Starting phenix.real_space_refine on Sat Feb 24 08:13:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gq5_34198/02_2024/8gq5_34198.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gq5_34198/02_2024/8gq5_34198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gq5_34198/02_2024/8gq5_34198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gq5_34198/02_2024/8gq5_34198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gq5_34198/02_2024/8gq5_34198.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gq5_34198/02_2024/8gq5_34198.pdb" } resolution = 2.7 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= 0.030 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 208 5.16 5 C 26720 2.51 5 N 7600 2.21 5 O 8064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 400": "OE1" <-> "OE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "B GLU 400": "OE1" <-> "OE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "C GLU 400": "OE1" <-> "OE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "D GLU 400": "OE1" <-> "OE2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "E GLU 400": "OE1" <-> "OE2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "F GLU 400": "OE1" <-> "OE2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "G GLU 400": "OE1" <-> "OE2" Residue "G ARG 403": "NH1" <-> "NH2" Residue "H GLU 400": "OE1" <-> "OE2" Residue "H ARG 403": "NH1" <-> "NH2" Residue "I GLU 400": "OE1" <-> "OE2" Residue "I ARG 403": "NH1" <-> "NH2" Residue "J GLU 400": "OE1" <-> "OE2" Residue "J ARG 403": "NH1" <-> "NH2" Residue "K GLU 400": "OE1" <-> "OE2" Residue "K ARG 403": "NH1" <-> "NH2" Residue "L GLU 400": "OE1" <-> "OE2" Residue "L ARG 403": "NH1" <-> "NH2" Residue "M GLU 400": "OE1" <-> "OE2" Residue "M ARG 403": "NH1" <-> "NH2" Residue "N GLU 400": "OE1" <-> "OE2" Residue "N ARG 403": "NH1" <-> "NH2" Residue "O GLU 400": "OE1" <-> "OE2" Residue "O ARG 403": "NH1" <-> "NH2" Residue "P GLU 400": "OE1" <-> "OE2" Residue "P ARG 403": "NH1" <-> "NH2" 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: 42592 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "a" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "B" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "b" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "C" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "c" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "D" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "d" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "E" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "e" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "F" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "f" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "G" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "g" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "H" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "h" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "I" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "i" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "J" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "j" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "K" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "k" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "L" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "l" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "M" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "m" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "N" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "n" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "O" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "o" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "P" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "p" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Time building chain proxies: 21.11, per 1000 atoms: 0.50 Number of scatterers: 42592 At special positions: 0 Unit cell: (173.236, 173.236, 144.184, 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 208 16.00 O 8064 8.00 N 7600 7.00 C 26720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 96 " distance=2.02 Simple disulfide: pdb=" SG CYS c 23 " - pdb=" SG CYS c 96 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 23 " - pdb=" SG CYS e 96 " distance=2.03 Simple disulfide: pdb=" SG CYS f 23 " - pdb=" SG CYS f 96 " distance=2.02 Simple disulfide: pdb=" SG CYS g 23 " - pdb=" SG CYS g 96 " distance=2.03 Simple disulfide: pdb=" SG CYS h 23 " - pdb=" SG CYS h 96 " distance=2.03 Simple disulfide: pdb=" SG CYS i 23 " - pdb=" SG CYS i 96 " distance=2.02 Simple disulfide: pdb=" SG CYS j 23 " - pdb=" SG CYS j 96 " distance=2.02 Simple disulfide: pdb=" SG CYS k 23 " - pdb=" SG CYS k 96 " distance=2.02 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 96 " distance=2.03 Simple disulfide: pdb=" SG CYS m 23 " - pdb=" SG CYS m 96 " distance=2.03 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 96 " distance=2.02 Simple disulfide: pdb=" SG CYS o 23 " - pdb=" SG CYS o 96 " distance=2.02 Simple disulfide: pdb=" SG CYS p 23 " - pdb=" SG CYS p 96 " distance=2.02 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=0, symmetry=0 Time building additional restraints: 16.04 Conformation dependent library (CDL) restraints added in 7.8 seconds 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10080 Finding SS restraints... Secondary structure from input PDB file: 320 helices and 32 sheets defined 53.4% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.72 Creating SS restraints... Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.866A pdb=" N GLN A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 330' Processing helix chain 'A' and resid 331 through 336 removed outlier: 4.252A pdb=" N LEU A 334 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 Processing helix chain 'A' and resid 413 through 425 Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS A 430 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.621A pdb=" N ASP A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 475 removed outlier: 3.652A pdb=" N THR A 475 " --> pdb=" O THR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.768A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 496 through 500' Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.804A pdb=" N CYS A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS A 516 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU A 525 " --> pdb=" O GLN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 32 Processing helix chain 'a' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS a 65 " --> pdb=" O ASP a 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 330' Processing helix chain 'B' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU B 334 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 369 through 378 removed outlier: 4.044A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS B 430 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 447 through 454 removed outlier: 3.621A pdb=" N ASP B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.768A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 494 " --> pdb=" O TRP B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG B 499 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 496 through 500' Processing helix chain 'B' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS B 516 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG B 517 " --> pdb=" O LEU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU B 525 " --> pdb=" O GLN B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 32 Processing helix chain 'b' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS b 65 " --> pdb=" O ASP b 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 325 through 330' Processing helix chain 'C' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU C 334 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 369 through 378 removed outlier: 4.042A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 Processing helix chain 'C' and resid 413 through 425 Processing helix chain 'C' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS C 430 " --> pdb=" O SER C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 436 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR C 475 " --> pdb=" O THR C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 495 removed outlier: 3.768A pdb=" N TRP C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG C 499 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 496 through 500' Processing helix chain 'C' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS C 516 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG C 517 " --> pdb=" O LEU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU C 525 " --> pdb=" O GLN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 32 Processing helix chain 'c' and resid 61 through 65 removed outlier: 3.777A pdb=" N LYS c 65 " --> pdb=" O ASP c 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG D 329 " --> pdb=" O ASP D 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU D 330 " --> pdb=" O ASP D 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 330' Processing helix chain 'D' and resid 331 through 336 removed outlier: 4.252A pdb=" N LEU D 334 " --> pdb=" O VAL D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 368 Processing helix chain 'D' and resid 369 through 378 removed outlier: 4.042A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 413 through 425 Processing helix chain 'D' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS D 430 " --> pdb=" O SER D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 436 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 447 through 454 removed outlier: 3.621A pdb=" N ASP D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 475 removed outlier: 3.652A pdb=" N THR D 475 " --> pdb=" O THR D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 494 " --> pdb=" O TRP D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG D 499 " --> pdb=" O PRO D 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 496 through 500' Processing helix chain 'D' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 4.287A pdb=" N HIS D 516 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG D 517 " --> pdb=" O LEU D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU D 525 " --> pdb=" O GLN D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 32 Processing helix chain 'd' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS d 65 " --> pdb=" O ASP d 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG E 329 " --> pdb=" O ASP E 325 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 325 through 330' Processing helix chain 'E' and resid 331 through 336 removed outlier: 4.252A pdb=" N LEU E 334 " --> pdb=" O VAL E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 358 removed outlier: 4.031A pdb=" N GLN E 342 " --> pdb=" O ARG E 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 368 Processing helix chain 'E' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 413 through 425 Processing helix chain 'E' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS E 430 " --> pdb=" O SER E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 436 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR E 475 " --> pdb=" O THR E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 494 " --> pdb=" O TRP E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG E 499 " --> pdb=" O PRO E 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 496 through 500' Processing helix chain 'E' and resid 501 through 508 removed outlier: 3.804A pdb=" N CYS E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS E 516 " --> pdb=" O SER E 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG E 517 " --> pdb=" O LEU E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU E 525 " --> pdb=" O GLN E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET E 545 " --> pdb=" O ALA E 541 " (cutoff:3.500A) Processing helix chain 'e' and resid 28 through 32 Processing helix chain 'e' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS e 65 " --> pdb=" O ASP e 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG F 329 " --> pdb=" O ASP F 325 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU F 330 " --> pdb=" O ASP F 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 325 through 330' Processing helix chain 'F' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU F 334 " --> pdb=" O VAL F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 358 removed outlier: 4.031A pdb=" N GLN F 342 " --> pdb=" O ARG F 338 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 368 Processing helix chain 'F' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 413 through 425 Processing helix chain 'F' and resid 426 through 430 removed outlier: 3.623A pdb=" N CYS F 430 " --> pdb=" O SER F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 436 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 447 through 454 removed outlier: 3.621A pdb=" N ASP F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 475 removed outlier: 3.652A pdb=" N THR F 475 " --> pdb=" O THR F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 494 " --> pdb=" O TRP F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG F 499 " --> pdb=" O PRO F 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 496 through 500' Processing helix chain 'F' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 518 removed outlier: 4.287A pdb=" N HIS F 516 " --> pdb=" O SER F 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG F 517 " --> pdb=" O LEU F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 526 removed outlier: 4.047A pdb=" N GLU F 525 " --> pdb=" O GLN F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'f' and resid 28 through 32 Processing helix chain 'f' and resid 61 through 65 removed outlier: 3.777A pdb=" N LYS f 65 " --> pdb=" O ASP f 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG G 329 " --> pdb=" O ASP G 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU G 330 " --> pdb=" O ASP G 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 325 through 330' Processing helix chain 'G' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU G 334 " --> pdb=" O VAL G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 358 removed outlier: 4.029A pdb=" N GLN G 342 " --> pdb=" O ARG G 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 363 through 368 Processing helix chain 'G' and resid 369 through 378 removed outlier: 4.042A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 397 Processing helix chain 'G' and resid 413 through 425 Processing helix chain 'G' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS G 430 " --> pdb=" O SER G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 436 Processing helix chain 'G' and resid 439 through 444 Processing helix chain 'G' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP G 454 " --> pdb=" O GLU G 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 475 removed outlier: 3.652A pdb=" N THR G 475 " --> pdb=" O THR G 471 " (cutoff:3.500A) Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU G 494 " --> pdb=" O TRP G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG G 499 " --> pdb=" O PRO G 496 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 496 through 500' Processing helix chain 'G' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS G 516 " --> pdb=" O SER G 513 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG G 517 " --> pdb=" O LEU G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU G 525 " --> pdb=" O GLN G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET G 545 " --> pdb=" O ALA G 541 " (cutoff:3.500A) Processing helix chain 'g' and resid 28 through 32 Processing helix chain 'g' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS g 65 " --> pdb=" O ASP g 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG H 329 " --> pdb=" O ASP H 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU H 330 " --> pdb=" O ASP H 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 325 through 330' Processing helix chain 'H' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU H 334 " --> pdb=" O VAL H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN H 342 " --> pdb=" O ARG H 338 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 368 Processing helix chain 'H' and resid 369 through 378 removed outlier: 4.042A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 397 Processing helix chain 'H' and resid 413 through 425 Processing helix chain 'H' and resid 426 through 430 removed outlier: 3.623A pdb=" N CYS H 430 " --> pdb=" O SER H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 436 Processing helix chain 'H' and resid 439 through 444 Processing helix chain 'H' and resid 447 through 454 removed outlier: 3.621A pdb=" N ASP H 454 " --> pdb=" O GLU H 450 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR H 475 " --> pdb=" O THR H 471 " (cutoff:3.500A) Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.768A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU H 494 " --> pdb=" O TRP H 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG H 499 " --> pdb=" O PRO H 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 496 through 500' Processing helix chain 'H' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS H 508 " --> pdb=" O GLY H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS H 516 " --> pdb=" O SER H 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG H 517 " --> pdb=" O LEU H 514 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU H 525 " --> pdb=" O GLN H 521 " (cutoff:3.500A) Processing helix chain 'H' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET H 545 " --> pdb=" O ALA H 541 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 32 Processing helix chain 'h' and resid 61 through 65 removed outlier: 3.777A pdb=" N LYS h 65 " --> pdb=" O ASP h 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG I 329 " --> pdb=" O ASP I 325 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU I 330 " --> pdb=" O ASP I 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 325 through 330' Processing helix chain 'I' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU I 334 " --> pdb=" O VAL I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN I 342 " --> pdb=" O ARG I 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU I 358 " --> pdb=" O ALA I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 363 through 368 Processing helix chain 'I' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER I 373 " --> pdb=" O GLY I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 397 Processing helix chain 'I' and resid 413 through 425 Processing helix chain 'I' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS I 430 " --> pdb=" O SER I 427 " (cutoff:3.500A) Processing helix chain 'I' and resid 431 through 436 Processing helix chain 'I' and resid 439 through 444 Processing helix chain 'I' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP I 454 " --> pdb=" O GLU I 450 " (cutoff:3.500A) Processing helix chain 'I' and resid 459 through 475 removed outlier: 3.652A pdb=" N THR I 475 " --> pdb=" O THR I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 495 removed outlier: 3.768A pdb=" N TRP I 490 " --> pdb=" O ASN I 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU I 494 " --> pdb=" O TRP I 490 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG I 499 " --> pdb=" O PRO I 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN I 500 " --> pdb=" O ARG I 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 496 through 500' Processing helix chain 'I' and resid 501 through 508 removed outlier: 3.804A pdb=" N CYS I 508 " --> pdb=" O GLY I 504 " (cutoff:3.500A) Processing helix chain 'I' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS I 516 " --> pdb=" O SER I 513 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG I 517 " --> pdb=" O LEU I 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU I 525 " --> pdb=" O GLN I 521 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET I 545 " --> pdb=" O ALA I 541 " (cutoff:3.500A) Processing helix chain 'i' and resid 28 through 32 Processing helix chain 'i' and resid 61 through 65 removed outlier: 3.777A pdb=" N LYS i 65 " --> pdb=" O ASP i 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 330 removed outlier: 3.904A pdb=" N ARG J 329 " --> pdb=" O ASP J 325 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU J 330 " --> pdb=" O ASP J 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 325 through 330' Processing helix chain 'J' and resid 331 through 336 removed outlier: 4.254A pdb=" N LEU J 334 " --> pdb=" O VAL J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN J 342 " --> pdb=" O ARG J 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU J 358 " --> pdb=" O ALA J 354 " (cutoff:3.500A) Processing helix chain 'J' and resid 363 through 368 Processing helix chain 'J' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER J 373 " --> pdb=" O GLY J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 397 Processing helix chain 'J' and resid 413 through 425 Processing helix chain 'J' and resid 426 through 428 No H-bonds generated for 'chain 'J' and resid 426 through 428' Processing helix chain 'J' and resid 429 through 436 Processing helix chain 'J' and resid 439 through 444 Processing helix chain 'J' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP J 454 " --> pdb=" O GLU J 450 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR J 475 " --> pdb=" O THR J 471 " (cutoff:3.500A) Processing helix chain 'J' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP J 490 " --> pdb=" O ASN J 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU J 494 " --> pdb=" O TRP J 490 " (cutoff:3.500A) Processing helix chain 'J' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG J 499 " --> pdb=" O PRO J 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN J 500 " --> pdb=" O ARG J 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 496 through 500' Processing helix chain 'J' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS J 508 " --> pdb=" O GLY J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS J 516 " --> pdb=" O SER J 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG J 517 " --> pdb=" O LEU J 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 519 through 526 removed outlier: 4.047A pdb=" N GLU J 525 " --> pdb=" O GLN J 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET J 545 " --> pdb=" O ALA J 541 " (cutoff:3.500A) Processing helix chain 'j' and resid 28 through 32 Processing helix chain 'j' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS j 65 " --> pdb=" O ASP j 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG K 329 " --> pdb=" O ASP K 325 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU K 330 " --> pdb=" O ASP K 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 325 through 330' Processing helix chain 'K' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU K 334 " --> pdb=" O VAL K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN K 342 " --> pdb=" O ARG K 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU K 358 " --> pdb=" O ALA K 354 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 368 Processing helix chain 'K' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER K 373 " --> pdb=" O GLY K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 397 Processing helix chain 'K' and resid 413 through 425 Processing helix chain 'K' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS K 430 " --> pdb=" O SER K 427 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 436 Processing helix chain 'K' and resid 439 through 444 Processing helix chain 'K' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP K 454 " --> pdb=" O GLU K 450 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 475 removed outlier: 3.652A pdb=" N THR K 475 " --> pdb=" O THR K 471 " (cutoff:3.500A) Processing helix chain 'K' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP K 490 " --> pdb=" O ASN K 486 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU K 494 " --> pdb=" O TRP K 490 " (cutoff:3.500A) Processing helix chain 'K' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG K 499 " --> pdb=" O PRO K 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN K 500 " --> pdb=" O ARG K 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 496 through 500' Processing helix chain 'K' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS K 508 " --> pdb=" O GLY K 504 " (cutoff:3.500A) Processing helix chain 'K' and resid 513 through 518 removed outlier: 4.285A pdb=" N HIS K 516 " --> pdb=" O SER K 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG K 517 " --> pdb=" O LEU K 514 " (cutoff:3.500A) Processing helix chain 'K' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU K 525 " --> pdb=" O GLN K 521 " (cutoff:3.500A) Processing helix chain 'K' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET K 545 " --> pdb=" O ALA K 541 " (cutoff:3.500A) Processing helix chain 'k' and resid 28 through 32 Processing helix chain 'k' and resid 61 through 65 removed outlier: 3.777A pdb=" N LYS k 65 " --> pdb=" O ASP k 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG L 329 " --> pdb=" O ASP L 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU L 330 " --> pdb=" O ASP L 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 325 through 330' Processing helix chain 'L' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU L 334 " --> pdb=" O VAL L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 358 removed outlier: 4.031A pdb=" N GLN L 342 " --> pdb=" O ARG L 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU L 358 " --> pdb=" O ALA L 354 " (cutoff:3.500A) Processing helix chain 'L' and resid 363 through 368 Processing helix chain 'L' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER L 373 " --> pdb=" O GLY L 369 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 397 Processing helix chain 'L' and resid 413 through 425 Processing helix chain 'L' and resid 426 through 430 removed outlier: 3.623A pdb=" N CYS L 430 " --> pdb=" O SER L 427 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 436 Processing helix chain 'L' and resid 439 through 444 Processing helix chain 'L' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP L 454 " --> pdb=" O GLU L 450 " (cutoff:3.500A) Processing helix chain 'L' and resid 459 through 475 removed outlier: 3.652A pdb=" N THR L 475 " --> pdb=" O THR L 471 " (cutoff:3.500A) Processing helix chain 'L' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP L 490 " --> pdb=" O ASN L 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU L 494 " --> pdb=" O TRP L 490 " (cutoff:3.500A) Processing helix chain 'L' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG L 499 " --> pdb=" O PRO L 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN L 500 " --> pdb=" O ARG L 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 496 through 500' Processing helix chain 'L' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS L 508 " --> pdb=" O GLY L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 513 through 518 removed outlier: 4.287A pdb=" N HIS L 516 " --> pdb=" O SER L 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG L 517 " --> pdb=" O LEU L 514 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU L 525 " --> pdb=" O GLN L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET L 545 " --> pdb=" O ALA L 541 " (cutoff:3.500A) Processing helix chain 'l' and resid 28 through 32 Processing helix chain 'l' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS l 65 " --> pdb=" O ASP l 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG M 329 " --> pdb=" O ASP M 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU M 330 " --> pdb=" O ASP M 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 325 through 330' Processing helix chain 'M' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU M 334 " --> pdb=" O VAL M 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN M 342 " --> pdb=" O ARG M 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU M 358 " --> pdb=" O ALA M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 363 through 368 Processing helix chain 'M' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER M 373 " --> pdb=" O GLY M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 383 through 397 Processing helix chain 'M' and resid 413 through 425 Processing helix chain 'M' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS M 430 " --> pdb=" O SER M 427 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 436 Processing helix chain 'M' and resid 439 through 444 Processing helix chain 'M' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP M 454 " --> pdb=" O GLU M 450 " (cutoff:3.500A) Processing helix chain 'M' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR M 475 " --> pdb=" O THR M 471 " (cutoff:3.500A) Processing helix chain 'M' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP M 490 " --> pdb=" O ASN M 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU M 494 " --> pdb=" O TRP M 490 " (cutoff:3.500A) Processing helix chain 'M' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG M 499 " --> pdb=" O PRO M 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN M 500 " --> pdb=" O ARG M 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 496 through 500' Processing helix chain 'M' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS M 508 " --> pdb=" O GLY M 504 " (cutoff:3.500A) Processing helix chain 'M' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS M 516 " --> pdb=" O SER M 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG M 517 " --> pdb=" O LEU M 514 " (cutoff:3.500A) Processing helix chain 'M' and resid 519 through 526 removed outlier: 4.047A pdb=" N GLU M 525 " --> pdb=" O GLN M 521 " (cutoff:3.500A) Processing helix chain 'M' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET M 545 " --> pdb=" O ALA M 541 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 32 Processing helix chain 'm' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS m 65 " --> pdb=" O ASP m 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG N 329 " --> pdb=" O ASP N 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU N 330 " --> pdb=" O ASP N 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 325 through 330' Processing helix chain 'N' and resid 331 through 336 removed outlier: 4.252A pdb=" N LEU N 334 " --> pdb=" O VAL N 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN N 342 " --> pdb=" O ARG N 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU N 358 " --> pdb=" O ALA N 354 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 368 Processing helix chain 'N' and resid 369 through 378 removed outlier: 4.042A pdb=" N SER N 373 " --> pdb=" O GLY N 369 " (cutoff:3.500A) Processing helix chain 'N' and resid 383 through 397 Processing helix chain 'N' and resid 413 through 425 Processing helix chain 'N' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS N 430 " --> pdb=" O SER N 427 " (cutoff:3.500A) Processing helix chain 'N' and resid 431 through 436 Processing helix chain 'N' and resid 439 through 444 Processing helix chain 'N' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP N 454 " --> pdb=" O GLU N 450 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR N 475 " --> pdb=" O THR N 471 " (cutoff:3.500A) Processing helix chain 'N' and resid 486 through 495 removed outlier: 3.768A pdb=" N TRP N 490 " --> pdb=" O ASN N 486 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU N 494 " --> pdb=" O TRP N 490 " (cutoff:3.500A) Processing helix chain 'N' and resid 496 through 500 removed outlier: 3.635A pdb=" N ARG N 499 " --> pdb=" O PRO N 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN N 500 " --> pdb=" O ARG N 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 496 through 500' Processing helix chain 'N' and resid 501 through 508 removed outlier: 3.804A pdb=" N CYS N 508 " --> pdb=" O GLY N 504 " (cutoff:3.500A) Processing helix chain 'N' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS N 516 " --> pdb=" O SER N 513 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG N 517 " --> pdb=" O LEU N 514 " (cutoff:3.500A) Processing helix chain 'N' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU N 525 " --> pdb=" O GLN N 521 " (cutoff:3.500A) Processing helix chain 'N' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET N 545 " --> pdb=" O ALA N 541 " (cutoff:3.500A) Processing helix chain 'n' and resid 28 through 32 Processing helix chain 'n' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS n 65 " --> pdb=" O ASP n 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG O 329 " --> pdb=" O ASP O 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU O 330 " --> pdb=" O ASP O 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 325 through 330' Processing helix chain 'O' and resid 331 through 336 removed outlier: 4.254A pdb=" N LEU O 334 " --> pdb=" O VAL O 331 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN O 342 " --> pdb=" O ARG O 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU O 358 " --> pdb=" O ALA O 354 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 368 Processing helix chain 'O' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER O 373 " --> pdb=" O GLY O 369 " (cutoff:3.500A) Processing helix chain 'O' and resid 383 through 397 Processing helix chain 'O' and resid 413 through 425 Processing helix chain 'O' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS O 430 " --> pdb=" O SER O 427 " (cutoff:3.500A) Processing helix chain 'O' and resid 431 through 436 Processing helix chain 'O' and resid 439 through 444 Processing helix chain 'O' and resid 447 through 454 removed outlier: 3.621A pdb=" N ASP O 454 " --> pdb=" O GLU O 450 " (cutoff:3.500A) Processing helix chain 'O' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR O 475 " --> pdb=" O THR O 471 " (cutoff:3.500A) Processing helix chain 'O' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP O 490 " --> pdb=" O ASN O 486 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU O 494 " --> pdb=" O TRP O 490 " (cutoff:3.500A) Processing helix chain 'O' and resid 496 through 500 removed outlier: 3.635A pdb=" N ARG O 499 " --> pdb=" O PRO O 496 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN O 500 " --> pdb=" O ARG O 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 496 through 500' Processing helix chain 'O' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS O 508 " --> pdb=" O GLY O 504 " (cutoff:3.500A) Processing helix chain 'O' and resid 513 through 518 removed outlier: 4.285A pdb=" N HIS O 516 " --> pdb=" O SER O 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG O 517 " --> pdb=" O LEU O 514 " (cutoff:3.500A) Processing helix chain 'O' and resid 519 through 526 removed outlier: 4.047A pdb=" N GLU O 525 " --> pdb=" O GLN O 521 " (cutoff:3.500A) Processing helix chain 'O' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET O 545 " --> pdb=" O ALA O 541 " (cutoff:3.500A) Processing helix chain 'o' and resid 28 through 32 Processing helix chain 'o' and resid 61 through 65 removed outlier: 3.777A pdb=" N LYS o 65 " --> pdb=" O ASP o 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG P 329 " --> pdb=" O ASP P 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU P 330 " --> pdb=" O ASP P 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 325 through 330' Processing helix chain 'P' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU P 334 " --> pdb=" O VAL P 331 " (cutoff:3.500A) Processing helix chain 'P' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN P 342 " --> pdb=" O ARG P 338 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU P 358 " --> pdb=" O ALA P 354 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 368 Processing helix chain 'P' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER P 373 " --> pdb=" O GLY P 369 " (cutoff:3.500A) Processing helix chain 'P' and resid 383 through 397 Processing helix chain 'P' and resid 413 through 425 Processing helix chain 'P' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS P 430 " --> pdb=" O SER P 427 " (cutoff:3.500A) Processing helix chain 'P' and resid 431 through 436 Processing helix chain 'P' and resid 439 through 444 Processing helix chain 'P' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP P 454 " --> pdb=" O GLU P 450 " (cutoff:3.500A) Processing helix chain 'P' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR P 475 " --> pdb=" O THR P 471 " (cutoff:3.500A) Processing helix chain 'P' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP P 490 " --> pdb=" O ASN P 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU P 494 " --> pdb=" O TRP P 490 " (cutoff:3.500A) Processing helix chain 'P' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG P 499 " --> pdb=" O PRO P 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN P 500 " --> pdb=" O ARG P 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 496 through 500' Processing helix chain 'P' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS P 508 " --> pdb=" O GLY P 504 " (cutoff:3.500A) Processing helix chain 'P' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS P 516 " --> pdb=" O SER P 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG P 517 " --> pdb=" O LEU P 514 " (cutoff:3.500A) Processing helix chain 'P' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU P 525 " --> pdb=" O GLN P 521 " (cutoff:3.500A) Processing helix chain 'P' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET P 545 " --> pdb=" O ALA P 541 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 32 Processing helix chain 'p' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS p 65 " --> pdb=" O ASP p 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR a 78 " --> pdb=" O ASP a 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET a 35 " --> pdb=" O VAL a 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL a 51 " --> pdb=" O MET a 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP a 37 " --> pdb=" O VAL a 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN a 59 " --> pdb=" O VAL a 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'b' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR b 78 " --> pdb=" O ASP b 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET b 35 " --> pdb=" O VAL b 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL b 51 " --> pdb=" O MET b 35 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP b 37 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN b 59 " --> pdb=" O VAL b 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 6 through 8 removed outlier: 3.702A pdb=" N THR c 78 " --> pdb=" O ASP c 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET c 35 " --> pdb=" O VAL c 51 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL c 51 " --> pdb=" O MET c 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP c 37 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN c 59 " --> pdb=" O VAL c 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'd' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR d 78 " --> pdb=" O ASP d 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET d 35 " --> pdb=" O VAL d 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL d 51 " --> pdb=" O MET d 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP d 37 " --> pdb=" O VAL d 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN d 59 " --> pdb=" O VAL d 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR e 78 " --> pdb=" O ASP e 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'e' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET e 35 " --> pdb=" O VAL e 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL e 51 " --> pdb=" O MET e 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP e 37 " --> pdb=" O VAL e 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN e 59 " --> pdb=" O VAL e 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'f' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR f 78 " --> pdb=" O ASP f 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 11 through 13 removed outlier: 6.738A pdb=" N MET f 35 " --> pdb=" O VAL f 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL f 51 " --> pdb=" O MET f 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP f 37 " --> pdb=" O VAL f 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN f 59 " --> pdb=" O VAL f 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'g' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR g 78 " --> pdb=" O ASP g 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'g' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET g 35 " --> pdb=" O VAL g 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL g 51 " --> pdb=" O MET g 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP g 37 " --> pdb=" O VAL g 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN g 59 " --> pdb=" O VAL g 51 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'h' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR h 78 " --> pdb=" O ASP h 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'h' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET h 35 " --> pdb=" O VAL h 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL h 51 " --> pdb=" O MET h 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP h 37 " --> pdb=" O VAL h 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN h 59 " --> pdb=" O VAL h 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'i' and resid 6 through 8 removed outlier: 3.702A pdb=" N THR i 78 " --> pdb=" O ASP i 73 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'i' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET i 35 " --> pdb=" O VAL i 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL i 51 " --> pdb=" O MET i 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP i 37 " --> pdb=" O VAL i 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN i 59 " --> pdb=" O VAL i 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'j' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR j 78 " --> pdb=" O ASP j 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'j' and resid 11 through 13 removed outlier: 6.738A pdb=" N MET j 35 " --> pdb=" O VAL j 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL j 51 " --> pdb=" O MET j 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP j 37 " --> pdb=" O VAL j 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN j 59 " --> pdb=" O VAL j 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'k' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR k 78 " --> pdb=" O ASP k 73 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'k' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET k 35 " --> pdb=" O VAL k 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL k 51 " --> pdb=" O MET k 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP k 37 " --> pdb=" O VAL k 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN k 59 " --> pdb=" O VAL k 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'l' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR l 78 " --> pdb=" O ASP l 73 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'l' and resid 11 through 13 removed outlier: 6.738A pdb=" N MET l 35 " --> pdb=" O VAL l 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL l 51 " --> pdb=" O MET l 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP l 37 " --> pdb=" O VAL l 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN l 59 " --> pdb=" O VAL l 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'm' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR m 78 " --> pdb=" O ASP m 73 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'm' and resid 11 through 13 removed outlier: 6.738A pdb=" N MET m 35 " --> pdb=" O VAL m 51 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL m 51 " --> pdb=" O MET m 35 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP m 37 " --> pdb=" O VAL m 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN m 59 " --> pdb=" O VAL m 51 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'n' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR n 78 " --> pdb=" O ASP n 73 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'n' and resid 11 through 13 removed outlier: 6.736A pdb=" N MET n 35 " --> pdb=" O VAL n 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL n 51 " --> pdb=" O MET n 35 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP n 37 " --> pdb=" O VAL n 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN n 59 " --> pdb=" O VAL n 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'o' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR o 78 " --> pdb=" O ASP o 73 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'o' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET o 35 " --> pdb=" O VAL o 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL o 51 " --> pdb=" O MET o 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP o 37 " --> pdb=" O VAL o 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN o 59 " --> pdb=" O VAL o 51 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'p' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR p 78 " --> pdb=" O ASP p 73 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'p' and resid 11 through 13 removed outlier: 6.738A pdb=" N MET p 35 " --> pdb=" O VAL p 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL p 51 " --> pdb=" O MET p 35 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP p 37 " --> pdb=" O VAL p 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN p 59 " --> pdb=" O VAL p 51 " (cutoff:3.500A) 1921 hydrogen bonds defined for protein. 5190 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: 15.37 Time building geometry restraints manager: 17.27 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: 13685 1.34 - 1.45: 7253 1.45 - 1.57: 22102 1.57 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 43328 Sorted by residual: bond pdb=" CB THR C 502 " pdb=" CG2 THR C 502 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.77e+00 bond pdb=" CB THR D 502 " pdb=" CG2 THR D 502 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.74e+00 bond pdb=" CB THR I 502 " pdb=" CG2 THR I 502 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.74e+00 bond pdb=" CB THR P 502 " pdb=" CG2 THR P 502 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.74e+00 bond pdb=" CB THR K 502 " pdb=" CG2 THR K 502 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.73e+00 ... (remaining 43323 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.64: 1109 106.64 - 113.56: 23647 113.56 - 120.48: 18041 120.48 - 127.40: 15389 127.40 - 134.32: 390 Bond angle restraints: 58576 Sorted by residual: angle pdb=" CA LEU N 333 " pdb=" CB LEU N 333 " pdb=" CG LEU N 333 " ideal model delta sigma weight residual 116.30 128.76 -12.46 3.50e+00 8.16e-02 1.27e+01 angle pdb=" CA LEU E 333 " pdb=" CB LEU E 333 " pdb=" CG LEU E 333 " ideal model delta sigma weight residual 116.30 128.76 -12.46 3.50e+00 8.16e-02 1.27e+01 angle pdb=" CA LEU P 333 " pdb=" CB LEU P 333 " pdb=" CG LEU P 333 " ideal model delta sigma weight residual 116.30 128.75 -12.45 3.50e+00 8.16e-02 1.27e+01 angle pdb=" CA LEU M 333 " pdb=" CB LEU M 333 " pdb=" CG LEU M 333 " ideal model delta sigma weight residual 116.30 128.75 -12.45 3.50e+00 8.16e-02 1.26e+01 angle pdb=" CA LEU H 333 " pdb=" CB LEU H 333 " pdb=" CG LEU H 333 " ideal model delta sigma weight residual 116.30 128.75 -12.45 3.50e+00 8.16e-02 1.26e+01 ... (remaining 58571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 23213 16.06 - 32.13: 2487 32.13 - 48.19: 476 48.19 - 64.26: 128 64.26 - 80.32: 64 Dihedral angle restraints: 26368 sinusoidal: 10688 harmonic: 15680 Sorted by residual: dihedral pdb=" CA ASN d 99 " pdb=" C ASN d 99 " pdb=" N VAL d 100 " pdb=" CA VAL d 100 " ideal model delta harmonic sigma weight residual 180.00 155.97 24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASN f 99 " pdb=" C ASN f 99 " pdb=" N VAL f 100 " pdb=" CA VAL f 100 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASN j 99 " pdb=" C ASN j 99 " pdb=" N VAL j 100 " pdb=" CA VAL j 100 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 26365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4201 0.049 - 0.097: 1583 0.097 - 0.146: 539 0.146 - 0.194: 237 0.194 - 0.243: 48 Chirality restraints: 6608 Sorted by residual: chirality pdb=" CG LEU L 397 " pdb=" CB LEU L 397 " pdb=" CD1 LEU L 397 " pdb=" CD2 LEU L 397 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CG LEU K 397 " pdb=" CB LEU K 397 " pdb=" CD1 LEU K 397 " pdb=" CD2 LEU K 397 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CG LEU C 397 " pdb=" CB LEU C 397 " pdb=" CD1 LEU C 397 " pdb=" CD2 LEU C 397 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 6605 not shown) Planarity restraints: 7536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS N 361 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C LYS N 361 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS N 361 " 0.018 2.00e-02 2.50e+03 pdb=" N THR N 362 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 361 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.74e+00 pdb=" C LYS A 361 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS A 361 " 0.017 2.00e-02 2.50e+03 pdb=" N THR A 362 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 361 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.73e+00 pdb=" C LYS F 361 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS F 361 " 0.017 2.00e-02 2.50e+03 pdb=" N THR F 362 " 0.015 2.00e-02 2.50e+03 ... (remaining 7533 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 2359 2.71 - 3.26: 41837 3.26 - 3.81: 64755 3.81 - 4.35: 79292 4.35 - 4.90: 139564 Nonbonded interactions: 327807 Sorted by model distance: nonbonded pdb=" NE1 TRP D 412 " pdb=" OE2 GLU d 101 " model vdw 2.166 2.520 nonbonded pdb=" OH TYR J 380 " pdb=" O ARG j 31 " model vdw 2.228 2.440 nonbonded pdb=" OD1 ASP K 441 " pdb=" OH TYR K 503 " model vdw 2.252 2.440 nonbonded pdb=" OD1 ASP C 441 " pdb=" OH TYR C 503 " model vdw 2.252 2.440 nonbonded pdb=" OD1 ASP P 441 " pdb=" OH TYR P 503 " model vdw 2.252 2.440 ... (remaining 327802 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.890 Check model and map are aligned: 0.620 Set scattering table: 0.420 Process input model: 105.070 Find NCS groups from input model: 3.130 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.010 0.089 43328 Z= 0.626 Angle : 1.103 12.458 58576 Z= 0.566 Chirality : 0.064 0.243 6608 Planarity : 0.007 0.051 7536 Dihedral : 14.182 80.319 16240 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -3.24 (0.10), residues: 5360 helix: -1.71 (0.09), residues: 2304 sheet: -2.11 (0.15), residues: 976 loop : -2.48 (0.12), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP N 490 HIS 0.003 0.001 HIS G 547 PHE 0.019 0.002 PHE M 467 TYR 0.019 0.003 TYR A 348 ARG 0.016 0.002 ARG e 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1116 time to evaluate : 5.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 ASN cc_start: 0.8848 (t0) cc_final: 0.7885 (t0) REVERT: a 77 ASN cc_start: 0.8923 (m-40) cc_final: 0.8498 (m-40) REVERT: a 86 LEU cc_start: 0.9052 (mt) cc_final: 0.8820 (mp) REVERT: a 87 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8183 (mppt) REVERT: a 105 GLN cc_start: 0.7911 (pm20) cc_final: 0.7669 (pm20) REVERT: B 439 ASP cc_start: 0.8367 (p0) cc_final: 0.8119 (p0) REVERT: B 486 ASN cc_start: 0.8924 (t0) cc_final: 0.8210 (t0) REVERT: B 489 ASP cc_start: 0.8192 (m-30) cc_final: 0.7930 (m-30) REVERT: b 73 ASP cc_start: 0.8216 (t70) cc_final: 0.7992 (t0) REVERT: b 86 LEU cc_start: 0.9076 (mt) cc_final: 0.8842 (mm) REVERT: b 87 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8113 (mppt) REVERT: b 105 GLN cc_start: 0.8170 (pm20) cc_final: 0.7830 (pm20) REVERT: C 439 ASP cc_start: 0.8223 (p0) cc_final: 0.7966 (p0) REVERT: C 486 ASN cc_start: 0.8904 (t0) cc_final: 0.8023 (t0) REVERT: c 77 ASN cc_start: 0.8913 (m-40) cc_final: 0.8606 (m-40) REVERT: c 86 LEU cc_start: 0.9041 (mt) cc_final: 0.8785 (mp) REVERT: c 87 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8192 (mppt) REVERT: D 439 ASP cc_start: 0.8459 (p0) cc_final: 0.8135 (p0) REVERT: D 486 ASN cc_start: 0.8963 (t0) cc_final: 0.8261 (t0) REVERT: d 4 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8444 (mp10) REVERT: d 73 ASP cc_start: 0.8104 (t70) cc_final: 0.7847 (t0) REVERT: d 86 LEU cc_start: 0.9130 (mt) cc_final: 0.8842 (mm) REVERT: d 87 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8123 (mppt) REVERT: d 105 GLN cc_start: 0.8274 (pm20) cc_final: 0.8046 (pm20) REVERT: E 486 ASN cc_start: 0.8918 (t0) cc_final: 0.7979 (t0) REVERT: e 4 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8581 (mm-40) REVERT: e 14 GLN cc_start: 0.8702 (pm20) cc_final: 0.8324 (mp10) REVERT: e 77 ASN cc_start: 0.8907 (m-40) cc_final: 0.8613 (m-40) REVERT: e 87 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8086 (mppt) REVERT: e 105 GLN cc_start: 0.7986 (pm20) cc_final: 0.7765 (pm20) REVERT: F 486 ASN cc_start: 0.8986 (t0) cc_final: 0.8311 (t0) REVERT: f 86 LEU cc_start: 0.9136 (mt) cc_final: 0.8930 (mm) REVERT: f 87 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8204 (mppt) REVERT: f 105 GLN cc_start: 0.8190 (pm20) cc_final: 0.7897 (pm20) REVERT: G 439 ASP cc_start: 0.8186 (p0) cc_final: 0.7971 (p0) REVERT: G 486 ASN cc_start: 0.8895 (t0) cc_final: 0.7978 (t0) REVERT: g 4 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8517 (mm-40) REVERT: g 14 GLN cc_start: 0.8739 (pm20) cc_final: 0.8441 (mp10) REVERT: g 73 ASP cc_start: 0.8386 (t70) cc_final: 0.8115 (t0) REVERT: g 77 ASN cc_start: 0.8794 (m-40) cc_final: 0.8451 (m110) REVERT: g 86 LEU cc_start: 0.9249 (mt) cc_final: 0.9030 (mm) REVERT: g 87 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8257 (mppt) REVERT: H 486 ASN cc_start: 0.8960 (t0) cc_final: 0.8457 (t0) REVERT: h 86 LEU cc_start: 0.9100 (mt) cc_final: 0.8899 (mm) REVERT: h 87 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8185 (mppt) REVERT: I 486 ASN cc_start: 0.8979 (t0) cc_final: 0.8310 (t0) REVERT: I 489 ASP cc_start: 0.8211 (m-30) cc_final: 0.7988 (m-30) REVERT: I 516 HIS cc_start: 0.8304 (p90) cc_final: 0.7055 (p90) REVERT: i 4 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8473 (mm-40) REVERT: i 86 LEU cc_start: 0.9042 (mt) cc_final: 0.8784 (mp) REVERT: i 87 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7781 (mppt) REVERT: i 105 GLN cc_start: 0.8100 (pm20) cc_final: 0.7755 (pm20) REVERT: J 486 ASN cc_start: 0.8869 (t0) cc_final: 0.8072 (t0) REVERT: j 4 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8496 (mm-40) REVERT: j 86 LEU cc_start: 0.9205 (mt) cc_final: 0.8767 (mm) REVERT: j 87 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8005 (mppt) REVERT: j 105 GLN cc_start: 0.7994 (pm20) cc_final: 0.7542 (pm20) REVERT: K 486 ASN cc_start: 0.8898 (t0) cc_final: 0.7913 (t0) REVERT: k 14 GLN cc_start: 0.8587 (pm20) cc_final: 0.8294 (mp10) REVERT: k 86 LEU cc_start: 0.9191 (mt) cc_final: 0.8915 (mm) REVERT: k 87 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8110 (mppt) REVERT: k 105 GLN cc_start: 0.8014 (pm20) cc_final: 0.7727 (pm20) REVERT: L 486 ASN cc_start: 0.8831 (t0) cc_final: 0.7913 (t0) REVERT: l 4 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8551 (mm-40) REVERT: l 7 GLU cc_start: 0.8437 (mp0) cc_final: 0.7981 (mp0) REVERT: l 86 LEU cc_start: 0.9285 (mt) cc_final: 0.8975 (mm) REVERT: l 87 LYS cc_start: 0.8494 (mmtt) cc_final: 0.7977 (mppt) REVERT: l 105 GLN cc_start: 0.7951 (pm20) cc_final: 0.7361 (pm20) REVERT: M 486 ASN cc_start: 0.8851 (t0) cc_final: 0.7980 (t0) REVERT: M 516 HIS cc_start: 0.8216 (p90) cc_final: 0.7905 (p90) REVERT: m 4 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8565 (mm-40) REVERT: m 14 GLN cc_start: 0.8551 (pm20) cc_final: 0.8350 (mp10) REVERT: m 86 LEU cc_start: 0.9159 (mt) cc_final: 0.8896 (mm) REVERT: m 87 LYS cc_start: 0.8668 (mmtt) cc_final: 0.8141 (mppt) REVERT: m 105 GLN cc_start: 0.8002 (pm20) cc_final: 0.7801 (pm20) REVERT: N 486 ASN cc_start: 0.8834 (t0) cc_final: 0.7940 (t0) REVERT: N 516 HIS cc_start: 0.8361 (p90) cc_final: 0.8143 (p90) REVERT: n 4 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8497 (mm-40) REVERT: n 7 GLU cc_start: 0.8485 (mp0) cc_final: 0.7923 (mp0) REVERT: n 46 ARG cc_start: 0.8481 (mtt90) cc_final: 0.8257 (mtt90) REVERT: n 86 LEU cc_start: 0.9197 (mt) cc_final: 0.8978 (mm) REVERT: n 87 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7821 (mppt) REVERT: n 105 GLN cc_start: 0.8005 (pm20) cc_final: 0.7443 (pm20) REVERT: O 486 ASN cc_start: 0.8943 (t0) cc_final: 0.8248 (t0) REVERT: O 489 ASP cc_start: 0.8217 (m-30) cc_final: 0.7998 (m-30) REVERT: O 516 HIS cc_start: 0.8292 (p90) cc_final: 0.7188 (p90) REVERT: o 4 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8570 (mm-40) REVERT: o 14 GLN cc_start: 0.8642 (pm20) cc_final: 0.8418 (mp10) REVERT: o 87 LYS cc_start: 0.8574 (mmtt) cc_final: 0.8000 (mppt) REVERT: P 486 ASN cc_start: 0.8864 (t0) cc_final: 0.7984 (t0) REVERT: p 4 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8550 (mm-40) REVERT: p 86 LEU cc_start: 0.9167 (mt) cc_final: 0.8875 (mm) REVERT: p 87 LYS cc_start: 0.8517 (mmtt) cc_final: 0.7961 (mppt) REVERT: p 105 GLN cc_start: 0.8089 (pm20) cc_final: 0.7602 (pm20) outliers start: 0 outliers final: 5 residues processed: 1116 average time/residue: 1.5943 time to fit residues: 2150.4407 Evaluate side-chains 881 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 876 time to evaluate : 4.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain j residue 73 ASP Chi-restraints excluded: chain l residue 73 ASP Chi-restraints excluded: chain N residue 483 ASP Chi-restraints excluded: chain n residue 73 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 0.9980 chunk 400 optimal weight: 0.8980 chunk 222 optimal weight: 5.9990 chunk 136 optimal weight: 0.3980 chunk 269 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 413 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 251 optimal weight: 0.9990 chunk 308 optimal weight: 0.8980 chunk 479 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN A 436 GLN a 97 ASN B 328 GLN B 436 GLN b 97 ASN C 328 GLN C 436 GLN c 97 ASN D 328 GLN D 436 GLN d 97 ASN E 328 GLN E 436 GLN e 97 ASN F 328 GLN F 436 GLN f 97 ASN G 328 GLN G 436 GLN g 97 ASN H 328 GLN ** H 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 436 GLN h 97 ASN I 328 GLN I 436 GLN I 516 HIS i 97 ASN J 328 GLN J 436 GLN j 97 ASN K 328 GLN K 436 GLN ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 97 ASN L 328 GLN L 436 GLN l 14 GLN l 97 ASN M 328 GLN M 436 GLN m 97 ASN N 328 GLN N 436 GLN n 14 GLN n 97 ASN O 328 GLN O 436 GLN O 516 HIS o 97 ASN P 328 GLN ** P 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 436 GLN p 14 GLN p 97 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 43328 Z= 0.174 Angle : 0.612 6.163 58576 Z= 0.307 Chirality : 0.040 0.137 6608 Planarity : 0.005 0.041 7536 Dihedral : 4.886 23.776 6026 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.65 % Allowed : 11.88 % Favored : 86.47 % 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 (0.11), residues: 5360 helix: -0.42 (0.11), residues: 2304 sheet: -1.50 (0.16), residues: 976 loop : -1.33 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 103 HIS 0.005 0.001 HIS E 516 PHE 0.008 0.001 PHE H 466 TYR 0.010 0.001 TYR h 54 ARG 0.008 0.001 ARG L 543 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1054 time to evaluate : 5.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 ASN cc_start: 0.8739 (t0) cc_final: 0.8289 (t0) REVERT: A 516 HIS cc_start: 0.8285 (p90) cc_final: 0.7971 (p90) REVERT: a 4 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8609 (mm-40) REVERT: a 73 ASP cc_start: 0.8243 (t0) cc_final: 0.7949 (t0) REVERT: a 77 ASN cc_start: 0.9007 (m-40) cc_final: 0.8638 (m-40) REVERT: a 78 THR cc_start: 0.9353 (m) cc_final: 0.9111 (m) REVERT: B 439 ASP cc_start: 0.8250 (p0) cc_final: 0.7935 (p0) REVERT: B 484 ARG cc_start: 0.8079 (tpp-160) cc_final: 0.7806 (mmp80) REVERT: B 516 HIS cc_start: 0.8024 (p90) cc_final: 0.7392 (p-80) REVERT: B 517 ARG cc_start: 0.8431 (ptm160) cc_final: 0.8182 (ptp-110) REVERT: b 4 GLN cc_start: 0.8742 (mp10) cc_final: 0.8463 (mp10) REVERT: b 87 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7950 (mppt) REVERT: C 439 ASP cc_start: 0.8145 (p0) cc_final: 0.7903 (p0) REVERT: C 486 ASN cc_start: 0.8780 (t0) cc_final: 0.8430 (t0) REVERT: c 4 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8606 (mp10) REVERT: c 77 ASN cc_start: 0.9063 (m-40) cc_final: 0.8684 (m-40) REVERT: c 86 LEU cc_start: 0.8956 (mt) cc_final: 0.8507 (mp) REVERT: c 87 LYS cc_start: 0.8407 (mmtt) cc_final: 0.7893 (mppt) REVERT: D 439 ASP cc_start: 0.8297 (p0) cc_final: 0.7927 (p0) REVERT: D 486 ASN cc_start: 0.8728 (t0) cc_final: 0.8475 (t0) REVERT: d 7 GLU cc_start: 0.8442 (mp0) cc_final: 0.8020 (mp0) REVERT: d 73 ASP cc_start: 0.8007 (t70) cc_final: 0.7792 (t0) REVERT: d 87 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7723 (mppt) REVERT: E 486 ASN cc_start: 0.8738 (t0) cc_final: 0.8341 (t0) REVERT: e 4 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8480 (mm-40) REVERT: e 7 GLU cc_start: 0.8377 (mp0) cc_final: 0.7848 (mp0) REVERT: e 14 GLN cc_start: 0.8709 (pm20) cc_final: 0.8273 (mp10) REVERT: e 77 ASN cc_start: 0.9033 (m-40) cc_final: 0.8668 (m-40) REVERT: e 105 GLN cc_start: 0.7775 (pm20) cc_final: 0.7555 (pm20) REVERT: F 486 ASN cc_start: 0.8727 (t0) cc_final: 0.8432 (t0) REVERT: f 4 GLN cc_start: 0.8710 (mp10) cc_final: 0.8426 (mp10) REVERT: f 86 LEU cc_start: 0.9110 (mt) cc_final: 0.8835 (mm) REVERT: f 87 LYS cc_start: 0.8256 (mmtt) cc_final: 0.7755 (mppt) REVERT: G 486 ASN cc_start: 0.8762 (t0) cc_final: 0.8383 (t0) REVERT: g 4 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8450 (mm-40) REVERT: g 14 GLN cc_start: 0.8756 (pm20) cc_final: 0.8422 (mp10) REVERT: g 73 ASP cc_start: 0.8235 (t70) cc_final: 0.7976 (t0) REVERT: g 76 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8971 (pmtt) REVERT: g 77 ASN cc_start: 0.8980 (m-40) cc_final: 0.8586 (m110) REVERT: H 486 ASN cc_start: 0.8816 (t0) cc_final: 0.8594 (t0) REVERT: h 4 GLN cc_start: 0.8775 (mp10) cc_final: 0.8499 (mp10) REVERT: h 86 LEU cc_start: 0.9056 (mt) cc_final: 0.8851 (mm) REVERT: h 87 LYS cc_start: 0.8319 (mmtt) cc_final: 0.8015 (mppt) REVERT: I 516 HIS cc_start: 0.7977 (p-80) cc_final: 0.7713 (p90) REVERT: I 517 ARG cc_start: 0.8268 (ptp-170) cc_final: 0.7842 (ptp-170) REVERT: i 7 GLU cc_start: 0.8134 (mp0) cc_final: 0.7861 (mp0) REVERT: i 73 ASP cc_start: 0.8345 (t0) cc_final: 0.8129 (t0) REVERT: i 86 LEU cc_start: 0.9021 (mt) cc_final: 0.8781 (mm) REVERT: i 87 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7914 (mppt) REVERT: j 4 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8493 (mm-40) REVERT: j 7 GLU cc_start: 0.8137 (mp0) cc_final: 0.7929 (mp0) REVERT: j 73 ASP cc_start: 0.8050 (t0) cc_final: 0.7633 (t0) REVERT: j 86 LEU cc_start: 0.9188 (mt) cc_final: 0.8758 (mm) REVERT: j 87 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7858 (mppt) REVERT: K 486 ASN cc_start: 0.8786 (t0) cc_final: 0.8539 (t0) REVERT: K 516 HIS cc_start: 0.8267 (p-80) cc_final: 0.6841 (p90) REVERT: k 14 GLN cc_start: 0.8584 (pm20) cc_final: 0.8217 (mp10) REVERT: k 86 LEU cc_start: 0.9190 (mt) cc_final: 0.8830 (mm) REVERT: k 87 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8018 (mppt) REVERT: L 486 ASN cc_start: 0.8657 (t0) cc_final: 0.8270 (t0) REVERT: l 4 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8423 (mm-40) REVERT: l 86 LEU cc_start: 0.9189 (mt) cc_final: 0.8876 (mm) REVERT: l 87 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7814 (mppt) REVERT: l 105 GLN cc_start: 0.7862 (pm20) cc_final: 0.7556 (mp10) REVERT: M 486 ASN cc_start: 0.8749 (t0) cc_final: 0.8451 (t0) REVERT: m 14 GLN cc_start: 0.8546 (pm20) cc_final: 0.8282 (mp10) REVERT: m 86 LEU cc_start: 0.9157 (mt) cc_final: 0.8790 (mm) REVERT: m 87 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8106 (mppt) REVERT: N 486 ASN cc_start: 0.8670 (t0) cc_final: 0.8387 (t0) REVERT: n 7 GLU cc_start: 0.8310 (mp0) cc_final: 0.7846 (mp0) REVERT: n 46 ARG cc_start: 0.8468 (mtt90) cc_final: 0.8259 (mtt90) REVERT: n 73 ASP cc_start: 0.8157 (t0) cc_final: 0.7719 (t0) REVERT: n 86 LEU cc_start: 0.9137 (mt) cc_final: 0.8904 (mm) REVERT: n 87 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7739 (mppt) REVERT: n 105 GLN cc_start: 0.7927 (pm20) cc_final: 0.7285 (pm20) REVERT: O 516 HIS cc_start: 0.8008 (p-80) cc_final: 0.7537 (p-80) REVERT: O 517 ARG cc_start: 0.8227 (ptp-170) cc_final: 0.7947 (ptp-110) REVERT: o 14 GLN cc_start: 0.8655 (pm20) cc_final: 0.8440 (mp10) REVERT: o 86 LEU cc_start: 0.9094 (mt) cc_final: 0.8731 (mm) REVERT: o 87 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8056 (mppt) REVERT: p 4 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8477 (mm-40) REVERT: p 7 GLU cc_start: 0.8172 (mp0) cc_final: 0.7658 (mp0) REVERT: p 73 ASP cc_start: 0.8334 (t0) cc_final: 0.7996 (t0) REVERT: p 86 LEU cc_start: 0.9103 (mt) cc_final: 0.8760 (mm) REVERT: p 87 LYS cc_start: 0.8397 (mmtt) cc_final: 0.7971 (mppt) REVERT: p 105 GLN cc_start: 0.7811 (pm20) cc_final: 0.7600 (pm20) outliers start: 77 outliers final: 24 residues processed: 1078 average time/residue: 1.5067 time to fit residues: 1986.2184 Evaluate side-chains 954 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 928 time to evaluate : 5.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain c residue 4 GLN Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 76 LYS Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain I residue 481 THR Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 21 LEU Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 399 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 chunk 132 optimal weight: 40.0000 chunk 480 optimal weight: 2.9990 chunk 518 optimal weight: 0.9990 chunk 427 optimal weight: 8.9990 chunk 476 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 385 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 GLN ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 105 GLN i 4 GLN J 418 GLN ** J 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 105 GLN k 4 GLN k 105 GLN ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 43328 Z= 0.412 Angle : 0.647 8.014 58576 Z= 0.331 Chirality : 0.044 0.144 6608 Planarity : 0.004 0.058 7536 Dihedral : 5.023 26.693 6016 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.95 % Allowed : 13.77 % Favored : 82.28 % 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: -1.08 (0.12), residues: 5360 helix: -0.05 (0.11), residues: 2304 sheet: -1.31 (0.16), residues: 992 loop : -0.99 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP a 103 HIS 0.008 0.001 HIS P 516 PHE 0.010 0.001 PHE P 466 TYR 0.017 0.002 TYR M 479 ARG 0.008 0.001 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 914 time to evaluate : 4.754 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: A 486 ASN cc_start: 0.8793 (t0) cc_final: 0.8462 (t0) REVERT: a 4 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8736 (mm-40) REVERT: a 73 ASP cc_start: 0.8351 (t0) cc_final: 0.8004 (t0) REVERT: a 77 ASN cc_start: 0.9035 (m-40) cc_final: 0.8685 (m-40) REVERT: a 78 THR cc_start: 0.9356 (m) cc_final: 0.9139 (m) REVERT: B 423 GLN cc_start: 0.8756 (tt0) cc_final: 0.8534 (tt0) REVERT: B 439 ASP cc_start: 0.8319 (p0) cc_final: 0.8088 (p0) REVERT: b 73 ASP cc_start: 0.8224 (t0) cc_final: 0.7683 (t0) REVERT: C 486 ASN cc_start: 0.8788 (t0) cc_final: 0.8567 (t0) REVERT: c 76 LYS cc_start: 0.9196 (pmtt) cc_final: 0.8988 (pmtt) REVERT: c 77 ASN cc_start: 0.9046 (m-40) cc_final: 0.8719 (m-40) REVERT: c 78 THR cc_start: 0.9390 (m) cc_final: 0.9134 (m) REVERT: c 86 LEU cc_start: 0.9106 (mt) cc_final: 0.8898 (mm) REVERT: c 87 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8351 (ttmm) REVERT: c 89 GLU cc_start: 0.8642 (pm20) cc_final: 0.8181 (pm20) REVERT: D 423 GLN cc_start: 0.8782 (tt0) cc_final: 0.8554 (tt0) REVERT: D 439 ASP cc_start: 0.8343 (p0) cc_final: 0.8085 (p0) REVERT: D 486 ASN cc_start: 0.8826 (t0) cc_final: 0.8552 (t0) REVERT: d 73 ASP cc_start: 0.8253 (t70) cc_final: 0.7989 (t0) REVERT: d 76 LYS cc_start: 0.9287 (pmmt) cc_final: 0.9080 (pmtt) REVERT: E 486 ASN cc_start: 0.8797 (t0) cc_final: 0.8593 (t0) REVERT: e 4 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8493 (mm-40) REVERT: e 14 GLN cc_start: 0.8676 (pm20) cc_final: 0.8306 (mp10) REVERT: e 77 ASN cc_start: 0.9040 (m-40) cc_final: 0.8742 (m-40) REVERT: e 78 THR cc_start: 0.9390 (m) cc_final: 0.9124 (m) REVERT: F 486 ASN cc_start: 0.8827 (t0) cc_final: 0.8607 (t0) REVERT: f 4 GLN cc_start: 0.8784 (mp10) cc_final: 0.8480 (mp10) REVERT: f 73 ASP cc_start: 0.8261 (t0) cc_final: 0.7618 (t0) REVERT: G 486 ASN cc_start: 0.8768 (t0) cc_final: 0.8529 (t0) REVERT: g 4 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8556 (mm-40) REVERT: g 7 GLU cc_start: 0.8388 (mp0) cc_final: 0.8165 (mp0) REVERT: g 14 GLN cc_start: 0.8690 (pm20) cc_final: 0.8365 (mp10) REVERT: g 73 ASP cc_start: 0.8322 (t70) cc_final: 0.8098 (t0) REVERT: g 77 ASN cc_start: 0.9044 (m-40) cc_final: 0.8618 (m110) REVERT: h 4 GLN cc_start: 0.8834 (mp10) cc_final: 0.8538 (mp10) REVERT: h 73 ASP cc_start: 0.8284 (t0) cc_final: 0.7614 (t0) REVERT: h 76 LYS cc_start: 0.9269 (pmmt) cc_final: 0.9055 (pmtt) REVERT: I 516 HIS cc_start: 0.8167 (p-80) cc_final: 0.7387 (p90) REVERT: I 517 ARG cc_start: 0.8233 (ptp-110) cc_final: 0.7653 (ptp-110) REVERT: i 4 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8444 (mm-40) REVERT: i 73 ASP cc_start: 0.8426 (t0) cc_final: 0.8224 (t0) REVERT: i 86 LEU cc_start: 0.9135 (mt) cc_final: 0.8779 (mm) REVERT: i 87 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8035 (mppt) REVERT: j 4 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8501 (mm-40) REVERT: j 73 ASP cc_start: 0.8317 (t0) cc_final: 0.8076 (t0) REVERT: j 86 LEU cc_start: 0.9222 (mt) cc_final: 0.9021 (mm) REVERT: K 486 ASN cc_start: 0.8811 (t0) cc_final: 0.8533 (t0) REVERT: k 4 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8506 (mm-40) REVERT: k 14 GLN cc_start: 0.8653 (pm20) cc_final: 0.8256 (mp10) REVERT: k 86 LEU cc_start: 0.9240 (mt) cc_final: 0.8929 (mm) REVERT: k 87 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8022 (mppt) REVERT: L 486 ASN cc_start: 0.8749 (t0) cc_final: 0.8181 (t0) REVERT: l 4 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8501 (mm-40) REVERT: l 7 GLU cc_start: 0.8144 (mp0) cc_final: 0.7830 (mp0) REVERT: l 73 ASP cc_start: 0.8419 (t0) cc_final: 0.8200 (t0) REVERT: l 86 LEU cc_start: 0.9229 (mt) cc_final: 0.8932 (mm) REVERT: l 87 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8000 (mppt) REVERT: M 486 ASN cc_start: 0.8835 (t0) cc_final: 0.8623 (t0) REVERT: m 14 GLN cc_start: 0.8651 (pm20) cc_final: 0.8323 (mp10) REVERT: m 86 LEU cc_start: 0.9218 (mt) cc_final: 0.8904 (mm) REVERT: m 87 LYS cc_start: 0.8518 (mmtt) cc_final: 0.8072 (mppt) REVERT: N 423 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8551 (tt0) REVERT: n 7 GLU cc_start: 0.8388 (mp0) cc_final: 0.7832 (mp0) REVERT: n 46 ARG cc_start: 0.8525 (mtt90) cc_final: 0.8297 (mtt90) REVERT: n 73 ASP cc_start: 0.8288 (t0) cc_final: 0.8025 (t0) REVERT: n 86 LEU cc_start: 0.9197 (mt) cc_final: 0.8914 (mm) REVERT: n 87 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8038 (mppt) REVERT: n 105 GLN cc_start: 0.7871 (pm20) cc_final: 0.7141 (pm20) REVERT: O 516 HIS cc_start: 0.8228 (p-80) cc_final: 0.7525 (p90) REVERT: O 517 ARG cc_start: 0.8244 (ptp-170) cc_final: 0.7746 (ptp-170) REVERT: o 14 GLN cc_start: 0.8657 (pm20) cc_final: 0.8357 (mp10) REVERT: P 439 ASP cc_start: 0.8329 (p0) cc_final: 0.8099 (p0) REVERT: P 516 HIS cc_start: 0.8400 (p90) cc_final: 0.8104 (p90) REVERT: P 517 ARG cc_start: 0.8424 (ptp-170) cc_final: 0.8216 (ptp-110) REVERT: p 4 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8494 (mm-40) REVERT: p 86 LEU cc_start: 0.9261 (mt) cc_final: 0.8983 (mm) REVERT: p 87 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8060 (mppt) REVERT: p 105 GLN cc_start: 0.7860 (pm20) cc_final: 0.7550 (pm20) outliers start: 184 outliers final: 78 residues processed: 989 average time/residue: 1.5413 time to fit residues: 1858.3991 Evaluate side-chains 931 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 852 time to evaluate : 5.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 508 CYS Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 439 ASP Chi-restraints excluded: chain F residue 508 CYS Chi-restraints excluded: chain f residue 21 LEU Chi-restraints excluded: chain f residue 69 THR Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 69 THR Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain I residue 481 THR Chi-restraints excluded: chain I residue 502 THR Chi-restraints excluded: chain I residue 508 CYS Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 502 THR Chi-restraints excluded: chain J residue 505 LEU Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 508 CYS Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 21 LEU Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain M residue 502 THR Chi-restraints excluded: chain M residue 508 CYS Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 69 THR Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain N residue 423 GLN Chi-restraints excluded: chain N residue 502 THR Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain O residue 481 THR Chi-restraints excluded: chain O residue 502 THR Chi-restraints excluded: chain O residue 508 CYS Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain P residue 378 VAL Chi-restraints excluded: chain P residue 481 THR Chi-restraints excluded: chain P residue 502 THR Chi-restraints excluded: chain p residue 21 LEU Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 2.9990 chunk 361 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 322 optimal weight: 1.9990 chunk 482 optimal weight: 0.0060 chunk 510 optimal weight: 0.6980 chunk 251 optimal weight: 2.9990 chunk 456 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 GLN ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 105 GLN ** H 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 105 GLN i 105 GLN ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 105 GLN ** l 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 43328 Z= 0.200 Angle : 0.576 8.442 58576 Z= 0.289 Chirality : 0.039 0.139 6608 Planarity : 0.004 0.037 7536 Dihedral : 4.725 24.183 6016 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.58 % Allowed : 17.44 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.12), residues: 5360 helix: 0.31 (0.11), residues: 2304 sheet: -1.27 (0.16), residues: 976 loop : -0.83 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 103 HIS 0.006 0.001 HIS K 516 PHE 0.006 0.001 PHE L 466 TYR 0.011 0.001 TYR h 54 ARG 0.008 0.000 ARG N 484 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 911 time to evaluate : 5.302 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: A 386 LYS cc_start: 0.8843 (ptmt) cc_final: 0.8163 (ptpp) REVERT: a 4 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8736 (mm-40) REVERT: a 73 ASP cc_start: 0.8323 (t0) cc_final: 0.7991 (t0) REVERT: a 77 ASN cc_start: 0.9012 (m-40) cc_final: 0.8672 (m-40) REVERT: a 89 GLU cc_start: 0.8655 (pm20) cc_final: 0.8406 (pm20) REVERT: B 423 GLN cc_start: 0.8638 (tt0) cc_final: 0.8393 (tt0) REVERT: B 439 ASP cc_start: 0.8236 (p0) cc_final: 0.7984 (p0) REVERT: B 486 ASN cc_start: 0.8720 (t0) cc_final: 0.8317 (t0) REVERT: b 4 GLN cc_start: 0.8817 (mp10) cc_final: 0.8580 (mp10) REVERT: c 4 GLN cc_start: 0.8835 (mp10) cc_final: 0.8587 (mp10) REVERT: c 77 ASN cc_start: 0.8999 (m-40) cc_final: 0.8689 (m-40) REVERT: c 78 THR cc_start: 0.9367 (m) cc_final: 0.9116 (m) REVERT: D 423 GLN cc_start: 0.8691 (tt0) cc_final: 0.8453 (tt0) REVERT: D 439 ASP cc_start: 0.8216 (p0) cc_final: 0.7979 (p0) REVERT: e 4 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8476 (mm-40) REVERT: e 14 GLN cc_start: 0.8725 (pm20) cc_final: 0.8288 (mp10) REVERT: e 77 ASN cc_start: 0.9011 (m-40) cc_final: 0.8716 (m-40) REVERT: e 78 THR cc_start: 0.9359 (m) cc_final: 0.9112 (m) REVERT: F 486 ASN cc_start: 0.8748 (t0) cc_final: 0.8539 (t0) REVERT: f 4 GLN cc_start: 0.8832 (mp10) cc_final: 0.8544 (mp10) REVERT: f 73 ASP cc_start: 0.8130 (t0) cc_final: 0.7911 (t0) REVERT: G 517 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8150 (ptm160) REVERT: g 4 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8547 (mm-40) REVERT: g 14 GLN cc_start: 0.8675 (pm20) cc_final: 0.8365 (mp10) REVERT: g 44 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8378 (mtmm) REVERT: g 73 ASP cc_start: 0.8296 (t70) cc_final: 0.8081 (t0) REVERT: g 77 ASN cc_start: 0.8994 (m-40) cc_final: 0.8571 (m110) REVERT: H 517 ARG cc_start: 0.8443 (ptm160) cc_final: 0.8174 (ptp-110) REVERT: h 73 ASP cc_start: 0.8195 (t0) cc_final: 0.7947 (t0) REVERT: I 516 HIS cc_start: 0.8166 (p-80) cc_final: 0.7485 (p90) REVERT: I 517 ARG cc_start: 0.8289 (ptp-110) cc_final: 0.7797 (ptp-110) REVERT: i 4 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8411 (mm-40) REVERT: i 89 GLU cc_start: 0.8626 (pm20) cc_final: 0.8387 (pm20) REVERT: J 517 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8209 (ptp-110) REVERT: j 4 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8417 (mm-40) REVERT: j 73 ASP cc_start: 0.8359 (t0) cc_final: 0.8138 (t0) REVERT: k 4 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8455 (mm-40) REVERT: k 14 GLN cc_start: 0.8617 (pm20) cc_final: 0.8244 (mp10) REVERT: L 486 ASN cc_start: 0.8642 (t0) cc_final: 0.7988 (t0) REVERT: l 4 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8487 (mm-40) REVERT: l 89 GLU cc_start: 0.8641 (pm20) cc_final: 0.8275 (pm20) REVERT: M 486 ASN cc_start: 0.8745 (t0) cc_final: 0.8526 (t0) REVERT: m 4 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8418 (mm110) REVERT: m 14 GLN cc_start: 0.8587 (pm20) cc_final: 0.8288 (mp10) REVERT: n 73 ASP cc_start: 0.8354 (t0) cc_final: 0.8125 (t0) REVERT: n 105 GLN cc_start: 0.7829 (pm20) cc_final: 0.7406 (mp10) REVERT: o 14 GLN cc_start: 0.8662 (pm20) cc_final: 0.8311 (mp10) REVERT: P 516 HIS cc_start: 0.8315 (p90) cc_final: 0.7810 (p90) REVERT: P 517 ARG cc_start: 0.8359 (ptp-110) cc_final: 0.8040 (ptp-110) REVERT: p 4 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8471 (mm-40) REVERT: p 89 GLU cc_start: 0.8786 (pm20) cc_final: 0.8576 (pm20) outliers start: 120 outliers final: 52 residues processed: 969 average time/residue: 1.5416 time to fit residues: 1830.8113 Evaluate side-chains 941 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 887 time to evaluate : 5.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 105 GLN Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 105 GLN Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 517 ARG Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain I residue 481 THR Chi-restraints excluded: chain I residue 523 LEU Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 517 ARG Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain K residue 523 LEU Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain l residue 21 LEU Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain O residue 481 THR Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain p residue 12 LEU Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 6.9990 chunk 289 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 380 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 435 optimal weight: 0.0970 chunk 352 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 260 optimal weight: 0.5980 chunk 458 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 ASN ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 486 ASN ** H 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 105 GLN ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 105 GLN ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 GLN ** O 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43328 Z= 0.220 Angle : 0.580 8.707 58576 Z= 0.292 Chirality : 0.040 0.131 6608 Planarity : 0.003 0.041 7536 Dihedral : 4.618 22.920 6016 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.79 % Allowed : 18.28 % Favored : 78.93 % 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: -0.47 (0.12), residues: 5360 helix: 0.50 (0.11), residues: 2304 sheet: -1.13 (0.17), residues: 976 loop : -0.66 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP n 103 HIS 0.004 0.001 HIS D 516 PHE 0.007 0.001 PHE k 68 TYR 0.011 0.001 TYR o 80 ARG 0.007 0.000 ARG m 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 910 time to evaluate : 5.124 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: A 386 LYS cc_start: 0.8848 (ptmt) cc_final: 0.8179 (ptpp) REVERT: A 486 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8638 (t0) REVERT: A 517 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8219 (pmm-80) REVERT: A 543 ARG cc_start: 0.8390 (ttm170) cc_final: 0.8039 (mtt-85) REVERT: a 4 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8691 (mm-40) REVERT: a 77 ASN cc_start: 0.9079 (m-40) cc_final: 0.8673 (m-40) REVERT: a 87 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7610 (ttmm) REVERT: a 89 GLU cc_start: 0.8638 (pm20) cc_final: 0.8238 (pm20) REVERT: B 423 GLN cc_start: 0.8666 (tt0) cc_final: 0.8440 (tt0) REVERT: B 439 ASP cc_start: 0.8214 (p0) cc_final: 0.7973 (p0) REVERT: C 486 ASN cc_start: 0.8884 (t0) cc_final: 0.8641 (t0) REVERT: c 4 GLN cc_start: 0.8848 (mp10) cc_final: 0.8644 (mp10) REVERT: c 77 ASN cc_start: 0.9005 (m-40) cc_final: 0.8686 (m-40) REVERT: c 78 THR cc_start: 0.9350 (m) cc_final: 0.9114 (m) REVERT: c 89 GLU cc_start: 0.8565 (pm20) cc_final: 0.8321 (pm20) REVERT: D 423 GLN cc_start: 0.8709 (tt0) cc_final: 0.8480 (tt0) REVERT: D 439 ASP cc_start: 0.8195 (p0) cc_final: 0.7967 (p0) REVERT: e 4 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8497 (mm-40) REVERT: e 14 GLN cc_start: 0.8683 (pm20) cc_final: 0.8309 (mp10) REVERT: e 77 ASN cc_start: 0.8982 (m-40) cc_final: 0.8687 (m-40) REVERT: e 78 THR cc_start: 0.9354 (m) cc_final: 0.9100 (m) REVERT: e 87 LYS cc_start: 0.8182 (mppt) cc_final: 0.7746 (ttmm) REVERT: F 543 ARG cc_start: 0.8374 (ttm170) cc_final: 0.8022 (mtt-85) REVERT: f 4 GLN cc_start: 0.8842 (mp10) cc_final: 0.8541 (mp10) REVERT: G 486 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8608 (t0) REVERT: g 4 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8527 (mm-40) REVERT: g 14 GLN cc_start: 0.8690 (pm20) cc_final: 0.8364 (mp10) REVERT: g 73 ASP cc_start: 0.8353 (t70) cc_final: 0.8079 (t0) REVERT: g 77 ASN cc_start: 0.8996 (m-40) cc_final: 0.8582 (m110) REVERT: g 89 GLU cc_start: 0.8564 (pm20) cc_final: 0.8355 (pm20) REVERT: i 4 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8391 (mm-40) REVERT: J 517 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8239 (ptp-110) REVERT: j 4 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8405 (mm-40) REVERT: j 73 ASP cc_start: 0.8400 (t0) cc_final: 0.8165 (t0) REVERT: k 4 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8459 (mm-40) REVERT: k 14 GLN cc_start: 0.8613 (pm20) cc_final: 0.8224 (mp10) REVERT: L 486 ASN cc_start: 0.8602 (t0) cc_final: 0.7968 (t0) REVERT: L 517 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8223 (ptp-110) REVERT: L 543 ARG cc_start: 0.8337 (ttm-80) cc_final: 0.8025 (mtt-85) REVERT: l 4 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8500 (mm-40) REVERT: M 486 ASN cc_start: 0.8669 (t0) cc_final: 0.8451 (t0) REVERT: m 4 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8517 (mm-40) REVERT: m 14 GLN cc_start: 0.8593 (pm20) cc_final: 0.8287 (mp10) REVERT: m 87 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8202 (ttmm) REVERT: N 517 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8165 (ptp-110) REVERT: n 7 GLU cc_start: 0.8011 (mp0) cc_final: 0.7599 (mp0) REVERT: n 73 ASP cc_start: 0.8390 (t0) cc_final: 0.8189 (t0) REVERT: o 14 GLN cc_start: 0.8656 (pm20) cc_final: 0.8364 (mp10) REVERT: P 516 HIS cc_start: 0.8322 (p90) cc_final: 0.7776 (p90) REVERT: P 517 ARG cc_start: 0.8361 (ptp-110) cc_final: 0.8024 (ptp-110) REVERT: p 4 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8459 (mm-40) outliers start: 130 outliers final: 64 residues processed: 962 average time/residue: 1.5603 time to fit residues: 1826.5018 Evaluate side-chains 938 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 866 time to evaluate : 4.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 87 LYS Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 486 ASN Chi-restraints excluded: chain G residue 544 GLU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain I residue 481 THR Chi-restraints excluded: chain I residue 544 GLU Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 505 LEU Chi-restraints excluded: chain J residue 517 ARG Chi-restraints excluded: chain J residue 545 MET Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain K residue 523 LEU Chi-restraints excluded: chain K residue 544 GLU Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 21 LEU Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 87 LYS Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain O residue 481 THR Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain P residue 378 VAL Chi-restraints excluded: chain P residue 481 THR Chi-restraints excluded: chain p residue 12 LEU Chi-restraints excluded: chain p residue 21 LEU Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 8.9990 chunk 459 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 299 optimal weight: 20.0000 chunk 125 optimal weight: 0.5980 chunk 510 optimal weight: 0.7980 chunk 424 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 chunk 268 optimal weight: 6.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 105 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 105 GLN ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 105 GLN ** I 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 105 GLN ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 105 GLN ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 43328 Z= 0.373 Angle : 0.629 9.434 58576 Z= 0.320 Chirality : 0.042 0.136 6608 Planarity : 0.004 0.047 7536 Dihedral : 4.798 26.256 6016 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.74 % Allowed : 19.31 % Favored : 76.95 % 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: -0.40 (0.12), residues: 5360 helix: 0.54 (0.11), residues: 2336 sheet: -1.17 (0.17), residues: 976 loop : -0.56 (0.15), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 103 HIS 0.006 0.001 HIS F 516 PHE 0.008 0.001 PHE p 68 TYR 0.016 0.002 TYR K 479 ARG 0.007 0.000 ARG m 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 871 time to evaluate : 4.965 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: A 386 LYS cc_start: 0.8802 (ptmt) cc_final: 0.8093 (ptpp) REVERT: a 4 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8764 (mm-40) REVERT: a 7 GLU cc_start: 0.8416 (mp0) cc_final: 0.8131 (mp0) REVERT: a 73 ASP cc_start: 0.8468 (t0) cc_final: 0.7922 (t0) REVERT: a 76 LYS cc_start: 0.9289 (pmmt) cc_final: 0.8978 (pmtt) REVERT: a 77 ASN cc_start: 0.9034 (m-40) cc_final: 0.8700 (m-40) REVERT: a 78 THR cc_start: 0.9383 (m) cc_final: 0.9150 (m) REVERT: a 87 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7905 (ttmm) REVERT: a 89 GLU cc_start: 0.8664 (pm20) cc_final: 0.8197 (pm20) REVERT: a 105 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7330 (pm20) REVERT: B 423 GLN cc_start: 0.8755 (tt0) cc_final: 0.8551 (tt0) REVERT: B 439 ASP cc_start: 0.8308 (p0) cc_final: 0.8035 (p0) REVERT: c 7 GLU cc_start: 0.8388 (mp0) cc_final: 0.8005 (mp0) REVERT: c 77 ASN cc_start: 0.9012 (m-40) cc_final: 0.8718 (m-40) REVERT: c 78 THR cc_start: 0.9348 (m) cc_final: 0.9127 (m) REVERT: c 105 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: D 423 GLN cc_start: 0.8775 (tt0) cc_final: 0.8556 (tt0) REVERT: D 439 ASP cc_start: 0.8296 (p0) cc_final: 0.8037 (p0) REVERT: d 4 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8374 (mp10) REVERT: d 35 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8140 (mtp) REVERT: e 4 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8545 (mm-40) REVERT: e 7 GLU cc_start: 0.8077 (mp0) cc_final: 0.7836 (mp0) REVERT: e 14 GLN cc_start: 0.8642 (pm20) cc_final: 0.8245 (mp10) REVERT: e 73 ASP cc_start: 0.8396 (t0) cc_final: 0.8163 (t0) REVERT: e 77 ASN cc_start: 0.8996 (m-40) cc_final: 0.8705 (m-40) REVERT: e 78 THR cc_start: 0.9344 (m) cc_final: 0.9104 (m) REVERT: e 87 LYS cc_start: 0.8295 (mppt) cc_final: 0.7965 (ttmm) REVERT: F 486 ASN cc_start: 0.8970 (t0) cc_final: 0.8689 (t0) REVERT: f 4 GLN cc_start: 0.8870 (mp10) cc_final: 0.8618 (mp10) REVERT: f 83 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8271 (mtp) REVERT: G 517 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8209 (ptm160) REVERT: g 14 GLN cc_start: 0.8651 (pm20) cc_final: 0.8350 (mp10) REVERT: g 73 ASP cc_start: 0.8382 (t70) cc_final: 0.8086 (t0) REVERT: g 76 LYS cc_start: 0.9316 (pmtt) cc_final: 0.9102 (pmtt) REVERT: g 77 ASN cc_start: 0.9007 (m-40) cc_final: 0.8603 (m110) REVERT: H 489 ASP cc_start: 0.8155 (p0) cc_final: 0.7887 (p0) REVERT: H 517 ARG cc_start: 0.8404 (ptm160) cc_final: 0.8134 (ptp-110) REVERT: i 4 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8406 (mm-40) REVERT: i 87 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7922 (ttmm) REVERT: i 89 GLU cc_start: 0.8657 (pm20) cc_final: 0.8361 (pm20) REVERT: J 489 ASP cc_start: 0.7987 (p0) cc_final: 0.7730 (p0) REVERT: j 4 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8408 (mm-40) REVERT: j 7 GLU cc_start: 0.8106 (mp0) cc_final: 0.7644 (mp0) REVERT: k 4 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8494 (mm-40) REVERT: k 14 GLN cc_start: 0.8647 (pm20) cc_final: 0.8288 (mp10) REVERT: L 486 ASN cc_start: 0.8581 (t0) cc_final: 0.7970 (t0) REVERT: L 517 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8271 (ptp-110) REVERT: l 4 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8542 (mm-40) REVERT: m 4 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8610 (mm-40) REVERT: m 14 GLN cc_start: 0.8628 (pm20) cc_final: 0.8276 (mp10) REVERT: m 87 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8204 (ttmm) REVERT: N 516 HIS cc_start: 0.8348 (p-80) cc_final: 0.7413 (p90) REVERT: N 517 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8243 (ptp-110) REVERT: o 14 GLN cc_start: 0.8658 (pm20) cc_final: 0.8340 (mp10) REVERT: P 516 HIS cc_start: 0.8346 (p90) cc_final: 0.7679 (p90) REVERT: P 517 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7992 (ptp-110) REVERT: p 4 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8421 (mm-40) REVERT: p 7 GLU cc_start: 0.8156 (mp0) cc_final: 0.7926 (mp0) outliers start: 174 outliers final: 83 residues processed: 947 average time/residue: 1.5284 time to fit residues: 1762.4766 Evaluate side-chains 953 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 859 time to evaluate : 5.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 87 LYS Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain a residue 105 GLN Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 83 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 105 GLN Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 59 ASN Chi-restraints excluded: chain f residue 83 MET Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 517 ARG Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 544 GLU Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain I residue 481 THR Chi-restraints excluded: chain I residue 517 ARG Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 87 LYS Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain J residue 385 THR Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 502 THR Chi-restraints excluded: chain J residue 517 ARG Chi-restraints excluded: chain J residue 545 MET Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 375 LYS Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain L residue 545 MET Chi-restraints excluded: chain l residue 62 ASP Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 21 LEU Chi-restraints excluded: chain m residue 87 LYS Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain N residue 545 MET Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain O residue 481 THR Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain o residue 102 THR Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain P residue 378 VAL Chi-restraints excluded: chain P residue 481 THR Chi-restraints excluded: chain P residue 517 ARG Chi-restraints excluded: chain p residue 12 LEU Chi-restraints excluded: chain p residue 83 MET Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 291 optimal weight: 0.6980 chunk 373 optimal weight: 0.5980 chunk 289 optimal weight: 0.6980 chunk 430 optimal weight: 9.9990 chunk 285 optimal weight: 0.9980 chunk 508 optimal weight: 0.9990 chunk 318 optimal weight: 0.7980 chunk 310 optimal weight: 0.8980 chunk 234 optimal weight: 30.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN a 105 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 105 GLN ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 486 ASN ** H 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 105 GLN ** I 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 105 GLN ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 105 GLN ** N 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 GLN ** O 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43328 Z= 0.165 Angle : 0.601 10.174 58576 Z= 0.298 Chirality : 0.039 0.182 6608 Planarity : 0.004 0.040 7536 Dihedral : 4.543 24.136 6016 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.49 % Allowed : 21.18 % Favored : 76.33 % 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: -0.22 (0.12), residues: 5360 helix: 0.65 (0.11), residues: 2368 sheet: -1.10 (0.17), residues: 976 loop : -0.42 (0.15), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 103 HIS 0.004 0.001 HIS D 516 PHE 0.008 0.001 PHE d 68 TYR 0.011 0.001 TYR o 80 ARG 0.007 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 949 time to evaluate : 5.339 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: A 386 LYS cc_start: 0.8806 (ptmt) cc_final: 0.8096 (ptpp) REVERT: A 543 ARG cc_start: 0.8359 (ttm170) cc_final: 0.7986 (mtt-85) REVERT: a 4 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8660 (mm-40) REVERT: a 73 ASP cc_start: 0.8463 (t0) cc_final: 0.7857 (t0) REVERT: a 76 LYS cc_start: 0.9307 (pmmt) cc_final: 0.9005 (pmtt) REVERT: a 77 ASN cc_start: 0.8981 (m-40) cc_final: 0.8692 (m-40) REVERT: a 78 THR cc_start: 0.9333 (m) cc_final: 0.9086 (m) REVERT: a 87 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7454 (ttmm) REVERT: a 89 GLU cc_start: 0.8673 (pm20) cc_final: 0.8234 (pm20) REVERT: B 439 ASP cc_start: 0.8166 (p0) cc_final: 0.7908 (p0) REVERT: C 543 ARG cc_start: 0.8338 (ttm170) cc_final: 0.7950 (mtt-85) REVERT: c 4 GLN cc_start: 0.8807 (mp10) cc_final: 0.8530 (mp10) REVERT: c 77 ASN cc_start: 0.8955 (m-40) cc_final: 0.8669 (m-40) REVERT: c 78 THR cc_start: 0.9314 (m) cc_final: 0.9070 (m) REVERT: c 87 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7809 (ttmm) REVERT: D 439 ASP cc_start: 0.8165 (p0) cc_final: 0.7930 (p0) REVERT: D 489 ASP cc_start: 0.8113 (p0) cc_final: 0.7893 (p0) REVERT: d 4 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8365 (mp10) REVERT: E 450 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: e 14 GLN cc_start: 0.8685 (pm20) cc_final: 0.8322 (mp10) REVERT: e 77 ASN cc_start: 0.8957 (m-40) cc_final: 0.8645 (m110) REVERT: e 78 THR cc_start: 0.9312 (m) cc_final: 0.9062 (m) REVERT: e 87 LYS cc_start: 0.7912 (mppt) cc_final: 0.7580 (ttmm) REVERT: F 486 ASN cc_start: 0.8888 (t0) cc_final: 0.8650 (t0) REVERT: f 4 GLN cc_start: 0.8871 (mp10) cc_final: 0.8568 (mp10) REVERT: g 14 GLN cc_start: 0.8633 (pm20) cc_final: 0.8334 (mp10) REVERT: g 73 ASP cc_start: 0.8309 (t70) cc_final: 0.8096 (t0) REVERT: g 77 ASN cc_start: 0.8986 (m-40) cc_final: 0.8674 (m-40) REVERT: g 87 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7826 (ttmm) REVERT: i 4 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8285 (mm-40) REVERT: J 517 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8233 (ptp-110) REVERT: j 4 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8424 (mm-40) REVERT: k 4 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8429 (mm-40) REVERT: k 14 GLN cc_start: 0.8608 (pm20) cc_final: 0.8243 (mp10) REVERT: k 87 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7855 (ttmm) REVERT: L 423 GLN cc_start: 0.8683 (tt0) cc_final: 0.8356 (tt0) REVERT: L 486 ASN cc_start: 0.8498 (t0) cc_final: 0.8161 (t0) REVERT: L 517 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8221 (ptp-110) REVERT: L 543 ARG cc_start: 0.8308 (ttm-80) cc_final: 0.8041 (mtt-85) REVERT: l 4 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8521 (mm-40) REVERT: l 77 ASN cc_start: 0.8837 (m-40) cc_final: 0.8493 (m110) REVERT: m 4 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8598 (mm-40) REVERT: m 14 GLN cc_start: 0.8577 (pm20) cc_final: 0.8242 (mp10) REVERT: m 87 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7874 (ttmm) REVERT: N 516 HIS cc_start: 0.8388 (p-80) cc_final: 0.7187 (p90) REVERT: N 517 ARG cc_start: 0.8458 (pmm-80) cc_final: 0.8163 (ptp-170) REVERT: n 4 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8697 (mm-40) REVERT: n 7 GLU cc_start: 0.8017 (mp0) cc_final: 0.7578 (mp0) REVERT: n 77 ASN cc_start: 0.8836 (m-40) cc_final: 0.8513 (m110) REVERT: o 14 GLN cc_start: 0.8629 (pm20) cc_final: 0.8368 (mp10) REVERT: P 516 HIS cc_start: 0.8326 (p90) cc_final: 0.7725 (p90) REVERT: P 517 ARG cc_start: 0.8320 (ptp-110) cc_final: 0.7979 (ptp-110) REVERT: p 4 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8482 (mm-40) outliers start: 116 outliers final: 73 residues processed: 992 average time/residue: 1.5316 time to fit residues: 1853.5239 Evaluate side-chains 996 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 917 time to evaluate : 4.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 87 LYS Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 517 ARG Chi-restraints excluded: chain G residue 544 GLU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 544 GLU Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 105 GLN Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain J residue 517 ARG Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 544 GLU Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 545 MET Chi-restraints excluded: chain l residue 21 LEU Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 87 LYS Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 545 MET Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain O residue 481 THR Chi-restraints excluded: chain O residue 544 GLU Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain o residue 102 THR Chi-restraints excluded: chain P residue 378 VAL Chi-restraints excluded: chain P residue 385 THR Chi-restraints excluded: chain p residue 83 MET Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 303 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 99 optimal weight: 30.0000 chunk 98 optimal weight: 0.7980 chunk 323 optimal weight: 0.2980 chunk 346 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 400 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 486 ASN ** H 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 105 GLN ** I 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 105 GLN ** J 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 105 GLN ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 105 GLN ** P 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43328 Z= 0.196 Angle : 0.609 10.679 58576 Z= 0.301 Chirality : 0.040 0.199 6608 Planarity : 0.004 0.039 7536 Dihedral : 4.494 22.232 6016 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.28 % Allowed : 21.93 % Favored : 75.79 % 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: -0.13 (0.12), residues: 5360 helix: 0.79 (0.11), residues: 2336 sheet: -1.05 (0.17), residues: 976 loop : -0.44 (0.15), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 490 HIS 0.005 0.001 HIS H 516 PHE 0.011 0.001 PHE d 68 TYR 0.010 0.001 TYR k 80 ARG 0.009 0.000 ARG E 543 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 922 time to evaluate : 5.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8808 (ptmt) cc_final: 0.8094 (ptpp) REVERT: A 486 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.7804 (t0) REVERT: A 543 ARG cc_start: 0.8362 (ttm170) cc_final: 0.8001 (mtt-85) REVERT: a 4 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8649 (mm-40) REVERT: a 73 ASP cc_start: 0.8412 (t0) cc_final: 0.7770 (t0) REVERT: a 76 LYS cc_start: 0.9309 (pmmt) cc_final: 0.9002 (pmtt) REVERT: a 77 ASN cc_start: 0.8972 (m-40) cc_final: 0.8687 (m-40) REVERT: a 78 THR cc_start: 0.9326 (m) cc_final: 0.9070 (m) REVERT: B 439 ASP cc_start: 0.8168 (p0) cc_final: 0.7917 (p0) REVERT: B 489 ASP cc_start: 0.8231 (p0) cc_final: 0.8015 (p0) REVERT: B 517 ARG cc_start: 0.8243 (ptp-110) cc_final: 0.7962 (ptp-110) REVERT: C 543 ARG cc_start: 0.8349 (ttm170) cc_final: 0.7972 (mtt-85) REVERT: c 77 ASN cc_start: 0.8919 (m-40) cc_final: 0.8667 (m-40) REVERT: c 78 THR cc_start: 0.9303 (m) cc_final: 0.9058 (m) REVERT: c 87 LYS cc_start: 0.8043 (ttmm) cc_final: 0.7792 (ttmm) REVERT: D 439 ASP cc_start: 0.8159 (p0) cc_final: 0.7921 (p0) REVERT: d 4 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8366 (mp10) REVERT: E 450 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: e 7 GLU cc_start: 0.8066 (mp0) cc_final: 0.7589 (mp0) REVERT: e 14 GLN cc_start: 0.8669 (pm20) cc_final: 0.8326 (mp10) REVERT: e 77 ASN cc_start: 0.8923 (m-40) cc_final: 0.8690 (m-40) REVERT: e 78 THR cc_start: 0.9303 (m) cc_final: 0.9049 (m) REVERT: e 87 LYS cc_start: 0.7860 (mppt) cc_final: 0.7556 (ttmm) REVERT: e 89 GLU cc_start: 0.8662 (pm20) cc_final: 0.8438 (pm20) REVERT: e 105 GLN cc_start: 0.7455 (mp10) cc_final: 0.7195 (pm20) REVERT: f 4 GLN cc_start: 0.8880 (mp10) cc_final: 0.8622 (mp10) REVERT: G 486 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.7723 (t0) REVERT: G 517 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8143 (ptm160) REVERT: g 7 GLU cc_start: 0.8356 (mp0) cc_final: 0.7998 (mp0) REVERT: g 14 GLN cc_start: 0.8645 (pm20) cc_final: 0.8360 (mp10) REVERT: g 73 ASP cc_start: 0.8384 (t70) cc_final: 0.8113 (t0) REVERT: g 77 ASN cc_start: 0.8981 (m-40) cc_final: 0.8603 (m110) REVERT: g 87 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7750 (ttmm) REVERT: g 105 GLN cc_start: 0.7726 (pm20) cc_final: 0.7443 (pm20) REVERT: i 4 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8286 (mm-40) REVERT: J 517 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8249 (ptp-110) REVERT: j 4 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8426 (mm-40) REVERT: j 7 GLU cc_start: 0.8037 (mp0) cc_final: 0.7781 (mp0) REVERT: K 484 ARG cc_start: 0.7972 (tpp-160) cc_final: 0.7756 (mmp80) REVERT: K 486 ASN cc_start: 0.8451 (t0) cc_final: 0.8025 (t0) REVERT: K 489 ASP cc_start: 0.8025 (p0) cc_final: 0.7599 (p0) REVERT: k 4 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8427 (mm-40) REVERT: k 14 GLN cc_start: 0.8610 (pm20) cc_final: 0.8246 (mp10) REVERT: k 89 GLU cc_start: 0.8736 (pm20) cc_final: 0.8532 (pm20) REVERT: L 423 GLN cc_start: 0.8694 (tt0) cc_final: 0.8359 (tt0) REVERT: L 486 ASN cc_start: 0.8484 (t0) cc_final: 0.8116 (t0) REVERT: L 517 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8291 (ptp-110) REVERT: L 543 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.8028 (mtt-85) REVERT: l 4 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8465 (mm-40) REVERT: l 7 GLU cc_start: 0.8019 (mp0) cc_final: 0.7599 (mp0) REVERT: l 77 ASN cc_start: 0.8840 (m-40) cc_final: 0.8501 (m110) REVERT: M 543 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.8028 (mtt-85) REVERT: m 4 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8638 (mm-40) REVERT: m 14 GLN cc_start: 0.8591 (pm20) cc_final: 0.8254 (mp10) REVERT: m 87 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7675 (ttmm) REVERT: N 516 HIS cc_start: 0.8394 (p-80) cc_final: 0.7199 (p90) REVERT: N 517 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8216 (ptp-170) REVERT: n 4 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8700 (mm-40) REVERT: n 77 ASN cc_start: 0.8825 (m-40) cc_final: 0.8512 (m110) REVERT: o 14 GLN cc_start: 0.8656 (pm20) cc_final: 0.8395 (mp10) REVERT: P 516 HIS cc_start: 0.8324 (p90) cc_final: 0.7699 (p90) REVERT: P 517 ARG cc_start: 0.8322 (ptp-110) cc_final: 0.7968 (ptp-110) REVERT: p 4 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8486 (mm-40) REVERT: p 7 GLU cc_start: 0.8044 (mp0) cc_final: 0.7596 (mp0) outliers start: 106 outliers final: 71 residues processed: 967 average time/residue: 1.5496 time to fit residues: 1828.9170 Evaluate side-chains 976 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 897 time to evaluate : 4.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 83 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 486 ASN Chi-restraints excluded: chain G residue 517 ARG Chi-restraints excluded: chain G residue 544 GLU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 544 GLU Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain I residue 481 THR Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain J residue 502 THR Chi-restraints excluded: chain J residue 517 ARG Chi-restraints excluded: chain J residue 544 GLU Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 523 LEU Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain l residue 21 LEU Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 87 LYS Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 502 THR Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain N residue 545 MET Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain O residue 481 THR Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain o residue 102 THR Chi-restraints excluded: chain P residue 385 THR Chi-restraints excluded: chain p residue 21 LEU Chi-restraints excluded: chain p residue 83 MET Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 30.0000 chunk 487 optimal weight: 3.9990 chunk 444 optimal weight: 0.7980 chunk 474 optimal weight: 1.9990 chunk 285 optimal weight: 0.7980 chunk 206 optimal weight: 5.9990 chunk 372 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 428 optimal weight: 4.9990 chunk 448 optimal weight: 0.8980 chunk 472 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 105 GLN ** I 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 105 GLN ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 105 GLN ** N 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 43328 Z= 0.190 Angle : 0.622 11.333 58576 Z= 0.307 Chirality : 0.040 0.208 6608 Planarity : 0.004 0.039 7536 Dihedral : 4.468 22.340 6016 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.00 % Allowed : 22.42 % Favored : 75.58 % 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: 0.14 (0.12), residues: 5360 helix: 1.10 (0.11), residues: 2240 sheet: -1.02 (0.17), residues: 976 loop : -0.28 (0.15), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 490 HIS 0.006 0.001 HIS H 516 PHE 0.010 0.001 PHE j 68 TYR 0.011 0.001 TYR k 80 ARG 0.009 0.000 ARG E 543 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 918 time to evaluate : 5.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8856 (ptmt) cc_final: 0.8185 (ptpp) REVERT: A 486 ASN cc_start: 0.8531 (t0) cc_final: 0.8322 (t0) REVERT: A 543 ARG cc_start: 0.8375 (ttm170) cc_final: 0.8067 (mtt-85) REVERT: a 4 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8647 (mm-40) REVERT: a 44 LYS cc_start: 0.8838 (mtmm) cc_final: 0.8454 (mtmm) REVERT: a 73 ASP cc_start: 0.8410 (t0) cc_final: 0.7772 (t0) REVERT: a 76 LYS cc_start: 0.9305 (pmmt) cc_final: 0.8994 (pmtt) REVERT: a 77 ASN cc_start: 0.8977 (m-40) cc_final: 0.8726 (m-40) REVERT: a 78 THR cc_start: 0.9324 (m) cc_final: 0.9072 (m) REVERT: a 87 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7796 (ttmm) REVERT: B 439 ASP cc_start: 0.8135 (p0) cc_final: 0.7888 (p0) REVERT: B 517 ARG cc_start: 0.8212 (ptp-110) cc_final: 0.7929 (ptp-110) REVERT: C 486 ASN cc_start: 0.8674 (t0) cc_final: 0.8379 (t0) REVERT: C 489 ASP cc_start: 0.8187 (p0) cc_final: 0.7878 (p0) REVERT: C 517 ARG cc_start: 0.8416 (ptm160) cc_final: 0.8052 (ptp-170) REVERT: C 543 ARG cc_start: 0.8337 (ttm170) cc_final: 0.7977 (mtt-85) REVERT: c 77 ASN cc_start: 0.8929 (m-40) cc_final: 0.8693 (m-40) REVERT: c 78 THR cc_start: 0.9306 (m) cc_final: 0.9072 (m) REVERT: c 87 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7821 (ttmm) REVERT: D 439 ASP cc_start: 0.8168 (p0) cc_final: 0.7914 (p0) REVERT: D 543 ARG cc_start: 0.8385 (ttm170) cc_final: 0.8010 (mtt-85) REVERT: d 4 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8372 (mp10) REVERT: E 450 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: E 486 ASN cc_start: 0.8591 (t0) cc_final: 0.8356 (t0) REVERT: E 489 ASP cc_start: 0.8124 (p0) cc_final: 0.7905 (p0) REVERT: e 7 GLU cc_start: 0.8035 (mp0) cc_final: 0.7706 (mp0) REVERT: e 14 GLN cc_start: 0.8662 (pm20) cc_final: 0.8321 (mp10) REVERT: e 77 ASN cc_start: 0.8926 (m-40) cc_final: 0.8639 (m110) REVERT: e 78 THR cc_start: 0.9298 (m) cc_final: 0.9053 (m) REVERT: e 87 LYS cc_start: 0.7838 (mppt) cc_final: 0.7621 (ttmm) REVERT: e 105 GLN cc_start: 0.7407 (mp10) cc_final: 0.7201 (pm20) REVERT: F 486 ASN cc_start: 0.8768 (t0) cc_final: 0.7745 (t0) REVERT: f 4 GLN cc_start: 0.8880 (mp10) cc_final: 0.8620 (mp10) REVERT: g 7 GLU cc_start: 0.8335 (mp0) cc_final: 0.7945 (mp0) REVERT: g 73 ASP cc_start: 0.8403 (t70) cc_final: 0.8157 (t0) REVERT: g 77 ASN cc_start: 0.8966 (m-40) cc_final: 0.8590 (m110) REVERT: g 87 LYS cc_start: 0.7936 (ttmm) cc_final: 0.7691 (ttmm) REVERT: g 105 GLN cc_start: 0.7783 (pm20) cc_final: 0.7497 (pm20) REVERT: i 4 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8291 (mm-40) REVERT: J 517 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8186 (ptp-110) REVERT: j 4 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8467 (mm-40) REVERT: j 7 GLU cc_start: 0.7996 (mp0) cc_final: 0.7762 (mp0) REVERT: K 484 ARG cc_start: 0.7946 (tpp-160) cc_final: 0.7733 (mmp80) REVERT: K 486 ASN cc_start: 0.8505 (t0) cc_final: 0.8046 (t0) REVERT: K 489 ASP cc_start: 0.8009 (p0) cc_final: 0.7533 (p0) REVERT: k 4 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8435 (mm-40) REVERT: k 14 GLN cc_start: 0.8626 (pm20) cc_final: 0.8272 (mp10) REVERT: L 486 ASN cc_start: 0.8449 (t0) cc_final: 0.8195 (t0) REVERT: L 543 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.7999 (mtt-85) REVERT: l 4 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8427 (mm-40) REVERT: l 77 ASN cc_start: 0.8844 (m-40) cc_final: 0.8523 (m110) REVERT: M 543 ARG cc_start: 0.8413 (ttm-80) cc_final: 0.8034 (mtt-85) REVERT: m 4 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8642 (mm-40) REVERT: m 14 GLN cc_start: 0.8587 (pm20) cc_final: 0.8256 (mp10) REVERT: m 87 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7713 (ttmm) REVERT: m 89 GLU cc_start: 0.8740 (pm20) cc_final: 0.8531 (pm20) REVERT: N 516 HIS cc_start: 0.8396 (p-80) cc_final: 0.7206 (p90) REVERT: N 517 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8210 (ptp-170) REVERT: n 4 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8715 (mm-40) REVERT: n 7 GLU cc_start: 0.7902 (mp0) cc_final: 0.7501 (mp0) REVERT: n 77 ASN cc_start: 0.8812 (m-40) cc_final: 0.8498 (m110) REVERT: o 4 GLN cc_start: 0.8789 (mp10) cc_final: 0.8543 (mp10) REVERT: o 14 GLN cc_start: 0.8651 (pm20) cc_final: 0.8391 (mp10) REVERT: P 489 ASP cc_start: 0.7883 (p0) cc_final: 0.7661 (p0) REVERT: P 516 HIS cc_start: 0.8327 (p90) cc_final: 0.7632 (p90) REVERT: P 517 ARG cc_start: 0.8317 (ptp-110) cc_final: 0.7931 (ptp-110) REVERT: p 4 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8474 (mm-40) outliers start: 93 outliers final: 74 residues processed: 963 average time/residue: 1.5506 time to fit residues: 1833.9031 Evaluate side-chains 970 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 892 time to evaluate : 6.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 83 MET Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 517 ARG Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 105 GLN Chi-restraints excluded: chain I residue 481 THR Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain J residue 517 ARG Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 517 ARG Chi-restraints excluded: chain K residue 523 LEU Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 375 LYS Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 83 MET Chi-restraints excluded: chain m residue 87 LYS Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 502 THR Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain O residue 481 THR Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain o residue 102 THR Chi-restraints excluded: chain P residue 385 THR Chi-restraints excluded: chain P residue 502 THR Chi-restraints excluded: chain p residue 21 LEU Chi-restraints excluded: chain p residue 83 MET Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 0.9980 chunk 501 optimal weight: 2.9990 chunk 306 optimal weight: 3.9990 chunk 237 optimal weight: 0.4980 chunk 348 optimal weight: 5.9990 chunk 526 optimal weight: 6.9990 chunk 484 optimal weight: 9.9990 chunk 418 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 323 optimal weight: 0.0980 chunk 256 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 14 GLN ** H 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43328 Z= 0.179 Angle : 0.630 11.857 58576 Z= 0.310 Chirality : 0.039 0.197 6608 Planarity : 0.004 0.043 7536 Dihedral : 4.428 20.949 6016 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.85 % Allowed : 22.68 % Favored : 75.47 % 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: 0.20 (0.12), residues: 5360 helix: 1.15 (0.11), residues: 2240 sheet: -0.98 (0.17), residues: 976 loop : -0.26 (0.15), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 490 HIS 0.008 0.001 HIS H 516 PHE 0.007 0.001 PHE d 68 TYR 0.011 0.001 TYR a 80 ARG 0.009 0.000 ARG N 484 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 928 time to evaluate : 5.068 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: A 386 LYS cc_start: 0.8858 (ptmt) cc_final: 0.8185 (ptpp) REVERT: A 517 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7989 (ptp-110) REVERT: a 4 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8646 (mm-40) REVERT: a 44 LYS cc_start: 0.8851 (mtmm) cc_final: 0.8477 (mtmm) REVERT: a 73 ASP cc_start: 0.8413 (t0) cc_final: 0.7770 (t0) REVERT: a 76 LYS cc_start: 0.9304 (pmmt) cc_final: 0.8992 (pmtt) REVERT: a 77 ASN cc_start: 0.8968 (m-40) cc_final: 0.8722 (m-40) REVERT: a 78 THR cc_start: 0.9319 (m) cc_final: 0.9075 (m) REVERT: a 87 LYS cc_start: 0.7989 (ttmm) cc_final: 0.7750 (ttmm) REVERT: B 439 ASP cc_start: 0.8115 (p0) cc_final: 0.7871 (p0) REVERT: B 517 ARG cc_start: 0.8211 (ptp-110) cc_final: 0.7927 (ptp-110) REVERT: B 543 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.8092 (mtt-85) REVERT: C 486 ASN cc_start: 0.8739 (t0) cc_final: 0.8517 (t0) REVERT: C 489 ASP cc_start: 0.8169 (p0) cc_final: 0.7854 (p0) REVERT: c 77 ASN cc_start: 0.8914 (m-40) cc_final: 0.8685 (m-40) REVERT: c 78 THR cc_start: 0.9307 (m) cc_final: 0.9055 (m) REVERT: c 87 LYS cc_start: 0.7921 (ttmm) cc_final: 0.7660 (ttmm) REVERT: D 439 ASP cc_start: 0.8141 (p0) cc_final: 0.7891 (p0) REVERT: D 543 ARG cc_start: 0.8373 (ttm170) cc_final: 0.8027 (mtt-85) REVERT: d 4 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8372 (mp10) REVERT: E 486 ASN cc_start: 0.8616 (t0) cc_final: 0.8308 (t0) REVERT: E 489 ASP cc_start: 0.8108 (p0) cc_final: 0.7839 (p0) REVERT: e 4 GLN cc_start: 0.8864 (mp10) cc_final: 0.8552 (mp10) REVERT: e 7 GLU cc_start: 0.7919 (mp0) cc_final: 0.7531 (mp0) REVERT: e 77 ASN cc_start: 0.8896 (m-40) cc_final: 0.8613 (m110) REVERT: e 78 THR cc_start: 0.9296 (m) cc_final: 0.9033 (m) REVERT: e 105 GLN cc_start: 0.7375 (mp10) cc_final: 0.7174 (pm20) REVERT: F 486 ASN cc_start: 0.8696 (t0) cc_final: 0.8413 (t0) REVERT: f 4 GLN cc_start: 0.8885 (mp10) cc_final: 0.8631 (mp10) REVERT: G 486 ASN cc_start: 0.8563 (t0) cc_final: 0.8340 (t0) REVERT: g 4 GLN cc_start: 0.8798 (mp10) cc_final: 0.8569 (mp10) REVERT: g 7 GLU cc_start: 0.8294 (mp0) cc_final: 0.7897 (mp0) REVERT: g 73 ASP cc_start: 0.8396 (t70) cc_final: 0.8132 (t0) REVERT: g 77 ASN cc_start: 0.8956 (m-40) cc_final: 0.8584 (m110) REVERT: g 105 GLN cc_start: 0.7785 (pm20) cc_final: 0.7482 (pm20) REVERT: i 4 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8319 (mm-40) REVERT: J 517 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8179 (ptp-110) REVERT: j 4 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8453 (mm-40) REVERT: j 7 GLU cc_start: 0.7973 (mp0) cc_final: 0.7527 (mp0) REVERT: j 77 ASN cc_start: 0.8799 (m-40) cc_final: 0.8452 (m110) REVERT: K 484 ARG cc_start: 0.7962 (tpp-160) cc_final: 0.7743 (mmp80) REVERT: K 486 ASN cc_start: 0.8504 (t0) cc_final: 0.8071 (t0) REVERT: K 489 ASP cc_start: 0.8025 (p0) cc_final: 0.7535 (p0) REVERT: K 517 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7793 (ptp-110) REVERT: k 4 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8433 (mm-40) REVERT: k 14 GLN cc_start: 0.8621 (pm20) cc_final: 0.8284 (mp10) REVERT: L 423 GLN cc_start: 0.8693 (tt0) cc_final: 0.8359 (tt0) REVERT: L 486 ASN cc_start: 0.8432 (t0) cc_final: 0.8171 (t0) REVERT: L 516 HIS cc_start: 0.8299 (p-80) cc_final: 0.8095 (p90) REVERT: L 543 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.8038 (mtt-85) REVERT: l 4 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8420 (mm-40) REVERT: l 7 GLU cc_start: 0.7849 (mp0) cc_final: 0.7458 (mp0) REVERT: l 77 ASN cc_start: 0.8837 (m-40) cc_final: 0.8530 (m110) REVERT: M 543 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.8040 (mtt-85) REVERT: m 4 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8590 (mm-40) REVERT: m 14 GLN cc_start: 0.8585 (pm20) cc_final: 0.8257 (mp10) REVERT: m 87 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7568 (ttmm) REVERT: m 89 GLU cc_start: 0.8731 (pm20) cc_final: 0.8525 (pm20) REVERT: N 403 ARG cc_start: 0.8347 (mtp85) cc_final: 0.8144 (mmm-85) REVERT: n 4 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8720 (mm-40) REVERT: n 77 ASN cc_start: 0.8809 (m-40) cc_final: 0.8524 (m110) REVERT: o 4 GLN cc_start: 0.8829 (mp10) cc_final: 0.8587 (mp10) REVERT: o 14 GLN cc_start: 0.8650 (pm20) cc_final: 0.8307 (mp10) REVERT: P 516 HIS cc_start: 0.8317 (p90) cc_final: 0.7802 (p90) REVERT: P 517 ARG cc_start: 0.8279 (ptp-110) cc_final: 0.7961 (ptp-110) REVERT: p 4 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8467 (mm-40) REVERT: p 77 ASN cc_start: 0.8818 (m-40) cc_final: 0.8443 (m110) outliers start: 86 outliers final: 73 residues processed: 970 average time/residue: 1.5540 time to fit residues: 1833.5107 Evaluate side-chains 984 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 907 time to evaluate : 5.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 21 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 83 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 13 VAL Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 517 ARG Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain J residue 517 ARG Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 517 ARG Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 83 MET Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 83 MET Chi-restraints excluded: chain m residue 87 LYS Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 502 THR Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain O residue 481 THR Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain o residue 83 MET Chi-restraints excluded: chain o residue 102 THR Chi-restraints excluded: chain P residue 385 THR Chi-restraints excluded: chain P residue 502 THR Chi-restraints excluded: chain p residue 12 LEU Chi-restraints excluded: chain p residue 21 LEU Chi-restraints excluded: chain p residue 83 MET Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 20.0000 chunk 446 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 386 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 419 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 430 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 14 GLN ** e 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 105 GLN ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 105 GLN ** O 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 105 GLN ** P 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.148875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.095221 restraints weight = 64595.359| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.63 r_work: 0.3194 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43328 Z= 0.191 Angle : 0.637 11.098 58576 Z= 0.315 Chirality : 0.040 0.202 6608 Planarity : 0.004 0.042 7536 Dihedral : 4.414 20.732 6016 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.68 % Allowed : 23.05 % 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: 0.25 (0.12), residues: 5360 helix: 1.19 (0.11), residues: 2240 sheet: -0.95 (0.17), residues: 976 loop : -0.25 (0.15), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 490 HIS 0.010 0.001 HIS H 516 PHE 0.007 0.001 PHE d 68 TYR 0.010 0.001 TYR c 80 ARG 0.009 0.000 ARG E 543 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23853.44 seconds wall clock time: 420 minutes 32.76 seconds (25232.76 seconds total)