excluded: chain I residue 577 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 217 SER Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 TYR Chi-restraints excluded: chain K residue 412 ILE Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 447 CYS Chi-restraints excluded: chain K residue 453 PHE Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 266 ILE Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 404 TYR Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 453 PHE Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 563 ASN Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 555 GLN Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 158 ASN Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 422 HIS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 154 PHE Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 396 GLU Chi-restraints excluded: chain H residue 411 VAL Chi-restraints excluded: chain H residue 449 GLU Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 490 LEU Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 577 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 217 SER Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 404 TYR Chi-restraints excluded: chain J residue 407 MET Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 404 TYR Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain L residue 447 CYS Chi-restraints excluded: chain L residue 453 PHE Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 563 ASN Chi-restraints excluded: chain L residue 577 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 240 optimal weight: 0.3980 chunk 642 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 418 optimal weight: 30.0000 chunk 176 optimal weight: 0.8980 chunk 714 optimal weight: 0.8980 chunk 592 optimal weight: 6.9990 chunk 330 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 236 optimal weight: 3.9990 chunk 374 optimal weight: 4.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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** ** B 555 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** K 99 ASN ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 563 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.6685 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= 0.197 Angle : 0.589 11.533 79776 Z= 0.298 Chirality : 0.043 0.157 8826 Planarity : 0.004 0.058 10464 Dihedral : 4.786 51.319 8292 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.15 % Allowed : 19.33 % Favored : 77.52 % 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: -0.64 (0.10), residues: 7440 helix: 0.85 (0.11), residues: 2226 sheet: 1.15 (0.15), residues: 1152 loop : -1.72 (0.09), residues: 4062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 488 HIS 0.006 0.001 HIS J 654 PHE 0.034 0.002 PHE H 500 TYR 0.015 0.001 TYR E 566 ARG 0.009 0.000 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 495 time to evaluate : 5.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 528 ILE cc_start: 0.5638 (tt) cc_final: 0.5387 (tt) REVERT: F 179 ARG cc_start: 0.6442 (mtp-110) cc_final: 0.6237 (mtm180) REVERT: F 332 PHE cc_start: 0.5752 (t80) cc_final: 0.5532 (t80) REVERT: F 477 ASP cc_start: 0.3858 (p0) cc_final: 0.3526 (p0) REVERT: F 668 TYR cc_start: 0.4117 (m-80) cc_final: 0.3560 (m-80) REVERT: I 179 MET cc_start: 0.2080 (mmm) cc_final: 0.1595 (ppp) REVERT: I 272 GLN cc_start: 0.7777 (mt0) cc_final: 0.7326 (tt0) REVERT: I 295 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: I 449 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5609 (mt-10) REVERT: I 483 MET cc_start: 0.7023 (mpp) cc_final: 0.6802 (mmt) REVERT: K 21 ARG cc_start: 0.6920 (ttp-170) cc_final: 0.4995 (ttp-170) REVERT: K 179 MET cc_start: 0.3166 (mmm) cc_final: 0.2710 (ppp) REVERT: K 404 TYR cc_start: 0.4186 (OUTLIER) cc_final: 0.2854 (m-10) REVERT: K 441 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7796 (mt) REVERT: K 453 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.6076 (p90) REVERT: K 490 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7322 (mm) REVERT: M 179 MET cc_start: 0.2129 (mmm) cc_final: 0.1030 (ppp) REVERT: M 231 ARG cc_start: 0.7122 (tpt170) cc_final: 0.6671 (mmp-170) REVERT: M 244 ARG cc_start: 0.7221 (ttp80) cc_final: 0.6979 (tmm-80) REVERT: M 272 GLN cc_start: 0.7832 (mt0) cc_final: 0.7182 (mm110) REVERT: M 295 GLU cc_start: 0.7653 (tp30) cc_final: 0.7326 (tp30) REVERT: M 299 MET cc_start: 0.7188 (tpp) cc_final: 0.6939 (tpt) REVERT: M 404 TYR cc_start: 0.5518 (OUTLIER) cc_final: 0.4855 (m-80) REVERT: M 407 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7527 (tpt) REVERT: M 453 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6409 (p90) REVERT: M 488 TRP cc_start: 0.7551 (t60) cc_final: 0.7287 (t60) REVERT: M 563 ASN cc_start: 0.7062 (OUTLIER) cc_final: 0.6851 (m110) REVERT: A 143 GLU cc_start: 0.3836 (OUTLIER) cc_final: 0.3060 (tt0) REVERT: A 171 MET cc_start: 0.6700 (tpp) cc_final: 0.6287 (tpp) REVERT: A 179 ARG cc_start: 0.6299 (mtp-110) cc_final: 0.6086 (mtm180) REVERT: C 144 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.6131 (mmm160) REVERT: C 179 ARG cc_start: 0.6391 (mtp-110) cc_final: 0.5803 (mtp180) REVERT: C 668 TYR cc_start: 0.4222 (OUTLIER) cc_final: 0.3658 (m-80) REVERT: E 179 ARG cc_start: 0.6376 (mtp-110) cc_final: 0.6162 (mtp85) REVERT: E 376 GLU cc_start: 0.6525 (mm-30) cc_final: 0.6264 (mm-30) REVERT: E 477 ASP cc_start: 0.4568 (p0) cc_final: 0.4287 (p0) REVERT: H 179 MET cc_start: 0.2622 (mmm) cc_final: 0.1757 (ppp) REVERT: H 231 ARG cc_start: 0.7105 (tpt170) cc_final: 0.6608 (mmm160) REVERT: H 272 GLN cc_start: 0.7725 (mt0) cc_final: 0.7229 (tt0) REVERT: H 295 GLU cc_start: 0.7663 (tp30) cc_final: 0.7381 (tp30) REVERT: H 404 TYR cc_start: 0.5094 (OUTLIER) cc_final: 0.4160 (m-80) REVERT: H 453 PHE cc_start: 0.6509 (OUTLIER) cc_final: 0.6241 (p90) REVERT: J 21 ARG cc_start: 0.7253 (ttp-170) cc_final: 0.5885 (ttp-170) REVERT: J 215 LYS cc_start: 0.7082 (tttm) cc_final: 0.6872 (tptt) REVERT: J 299 MET cc_start: 0.6930 (tpt) cc_final: 0.6713 (tpt) REVERT: J 404 TYR cc_start: 0.5117 (OUTLIER) cc_final: 0.4080 (m-80) REVERT: J 453 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6642 (p90) REVERT: J 490 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7014 (mm) REVERT: J 650 MET cc_start: 0.4183 (OUTLIER) cc_final: 0.3833 (ttm) REVERT: L 260 MET cc_start: 0.6493 (mpt) cc_final: 0.5445 (mmt) REVERT: L 347 LEU cc_start: 0.7572 (tp) cc_final: 0.7113 (tt) REVERT: L 353 GLU cc_start: 0.8569 (tm-30) cc_final: 0.7778 (tm-30) REVERT: L 404 TYR cc_start: 0.4354 (OUTLIER) cc_final: 0.3043 (m-80) REVERT: L 441 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7740 (mt) REVERT: L 453 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.6186 (p90) outliers start: 193 outliers final: 134 residues processed: 658 average time/residue: 0.5541 time to fit residues: 628.6407 Evaluate side-chains 603 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 447 time to evaluate : 4.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 500 PHE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 422 HIS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 525 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 506 ASN Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 555 GLN Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 295 GLU Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 447 CYS Chi-restraints excluded: chain I residue 449 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 577 VAL Chi-restraints excluded: chain I residue 604 ASP Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 217 SER Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 TYR Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 412 ILE Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 447 CYS Chi-restraints excluded: chain K residue 453 PHE Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 577 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 266 ILE Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 404 TYR Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 453 PHE Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 563 ASN Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 668 TYR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 422 HIS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 510 CYS Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 154 PHE Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 396 GLU Chi-restraints excluded: chain H residue 404 TYR Chi-restraints excluded: chain H residue 412 ILE Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 577 VAL Chi-restraints excluded: chain H residue 604 ASP Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 317 ARG Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 404 TYR Chi-restraints excluded: chain J residue 412 ILE Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 490 LEU Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 650 MET Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 404 TYR Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 447 CYS Chi-restraints excluded: chain L residue 453 PHE Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 577 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 688 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 406 optimal weight: 10.0000 chunk 521 optimal weight: 5.9990 chunk 404 optimal weight: 8.9990 chunk 601 optimal weight: 0.0070 chunk 398 optimal weight: 7.9990 chunk 711 optimal weight: 4.9990 chunk 445 optimal weight: 3.9990 chunk 433 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- 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** ** B 555 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 660 GLN K 85 ASN ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 660 GLN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 563 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 59010 Z= 0.217 Angle : 0.608 12.938 79776 Z= 0.308 Chirality : 0.044 0.272 8826 Planarity : 0.005 0.059 10464 Dihedral : 4.845 58.394 8292 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.68 % Allowed : 19.53 % Favored : 76.80 % 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: -0.64 (0.10), residues: 7440 helix: 0.88 (0.11), residues: 2196 sheet: 1.09 (0.15), residues: 1164 loop : -1.72 (0.09), residues: 4080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 488 HIS 0.009 0.001 HIS A 539 PHE 0.043 0.002 PHE H 500 TYR 0.016 0.001 TYR E 566 ARG 0.010 0.001 ARG A 694 *********************** 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 712 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 487 time to evaluate : 4.995 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: B 653 PHE cc_start: 0.2987 (OUTLIER) cc_final: 0.2674 (m-10) REVERT: B 668 TYR cc_start: 0.4037 (OUTLIER) cc_final: 0.3561 (m-80) REVERT: D 626 MET cc_start: 0.2400 (tpt) cc_final: 0.1906 (tpt) REVERT: F 477 ASP cc_start: 0.3769 (p0) cc_final: 0.3318 (p0) REVERT: F 500 PHE cc_start: 0.4576 (OUTLIER) cc_final: 0.3996 (m-10) REVERT: F 668 TYR cc_start: 0.3937 (m-80) cc_final: 0.3363 (m-80) REVERT: I 179 MET cc_start: 0.2419 (mmm) cc_final: 0.1936 (ppp) REVERT: I 295 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7130 (tm-30) REVERT: I 449 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5828 (mt-10) REVERT: I 483 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6761 (mmt) REVERT: I 488 TRP cc_start: 0.7741 (t60) cc_final: 0.7511 (t60) REVERT: I 500 PHE cc_start: 0.6723 (t80) cc_final: 0.6300 (t80) REVERT: K 21 ARG cc_start: 0.7001 (ttp-170) cc_final: 0.5269 (ttp-170) REVERT: K 179 MET cc_start: 0.3251 (mmm) cc_final: 0.2753 (ppp) REVERT: K 404 TYR cc_start: 0.4541 (OUTLIER) cc_final: 0.3232 (m-80) REVERT: K 441 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7867 (mt) REVERT: K 453 PHE cc_start: 0.6667 (OUTLIER) cc_final: 0.6090 (p90) REVERT: K 602 LEU cc_start: 0.3059 (OUTLIER) cc_final: 0.2852 (tt) REVERT: M 231 ARG cc_start: 0.7103 (tpt170) cc_final: 0.6688 (mmp-170) REVERT: M 244 ARG cc_start: 0.7218 (ttp80) cc_final: 0.7013 (tmm-80) REVERT: M 295 GLU cc_start: 0.7600 (tp30) cc_final: 0.7321 (tp30) REVERT: M 299 MET cc_start: 0.7200 (tpp) cc_final: 0.6902 (tpt) REVERT: M 404 TYR cc_start: 0.5567 (OUTLIER) cc_final: 0.4820 (m-80) REVERT: M 407 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7532 (tpt) REVERT: M 453 PHE cc_start: 0.6777 (OUTLIER) cc_final: 0.6248 (p90) REVERT: M 488 TRP cc_start: 0.7609 (t60) cc_final: 0.7320 (t60) REVERT: A 143 GLU cc_start: 0.3773 (OUTLIER) cc_final: 0.2910 (tt0) REVERT: A 171 MET cc_start: 0.6732 (tpp) cc_final: 0.6315 (tpp) REVERT: A 179 ARG cc_start: 0.6217 (mtp-110) cc_final: 0.6010 (mtm180) REVERT: A 222 MET cc_start: 0.4802 (OUTLIER) cc_final: 0.4572 (mtp) REVERT: E 474 MET cc_start: 0.3509 (mmm) cc_final: 0.3008 (tpt) REVERT: E 477 ASP cc_start: 0.4654 (p0) cc_final: 0.4381 (p0) REVERT: H 179 MET cc_start: 0.2598 (mmm) cc_final: 0.1785 (ppp) REVERT: H 231 ARG cc_start: 0.7104 (tpt170) cc_final: 0.6763 (mmp-170) REVERT: H 272 GLN cc_start: 0.7805 (mt0) cc_final: 0.7169 (mm110) REVERT: H 295 GLU cc_start: 0.7735 (tp30) cc_final: 0.7485 (tp30) REVERT: H 404 TYR cc_start: 0.4892 (OUTLIER) cc_final: 0.3984 (m-80) REVERT: J 21 ARG cc_start: 0.7203 (ttp-170) cc_final: 0.6420 (ttp-170) REVERT: J 179 MET cc_start: 0.1629 (mmm) cc_final: 0.0669 (ppp) REVERT: J 299 MET cc_start: 0.6990 (tpt) cc_final: 0.6736 (tpt) REVERT: J 404 TYR cc_start: 0.5191 (OUTLIER) cc_final: 0.4512 (m-80) REVERT: J 407 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7499 (tpt) REVERT: J 453 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6469 (p90) REVERT: J 490 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7062 (mm) REVERT: J 650 MET cc_start: 0.4366 (OUTLIER) cc_final: 0.3934 (ttm) REVERT: L 246 TYR cc_start: 0.6438 (m-80) cc_final: 0.6086 (m-80) REVERT: L 260 MET cc_start: 0.6475 (mpt) cc_final: 0.5439 (mmt) REVERT: L 404 TYR cc_start: 0.4655 (OUTLIER) cc_final: 0.3403 (m-80) REVERT: L 441 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7885 (mt) REVERT: L 453 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.6291 (p90) REVERT: L 563 ASN cc_start: 0.7314 (OUTLIER) cc_final: 0.7044 (t0) outliers start: 225 outliers final: 155 residues processed: 669 average time/residue: 0.5237 time to fit residues: 601.5739 Evaluate side-chains 615 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 435 time to evaluate : 4.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 500 PHE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 422 HIS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 525 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 500 PHE Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 555 GLN Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 260 MET Chi-restraints excluded: chain I residue 295 GLU Chi-restraints excluded: chain I residue 316 CYS Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 447 CYS Chi-restraints excluded: chain I residue 449 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 483 MET Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 545 GLU Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 577 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 217 SER Chi-restraints excluded: chain K residue 228 LYS Chi-restraints excluded: chain K residue 237 GLU Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 TYR Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 412 ILE Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 447 CYS Chi-restraints excluded: chain K residue 453 PHE Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 602 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 264 GLN Chi-restraints excluded: chain M residue 266 ILE Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 404 TYR Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 453 PHE Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 525 ASN Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 158 ASN Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 422 HIS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 594 ILE Chi-restraints excluded: chain E residue 671 THR Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 154 PHE Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 396 GLU Chi-restraints excluded: chain H residue 404 TYR Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 577 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 324 ASP Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 404 TYR Chi-restraints excluded: chain J residue 407 MET Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain J residue 490 LEU Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 650 MET Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 404 TYR Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 447 CYS Chi-restraints excluded: chain L residue 453 PHE Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 547 CYS Chi-restraints excluded: chain L residue 563 ASN Chi-restraints excluded: chain L residue 577 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 440 optimal weight: 8.9990 chunk 284 optimal weight: 8.9990 chunk 424 optimal weight: 7.9990 chunk 214 optimal weight: 7.9990 chunk 139 optimal weight: 0.0270 chunk 137 optimal weight: 7.9990 chunk 452 optimal weight: 20.0000 chunk 484 optimal weight: 10.0000 chunk 351 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 559 optimal weight: 7.9990 overall best weight: 6.4046 ------------------------------------------------------------------------------- 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** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN F 304 GLN F 442 ASN ** F 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN ** I 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 660 GLN ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 306 GLN ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 85 ASN ** M 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 563 ASN ** L 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.7944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 59010 Z= 0.425 Angle : 0.813 16.329 79776 Z= 0.419 Chirality : 0.049 0.226 8826 Planarity : 0.007 0.065 10464 Dihedral : 6.120 57.961 8292 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 4.22 % Allowed : 19.80 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.09), residues: 7440 helix: -0.08 (0.10), residues: 2250 sheet: 0.23 (0.14), residues: 1242 loop : -2.13 (0.09), residues: 3948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP J 488 HIS 0.010 0.002 HIS J 466 PHE 0.035 0.003 PHE H 500 TYR 0.036 0.003 TYR A 250 ARG 0.015 0.001 ARG L 389 *********************** 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 684 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 426 time to evaluate : 5.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7159 (tpp) REVERT: B 518 MET cc_start: 0.8328 (mtm) cc_final: 0.7984 (mtp) REVERT: B 669 TYR cc_start: 0.6165 (OUTLIER) cc_final: 0.5727 (m-80) REVERT: D 626 MET cc_start: 0.2465 (tpt) cc_final: 0.2218 (tpt) REVERT: F 477 ASP cc_start: 0.4589 (p0) cc_final: 0.4061 (p0) REVERT: F 500 PHE cc_start: 0.4861 (OUTLIER) cc_final: 0.4030 (m-10) REVERT: I 179 MET cc_start: 0.2346 (mmm) cc_final: 0.1732 (ppp) REVERT: I 295 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: I 404 TYR cc_start: 0.5162 (OUTLIER) cc_final: 0.4276 (m-80) REVERT: I 441 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7668 (mt) REVERT: I 483 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6302 (mpp) REVERT: K 21 ARG cc_start: 0.7431 (ttp-170) cc_final: 0.5885 (ttp-170) REVERT: K 179 MET cc_start: 0.3655 (mmm) cc_final: 0.2843 (ppp) REVERT: K 246 TYR cc_start: 0.6587 (m-80) cc_final: 0.6103 (m-80) REVERT: K 404 TYR cc_start: 0.5026 (OUTLIER) cc_final: 0.3724 (m-80) REVERT: K 441 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7763 (mt) REVERT: K 453 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.6042 (p90) REVERT: M 179 MET cc_start: 0.2333 (mmm) cc_final: 0.1151 (ppp) REVERT: M 231 ARG cc_start: 0.7014 (tpt170) cc_final: 0.6683 (mmp-170) REVERT: M 404 TYR cc_start: 0.5376 (OUTLIER) cc_final: 0.4216 (m-80) REVERT: M 407 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7607 (tpt) REVERT: M 429 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8538 (tp) REVERT: M 453 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.6270 (p90) REVERT: M 650 MET cc_start: 0.4700 (tmm) cc_final: 0.3410 (ttm) REVERT: A 222 MET cc_start: 0.5156 (OUTLIER) cc_final: 0.4815 (mtp) REVERT: A 262 TYR cc_start: 0.3901 (OUTLIER) cc_final: 0.3509 (m-80) REVERT: A 393 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7625 (tp) REVERT: A 634 VAL cc_start: 0.7104 (t) cc_final: 0.6903 (p) REVERT: A 669 TYR cc_start: 0.6022 (OUTLIER) cc_final: 0.5602 (m-80) REVERT: C 144 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.5311 (mmp80) REVERT: E 335 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5858 (mm-30) REVERT: H 179 MET cc_start: 0.2527 (mmm) cc_final: 0.1700 (ppp) REVERT: H 231 ARG cc_start: 0.6923 (tpt170) cc_final: 0.6563 (mmp-170) REVERT: H 295 GLU cc_start: 0.7732 (tp30) cc_final: 0.7336 (tp30) REVERT: H 404 TYR cc_start: 0.5328 (OUTLIER) cc_final: 0.4503 (m-80) REVERT: H 449 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6271 (mt-10) REVERT: H 453 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.6415 (p90) REVERT: J 21 ARG cc_start: 0.7406 (ttp-170) cc_final: 0.6702 (ttp-170) REVERT: J 317 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6592 (mmt-90) REVERT: J 404 TYR cc_start: 0.5508 (OUTLIER) cc_final: 0.4650 (m-80) REVERT: J 407 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7541 (tpt) REVERT: J 453 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.6351 (p90) REVERT: L 106 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7839 (mp) REVERT: L 154 PHE cc_start: 0.4874 (OUTLIER) cc_final: 0.4531 (t80) REVERT: L 260 MET cc_start: 0.6734 (mpt) cc_final: 0.5770 (mmt) REVERT: L 404 TYR cc_start: 0.5128 (OUTLIER) cc_final: 0.3876 (m-80) REVERT: L 441 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7875 (mt) REVERT: L 453 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.5983 (p90) outliers start: 258 outliers final: 167 residues processed: 650 average time/residue: 0.5060 time to fit residues: 572.7688 Evaluate side-chains 573 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 374 time to evaluate : 4.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 500 PHE Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 669 TYR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 158 ASN Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 422 HIS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 525 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 500 PHE Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 555 GLN Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 260 MET Chi-restraints excluded: chain I residue 295 GLU Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 392 THR Chi-restraints excluded: chain I residue 404 TYR Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 437 ILE Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 447 CYS Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 483 MET Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 545 GLU Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 577 VAL Chi-restraints excluded: chain I residue 604 ASP Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 217 SER Chi-restraints excluded: chain K residue 228 LYS Chi-restraints excluded: chain K residue 237 GLU Chi-restraints excluded: chain K residue 260 MET Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 TYR Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 412 ILE Chi-restraints excluded: chain K residue 441 ILE Chi-restraints excluded: chain K residue 447 CYS Chi-restraints excluded: chain K residue 453 PHE Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 577 VAL Chi-restraints excluded: chain K residue 602 LEU Chi-restraints excluded: chain K residue 664 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 266 ILE Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 404 TYR Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 453 PHE Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 545 GLU Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 604 ASP Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 669 TYR Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 525 ASN Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 555 GLN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 668 TYR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 158 ASN Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 375 ASP Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 422 HIS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 154 PHE Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 396 GLU Chi-restraints excluded: chain H residue 404 TYR Chi-restraints excluded: chain H residue 411 VAL Chi-restraints excluded: chain H residue 449 GLU Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 545 GLU Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 577 VAL Chi-restraints excluded: chain H residue 604 ASP Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 312 THR Chi-restraints excluded: chain J residue 317 ARG Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 404 TYR Chi-restraints excluded: chain J residue 407 MET Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 545 GLU Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 154 PHE Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 228 LYS Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 404 TYR Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 447 CYS Chi-restraints excluded: chain L residue 453 PHE Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 547 CYS Chi-restraints excluded: chain L residue 577 VAL 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: 0.3980 chunk 621 optimal weight: 10.0000 chunk 662 optimal weight: 5.9990 chunk 398 optimal weight: 4.9990 chunk 288 optimal weight: 0.9990 chunk 520 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 598 optimal weight: 20.0000 chunk 626 optimal weight: 0.9990 chunk 660 optimal weight: 0.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- 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** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 ASN ** F 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 660 GLN ** K 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 491 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** ** L 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.7853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 59010 Z= 0.176 Angle : 0.613 17.065 79776 Z= 0.312 Chirality : 0.044 0.179 8826 Planarity : 0.005 0.077 10464 Dihedral : 5.081 57.652 8292 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.37 % Allowed : 22.08 % Favored : 75.56 % 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: 0.59 (0.11), residues: 2274 sheet: 0.74 (0.15), residues: 1122 loop : -1.88 (0.09), residues: 4044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 251 HIS 0.007 0.001 HIS M 52 PHE 0.025 0.001 PHE H 500 TYR 0.014 0.001 TYR E 566 ARG 0.010 0.000 ARG B 694 *********************** 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 631 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 486 time to evaluate : 5.006 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: B 422 HIS cc_start: 0.5168 (OUTLIER) cc_final: 0.4554 (m-70) REVERT: D 566 TYR cc_start: 0.5483 (m-80) cc_final: 0.4973 (m-80) REVERT: D 626 MET cc_start: 0.2614 (tpt) cc_final: 0.2404 (tpt) REVERT: D 694 ARG cc_start: 0.6642 (mmt90) cc_final: 0.6338 (mtt-85) REVERT: F 422 HIS cc_start: 0.4656 (OUTLIER) cc_final: 0.4057 (m-70) REVERT: F 477 ASP cc_start: 0.4617 (p0) cc_final: 0.4124 (p0) REVERT: F 500 PHE cc_start: 0.4717 (OUTLIER) cc_final: 0.4074 (m-10) REVERT: I 179 MET cc_start: 0.2297 (mmm) cc_final: 0.1950 (ppp) REVERT: I 272 GLN cc_start: 0.7712 (mt0) cc_final: 0.7151 (mm110) REVERT: I 404 TYR cc_start: 0.4947 (OUTLIER) cc_final: 0.4242 (m-80) REVERT: I 483 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6335 (mpp) REVERT: I 631 LEU cc_start: 0.5754 (OUTLIER) cc_final: 0.4748 (mt) REVERT: K 124 MET cc_start: 0.5952 (tmm) cc_final: 0.5740 (ttp) REVERT: K 225 PHE cc_start: 0.7867 (t80) cc_final: 0.7651 (t80) REVERT: K 404 TYR cc_start: 0.4662 (OUTLIER) cc_final: 0.3728 (m-80) REVERT: K 453 PHE cc_start: 0.6626 (OUTLIER) cc_final: 0.6118 (p90) REVERT: K 602 LEU cc_start: 0.3637 (OUTLIER) cc_final: 0.3365 (tt) REVERT: K 650 MET cc_start: 0.5727 (tmm) cc_final: 0.5313 (ptp) REVERT: M 21 ARG cc_start: 0.7277 (ttp-170) cc_final: 0.6749 (tmm-80) REVERT: M 179 MET cc_start: 0.2075 (mmm) cc_final: 0.0958 (ppp) REVERT: M 231 ARG cc_start: 0.7020 (tpt170) cc_final: 0.6733 (mmp-170) REVERT: M 244 ARG cc_start: 0.7282 (ttp80) cc_final: 0.7041 (tmm-80) REVERT: M 272 GLN cc_start: 0.7764 (mt0) cc_final: 0.7204 (mm110) REVERT: M 286 GLU cc_start: 0.7217 (mp0) cc_final: 0.6965 (mp0) REVERT: M 404 TYR cc_start: 0.5361 (OUTLIER) cc_final: 0.4646 (m-80) REVERT: M 453 PHE cc_start: 0.6675 (OUTLIER) cc_final: 0.6331 (p90) REVERT: M 502 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.6035 (tp) REVERT: M 545 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7242 (pt0) REVERT: M 650 MET cc_start: 0.5629 (tmm) cc_final: 0.4020 (ttm) REVERT: A 222 MET cc_start: 0.5039 (OUTLIER) cc_final: 0.4753 (mtp) REVERT: A 266 ILE cc_start: 0.7935 (mm) cc_final: 0.7465 (mt) REVERT: A 673 ARG cc_start: 0.4775 (mtt90) cc_final: 0.4216 (mtm180) REVERT: E 474 MET cc_start: 0.3166 (mmm) cc_final: 0.2858 (tpt) REVERT: H 179 MET cc_start: 0.2286 (mmm) cc_final: 0.1576 (ppp) REVERT: H 231 ARG cc_start: 0.6995 (tpt170) cc_final: 0.6603 (mmm160) REVERT: H 272 GLN cc_start: 0.7843 (mt0) cc_final: 0.7191 (mm110) REVERT: H 295 GLU cc_start: 0.7844 (tp30) cc_final: 0.7547 (tp30) REVERT: H 404 TYR cc_start: 0.5137 (OUTLIER) cc_final: 0.4183 (m-80) REVERT: H 441 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7489 (mt) REVERT: H 650 MET cc_start: 0.5158 (tmm) cc_final: 0.4863 (ptm) REVERT: J 21 ARG cc_start: 0.7248 (ttp-170) cc_final: 0.6300 (ttp-170) REVERT: J 179 MET cc_start: 0.1657 (mmm) cc_final: 0.0818 (ppp) REVERT: J 272 GLN cc_start: 0.7724 (mt0) cc_final: 0.7186 (mm110) REVERT: J 295 GLU cc_start: 0.7233 (tp30) cc_final: 0.7022 (tp30) REVERT: J 404 TYR cc_start: 0.5377 (OUTLIER) cc_final: 0.4468 (m-80) REVERT: J 407 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7464 (tpt) REVERT: J 453 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6497 (p90) REVERT: J 490 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7049 (mm) REVERT: J 650 MET cc_start: 0.4516 (OUTLIER) cc_final: 0.4120 (ttm) REVERT: L 106 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7619 (mp) REVERT: L 246 TYR cc_start: 0.6379 (m-80) cc_final: 0.6091 (m-80) REVERT: L 353 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8318 (tm-30) REVERT: L 404 TYR cc_start: 0.4772 (OUTLIER) cc_final: 0.3747 (m-80) REVERT: L 453 PHE cc_start: 0.6664 (OUTLIER) cc_final: 0.6131 (p90) outliers start: 145 outliers final: 99 residues processed: 614 average time/residue: 0.5274 time to fit residues: 557.7886 Evaluate side-chains 553 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 430 time to evaluate : 4.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 500 PHE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 158 ASN Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 525 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 422 HIS Chi-restraints excluded: chain F residue 500 PHE Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 555 GLN Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 404 TYR Chi-restraints excluded: chain I residue 411 VAL Chi-restraints excluded: chain I residue 447 CYS Chi-restraints excluded: chain I residue 483 MET Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 604 ASP Chi-restraints excluded: chain I residue 631 LEU Chi-restraints excluded: chain K residue 217 SER Chi-restraints excluded: chain K residue 228 LYS Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 TYR Chi-restraints excluded: chain K residue 412 ILE Chi-restraints excluded: chain K residue 453 PHE Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 602 LEU Chi-restraints excluded: chain K residue 664 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 264 GLN Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 404 TYR Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 453 PHE Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 502 LEU Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 545 GLU Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain M residue 604 ASP Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 525 ASN Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 422 HIS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 154 PHE Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 404 TYR Chi-restraints excluded: chain H residue 411 VAL Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 545 GLU Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 604 ASP Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 404 TYR Chi-restraints excluded: chain J residue 407 MET Chi-restraints excluded: chain J residue 411 VAL Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain J residue 490 LEU Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 604 ASP Chi-restraints excluded: chain J residue 650 MET Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 217 SER Chi-restraints excluded: chain L residue 228 LYS Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 404 TYR Chi-restraints excluded: chain L residue 453 PHE Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 547 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 435 optimal weight: 0.4980 chunk 700 optimal weight: 0.0770 chunk 427 optimal weight: 4.9990 chunk 332 optimal weight: 0.9990 chunk 487 optimal weight: 0.4980 chunk 735 optimal weight: 6.9990 chunk 676 optimal weight: 6.9990 chunk 585 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 452 optimal weight: 9.9990 chunk 358 optimal weight: 10.0000 overall best weight: 1.4142 ------------------------------------------------------------------------------- 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** ** B 555 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 99 ASN I 660 GLN ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 ASN M 466 HIS H 99 ASN ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.7924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 59010 Z= 0.181 Angle : 0.610 16.916 79776 Z= 0.307 Chirality : 0.044 0.173 8826 Planarity : 0.005 0.056 10464 Dihedral : 4.865 58.415 8292 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.11 % Allowed : 22.61 % Favored : 75.28 % 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: -0.77 (0.10), residues: 7440 helix: 0.81 (0.11), residues: 2232 sheet: 0.90 (0.16), residues: 1080 loop : -1.74 (0.09), residues: 4128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 488 HIS 0.008 0.001 HIS A 539 PHE 0.036 0.001 PHE I 500 TYR 0.014 0.001 TYR A 250 ARG 0.008 0.000 ARG L 389 ********************** 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 590 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 461 time to evaluate : 4.971 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: B 422 HIS cc_start: 0.5164 (OUTLIER) cc_final: 0.4760 (m-70) REVERT: D 566 TYR cc_start: 0.5797 (m-80) cc_final: 0.5273 (m-80) REVERT: F 477 ASP cc_start: 0.4702 (p0) cc_final: 0.4183 (p0) REVERT: F 500 PHE cc_start: 0.5117 (OUTLIER) cc_final: 0.4412 (m-10) REVERT: I 179 MET cc_start: 0.2264 (mmm) cc_final: 0.1982 (ppp) REVERT: I 272 GLN cc_start: 0.7690 (mt0) cc_final: 0.7070 (mm110) REVERT: I 404 TYR cc_start: 0.4951 (OUTLIER) cc_final: 0.4144 (m-80) REVERT: I 483 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6163 (mpp) REVERT: I 631 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.4733 (mt) REVERT: K 404 TYR cc_start: 0.4746 (OUTLIER) cc_final: 0.3692 (m-80) REVERT: K 453 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.6157 (p90) REVERT: K 488 TRP cc_start: 0.7545 (t60) cc_final: 0.7224 (t60) REVERT: K 602 LEU cc_start: 0.3151 (OUTLIER) cc_final: 0.2901 (tt) REVERT: K 650 MET cc_start: 0.5182 (tmm) cc_final: 0.4943 (ptp) REVERT: M 21 ARG cc_start: 0.7329 (ttp-170) cc_final: 0.6678 (ttp-170) REVERT: M 179 MET cc_start: 0.2057 (mmm) cc_final: 0.0906 (ppp) REVERT: M 231 ARG cc_start: 0.6943 (tpt170) cc_final: 0.6698 (mmp-170) REVERT: M 244 ARG cc_start: 0.7329 (ttp80) cc_final: 0.7066 (tmm-80) REVERT: M 286 GLU cc_start: 0.7198 (mp0) cc_final: 0.6967 (mp0) REVERT: M 404 TYR cc_start: 0.5384 (OUTLIER) cc_final: 0.4630 (m-80) REVERT: M 453 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.6185 (p90) REVERT: M 545 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7212 (pt0) REVERT: M 650 MET cc_start: 0.5491 (tmm) cc_final: 0.3843 (ttm) REVERT: A 266 ILE cc_start: 0.7898 (mm) cc_final: 0.7422 (mt) REVERT: E 474 MET cc_start: 0.3276 (mmm) cc_final: 0.2966 (tpt) REVERT: H 179 MET cc_start: 0.2301 (mmm) cc_final: 0.1634 (ppp) REVERT: H 231 ARG cc_start: 0.6979 (tpt170) cc_final: 0.6606 (mmm160) REVERT: H 272 GLN cc_start: 0.7675 (mt0) cc_final: 0.6993 (mm-40) REVERT: H 295 GLU cc_start: 0.7845 (tp30) cc_final: 0.7565 (tp30) REVERT: H 404 TYR cc_start: 0.5071 (OUTLIER) cc_final: 0.4325 (m-80) REVERT: H 650 MET cc_start: 0.5503 (tmm) cc_final: 0.5152 (ptm) REVERT: J 21 ARG cc_start: 0.7303 (ttp-170) cc_final: 0.6285 (ttp-170) REVERT: J 179 MET cc_start: 0.1939 (mmm) cc_final: 0.0899 (ppp) REVERT: J 295 GLU cc_start: 0.7179 (tp30) cc_final: 0.6962 (tp30) REVERT: J 404 TYR cc_start: 0.5396 (OUTLIER) cc_final: 0.4413 (m-80) REVERT: J 407 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7421 (tpt) REVERT: J 453 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.6389 (p90) REVERT: J 490 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7063 (mm) REVERT: J 650 MET cc_start: 0.4683 (OUTLIER) cc_final: 0.4354 (ttm) REVERT: L 154 PHE cc_start: 0.4930 (OUTLIER) cc_final: 0.4485 (t80) REVERT: L 246 TYR cc_start: 0.6340 (m-80) cc_final: 0.6048 (m-80) REVERT: L 353 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8012 (tm-30) REVERT: L 404 TYR cc_start: 0.4801 (OUTLIER) cc_final: 0.3643 (m-80) REVERT: L 453 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.6136 (p90) outliers start: 129 outliers final: 95 residues processed: 575 average time/residue: 0.5098 time to fit residues: 512.0063 Evaluate side-chains 538 residues out of total 6120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 423 time to evaluate : 5.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 422 HIS Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain D residue 158 ASN Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 525 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 500 PHE Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 555 GLN Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 404 TYR Chi-restraints excluded: chain I residue 447 CYS Chi-restraints excluded: chain I residue 483 MET Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 546 VAL Chi-restraints excluded: chain I residue 604 ASP Chi-restraints excluded: chain I residue 631 LEU Chi-restraints excluded: chain K residue 228 LYS Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 404 TYR Chi-restraints excluded: chain K residue 453 PHE Chi-restraints excluded: chain K residue 506 THR Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 602 LEU Chi-restraints excluded: chain K residue 664 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 264 GLN Chi-restraints excluded: chain M residue 404 TYR Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 453 PHE Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 545 GLU Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 525 ASN Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 422 HIS Chi-restraints excluded: chain E residue 522 ILE Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 674 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 154 PHE Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 404 TYR Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 506 THR Chi-restraints excluded: chain H residue 545 GLU Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 568 LEU Chi-restraints excluded: chain H residue 643 VAL Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 317 ARG Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 404 TYR Chi-restraints excluded: chain J residue 407 MET Chi-restraints excluded: chain J residue 447 CYS Chi-restraints excluded: chain J residue 453 PHE Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain J residue 490 LEU Chi-restraints excluded: chain J residue 506 THR Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 650 MET Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 154 PHE Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain L residue 404 TYR Chi-restraints excluded: chain L residue 453 PHE Chi-restraints excluded: chain L residue 506 THR Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 547 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 465 optimal weight: 0.9990 chunk 623 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 539 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 586 optimal weight: 20.0000 chunk 245 optimal weight: 10.0000 chunk 602 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 GLN ** F 422 HIS ** 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 99 ASN ** K 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 ASN ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN ** H 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN J 660 GLN ** L 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.121860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.099232 restraints weight = 149815.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.098309 restraints weight = 120105.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.098817 restraints weight = 102503.227| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.8307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 59010 Z= 0.369 Angle : 0.744 16.580 79776 Z= 0.381 Chirality : 0.047 0.203 8826 Planarity : 0.006 0.061 10464 Dihedral : 5.641 57.565 8292 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 2.83 % Allowed : 22.14 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.09), residues: 7440 helix: 0.15 (0.11), residues: 2280 sheet: 0.25 (0.14), residues: 1230 loop : -2.06 (0.09), residues: 3930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP H 488 HIS 0.009 0.002 HIS A 539 PHE 0.052 0.002 PHE H 298 TYR 0.019 0.002 TYR A 250 ARG 0.011 0.001 ARG A 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11673.25 seconds wall clock time: 206 minutes 32.26 seconds (12392.26 seconds total)