Starting phenix.real_space_refine on Tue Apr 16 08:57:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p60_13213/04_2024/7p60_13213.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p60_13213/04_2024/7p60_13213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p60_13213/04_2024/7p60_13213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p60_13213/04_2024/7p60_13213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p60_13213/04_2024/7p60_13213.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p60_13213/04_2024/7p60_13213.pdb" } resolution = 3.8 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= 0.003 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 159 5.16 5 C 24939 2.51 5 N 6450 2.21 5 O 6858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 165": "OD1" <-> "OD2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 358": "OE1" <-> "OE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 691": "OD1" <-> "OD2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 38406 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "B" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "C" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "D" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "E" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "F" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "G" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "I" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Time building chain proxies: 18.36, per 1000 atoms: 0.48 Number of scatterers: 38406 At special positions: 0 Unit cell: (156.24, 153.636, 192.696, 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 159 16.00 O 6858 8.00 N 6450 7.00 C 24939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 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: 13.95 Conformation dependent library (CDL) restraints added in 6.0 seconds 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9006 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 29 sheets defined 49.0% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.679A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 146 Proline residue: A 126 - end of helix removed outlier: 4.925A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.652A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.665A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.526A pdb=" N GLY A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 299 through 304 removed outlier: 3.815A pdb=" N THR A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 344 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.395A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.786A pdb=" N LEU A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.753A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 515 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 543 removed outlier: 4.098A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 629 through 637 Processing helix chain 'A' and resid 655 through 661 removed outlier: 3.561A pdb=" N ILE A 658 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 701 through 707 Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 771 through 776 removed outlier: 3.695A pdb=" N CYS A 776 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 792 Processing helix chain 'A' and resid 795 through 808 removed outlier: 3.676A pdb=" N GLU A 808 " --> pdb=" O ARG A 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 4.041A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 4.940A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 removed outlier: 4.020A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 4.068A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 256 removed outlier: 4.144A pdb=" N GLU B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 287 removed outlier: 4.624A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 344 Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.120A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 411 Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 439 through 445 removed outlier: 3.615A pdb=" N PHE B 443 " --> pdb=" O ASP B 440 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 444 " --> pdb=" O THR B 441 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 445 " --> pdb=" O VAL B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 495 Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 509 through 515 removed outlier: 3.818A pdb=" N TYR B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 543 removed outlier: 3.613A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 607 through 611 removed outlier: 3.528A pdb=" N ILE B 610 " --> pdb=" O PRO B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.729A pdb=" N GLN B 636 " --> pdb=" O ILE B 633 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 660 removed outlier: 3.640A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.700A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 removed outlier: 3.750A pdb=" N GLY B 705 " --> pdb=" O ALA B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.655A pdb=" N CYS B 730 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.686A pdb=" N VAL B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 751 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 3.613A pdb=" N CYS B 776 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.583A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 4.829A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 3.882A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 removed outlier: 3.661A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 299 through 304 removed outlier: 3.824A pdb=" N THR C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 344 Processing helix chain 'C' and resid 355 through 360 Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.332A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 411 Processing helix chain 'C' and resid 412 through 420 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.568A pdb=" N VAL C 442 " --> pdb=" O PRO C 439 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 443 " --> pdb=" O ASP C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 504 through 508 Processing helix chain 'C' and resid 509 through 515 removed outlier: 3.816A pdb=" N ILE C 512 " --> pdb=" O PRO C 509 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 543 removed outlier: 4.128A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 Processing helix chain 'C' and resid 607 through 613 removed outlier: 3.981A pdb=" N ILE C 610 " --> pdb=" O PRO C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.501A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 removed outlier: 3.777A pdb=" N ILE C 658 " --> pdb=" O PRO C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 684 Processing helix chain 'C' and resid 701 through 707 removed outlier: 3.598A pdb=" N ILE C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.564A pdb=" N VAL C 750 " --> pdb=" O PRO C 747 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 751 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 776 removed outlier: 3.592A pdb=" N LEU C 773 " --> pdb=" O PRO C 770 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS C 776 " --> pdb=" O LEU C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 792 Processing helix chain 'C' and resid 795 through 808 removed outlier: 3.679A pdb=" N GLU C 808 " --> pdb=" O ARG C 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 21 removed outlier: 3.704A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 146 Proline residue: D 126 - end of helix removed outlier: 4.957A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.154A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 removed outlier: 4.099A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 256 removed outlier: 4.124A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 287 removed outlier: 4.440A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 344 Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 383 through 392 removed outlier: 4.066A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 411 Processing helix chain 'D' and resid 412 through 420 Processing helix chain 'D' and resid 439 through 445 removed outlier: 3.721A pdb=" N LEU D 445 " --> pdb=" O VAL D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 484 through 495 Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'D' and resid 509 through 515 removed outlier: 3.940A pdb=" N TYR D 513 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 543 removed outlier: 3.500A pdb=" N ASP D 538 " --> pdb=" O ILE D 535 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY D 539 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG D 541 " --> pdb=" O ASP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 566 Processing helix chain 'D' and resid 608 through 613 removed outlier: 3.652A pdb=" N SER D 612 " --> pdb=" O HIS D 608 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 613 " --> pdb=" O SER D 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 608 through 613' Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.829A pdb=" N GLN D 636 " --> pdb=" O ILE D 633 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS D 637 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 660 removed outlier: 3.522A pdb=" N ILE D 658 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 removed outlier: 3.770A pdb=" N CYS D 684 " --> pdb=" O LEU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 707 Processing helix chain 'D' and resid 724 through 730 Processing helix chain 'D' and resid 747 through 753 removed outlier: 3.757A pdb=" N GLY D 751 " --> pdb=" O SER D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 776 removed outlier: 3.618A pdb=" N CYS D 776 " --> pdb=" O LEU D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 795 through 808 Processing helix chain 'E' and resid 16 through 21 removed outlier: 3.572A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 146 removed outlier: 3.511A pdb=" N LYS E 123 " --> pdb=" O HIS E 119 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 4.820A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 3.840A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 176 removed outlier: 3.678A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.525A pdb=" N GLY E 237 " --> pdb=" O ASP E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 299 through 304 removed outlier: 3.787A pdb=" N THR E 303 " --> pdb=" O ILE E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 344 Processing helix chain 'E' and resid 354 through 360 removed outlier: 3.622A pdb=" N GLU E 358 " --> pdb=" O GLU E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 383 Processing helix chain 'E' and resid 383 through 392 removed outlier: 4.439A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 411 Processing helix chain 'E' and resid 412 through 419 Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.562A pdb=" N LEU E 445 " --> pdb=" O VAL E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 484 through 494 removed outlier: 3.563A pdb=" N GLU E 493 " --> pdb=" O ALA E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 515 removed outlier: 3.942A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 543 removed outlier: 4.024A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 Processing helix chain 'E' and resid 607 through 613 removed outlier: 3.853A pdb=" N ILE E 610 " --> pdb=" O PRO E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 629 through 637 Processing helix chain 'E' and resid 655 through 661 removed outlier: 3.802A pdb=" N ILE E 658 " --> pdb=" O PRO E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 684 Processing helix chain 'E' and resid 701 through 707 Processing helix chain 'E' and resid 724 through 730 Processing helix chain 'E' and resid 747 through 753 removed outlier: 3.702A pdb=" N VAL E 750 " --> pdb=" O PRO E 747 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY E 751 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 776 removed outlier: 3.800A pdb=" N LEU E 773 " --> pdb=" O PRO E 770 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS E 776 " --> pdb=" O LEU E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 792 Processing helix chain 'E' and resid 795 through 808 removed outlier: 3.663A pdb=" N GLU E 808 " --> pdb=" O ARG E 804 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 removed outlier: 3.855A pdb=" N ILE F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 102 through 117 Processing helix chain 'F' and resid 119 through 146 Proline residue: F 126 - end of helix removed outlier: 4.955A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 166 removed outlier: 4.348A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 176 removed outlier: 4.119A pdb=" N THR F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 256 removed outlier: 4.195A pdb=" N GLU F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 287 removed outlier: 4.584A pdb=" N HIS F 287 " --> pdb=" O VAL F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 343 Processing helix chain 'F' and resid 353 through 360 Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 383 through 392 removed outlier: 4.191A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 411 Processing helix chain 'F' and resid 412 through 420 Processing helix chain 'F' and resid 439 through 445 removed outlier: 3.799A pdb=" N LEU F 445 " --> pdb=" O VAL F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 484 through 495 Processing helix chain 'F' and resid 504 through 508 Processing helix chain 'F' and resid 509 through 515 removed outlier: 3.775A pdb=" N TYR F 513 " --> pdb=" O LEU F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 543 removed outlier: 3.874A pdb=" N GLY F 539 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG F 541 " --> pdb=" O ASP F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 566 Processing helix chain 'F' and resid 607 through 611 Processing helix chain 'F' and resid 631 through 636 removed outlier: 3.719A pdb=" N GLN F 636 " --> pdb=" O ILE F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 660 removed outlier: 3.501A pdb=" N ILE F 658 " --> pdb=" O PRO F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 684 removed outlier: 3.590A pdb=" N LEU F 681 " --> pdb=" O PRO F 678 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS F 684 " --> pdb=" O LEU F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 707 removed outlier: 3.621A pdb=" N LEU F 707 " --> pdb=" O ILE F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 730 Processing helix chain 'F' and resid 747 through 753 removed outlier: 3.803A pdb=" N GLY F 751 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 776 removed outlier: 3.579A pdb=" N CYS F 776 " --> pdb=" O LEU F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 792 Processing helix chain 'F' and resid 795 through 808 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.613A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 108 through 112 removed outlier: 3.827A pdb=" N GLU H 111 " --> pdb=" O TYR H 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR H 112 " --> pdb=" O TYR H 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 108 through 112' Processing sheet with id=AA1, first strand: chain 'A' and resid 292 through 296 Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.411A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU A 451 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N TYR A 477 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 453 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 474 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LYS A 501 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 476 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 498 " --> pdb=" O HIS A 522 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR A 524 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A 500 " --> pdb=" O THR A 524 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 549 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ASN A 575 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 551 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU A 713 " --> pdb=" O HIS A 737 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU A 736 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 459 through 461 removed outlier: 6.389A pdb=" N VAL A 459 " --> pdb=" O LYS A 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.824A pdb=" N LEU B 428 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LYS B 452 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 430 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLU B 454 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 432 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU B 549 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN B 575 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 551 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU B 572 " --> pdb=" O GLU B 597 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE B 599 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE B 574 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 619 " --> pdb=" O CYS B 643 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 645 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR B 668 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 667 " --> pdb=" O ASP B 691 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 460 through 461 Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.139A pdb=" N LEU C 428 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LYS C 452 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU C 430 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLU C 454 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU C 432 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 549 " --> pdb=" O SER C 573 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASN C 575 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU C 551 " --> pdb=" O ASN C 575 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 572 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE C 599 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE C 574 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 619 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR C 668 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 691 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU C 713 " --> pdb=" O HIS C 737 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU C 760 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 459 through 460 removed outlier: 6.325A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB2, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AB3, first strand: chain 'D' and resid 421 through 422 removed outlier: 6.467A pdb=" N LEU D 428 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LYS D 452 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU D 430 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLU D 454 " --> pdb=" O LEU D 430 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU D 432 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU D 451 " --> pdb=" O TRP D 475 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N TYR D 477 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU D 453 " --> pdb=" O TYR D 477 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU D 549 " --> pdb=" O SER D 573 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ASN D 575 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU D 551 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU D 572 " --> pdb=" O GLU D 597 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE D 599 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE D 574 " --> pdb=" O ILE D 599 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE D 619 " --> pdb=" O LYS D 645 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 644 " --> pdb=" O TYR D 668 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP D 691 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU D 713 " --> pdb=" O HIS D 737 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU D 736 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE D 759 " --> pdb=" O VAL D 785 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 460 through 461 Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AB6, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.542A pdb=" N LEU E 451 " --> pdb=" O TRP E 475 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N TYR E 477 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU E 453 " --> pdb=" O TYR E 477 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU E 549 " --> pdb=" O SER E 573 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ASN E 575 " --> pdb=" O LEU E 549 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU E 551 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE E 619 " --> pdb=" O LYS E 645 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR E 668 " --> pdb=" O LEU E 644 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU E 713 " --> pdb=" O HIS E 737 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU E 760 " --> pdb=" O LEU E 736 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 459 through 461 removed outlier: 6.278A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AB9, first strand: chain 'F' and resid 421 through 422 removed outlier: 6.283A pdb=" N LEU F 428 " --> pdb=" O VAL F 450 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LYS F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU F 430 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLU F 454 " --> pdb=" O LEU F 430 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU F 432 " --> pdb=" O GLU F 454 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU F 451 " --> pdb=" O TRP F 475 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N TYR F 477 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU F 453 " --> pdb=" O TYR F 477 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU F 474 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LYS F 501 " --> pdb=" O LEU F 474 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU F 476 " --> pdb=" O LYS F 501 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU F 549 " --> pdb=" O SER F 573 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ASN F 575 " --> pdb=" O LEU F 549 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU F 551 " --> pdb=" O ASN F 575 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU F 572 " --> pdb=" O GLU F 597 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE F 599 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE F 574 " --> pdb=" O ILE F 599 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE F 619 " --> pdb=" O LYS F 645 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU F 644 " --> pdb=" O TYR F 668 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP F 691 " --> pdb=" O LEU F 667 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU F 690 " --> pdb=" O ALA F 714 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU F 713 " --> pdb=" O HIS F 737 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 460 through 461 Processing sheet with id=AC2, first strand: chain 'F' and resid 759 through 760 removed outlier: 6.278A pdb=" N ILE F 759 " --> pdb=" O VAL F 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 13 removed outlier: 5.884A pdb=" N GLY G 10 " --> pdb=" O THR G 122 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER G 124 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL G 12 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP G 36 " --> pdb=" O ALA G 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.653A pdb=" N TYR G 114 " --> pdb=" O ALA G 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 13 removed outlier: 5.981A pdb=" N GLY I 10 " --> pdb=" O THR I 122 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N SER I 124 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL I 12 " --> pdb=" O SER I 124 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.652A pdb=" N TYR I 114 " --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'H' and resid 11 through 13 removed outlier: 8.278A pdb=" N GLU H 32 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA H 52 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.707A pdb=" N TYR H 114 " --> pdb=" O ALA H 98 " (cutoff:3.500A) 1756 hydrogen bonds defined for protein. 4434 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: 16.17 Time building geometry restraints manager: 15.18 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: 12145 1.34 - 1.46: 8946 1.46 - 1.58: 17966 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 39273 Sorted by residual: bond pdb=" CA TYR I 109 " pdb=" C TYR I 109 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.80e-02 3.09e+03 1.62e+00 bond pdb=" CA TYR G 109 " pdb=" C TYR G 109 " ideal model delta sigma weight residual 1.523 1.501 0.022 1.80e-02 3.09e+03 1.55e+00 bond pdb=" N LEU F 700 " pdb=" CA LEU F 700 " ideal model delta sigma weight residual 1.463 1.448 0.015 1.22e-02 6.72e+03 1.44e+00 bond pdb=" CA ILE E 438 " pdb=" CB ILE E 438 " ideal model delta sigma weight residual 1.537 1.524 0.014 1.29e-02 6.01e+03 1.13e+00 bond pdb=" CA ILE A 438 " pdb=" CB ILE A 438 " ideal model delta sigma weight residual 1.537 1.524 0.013 1.29e-02 6.01e+03 1.04e+00 ... (remaining 39268 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.34: 948 106.34 - 113.30: 21913 113.30 - 120.26: 14300 120.26 - 127.21: 15620 127.21 - 134.17: 463 Bond angle restraints: 53244 Sorted by residual: angle pdb=" N PHE E 372 " pdb=" CA PHE E 372 " pdb=" C PHE E 372 " ideal model delta sigma weight residual 114.04 107.81 6.23 1.24e+00 6.50e-01 2.52e+01 angle pdb=" N VAL D 397 " pdb=" CA VAL D 397 " pdb=" C VAL D 397 " ideal model delta sigma weight residual 111.90 107.91 3.99 8.10e-01 1.52e+00 2.43e+01 angle pdb=" N ILE E 535 " pdb=" CA ILE E 535 " pdb=" C ILE E 535 " ideal model delta sigma weight residual 112.96 108.71 4.25 1.00e+00 1.00e+00 1.80e+01 angle pdb=" N ILE C 535 " pdb=" CA ILE C 535 " pdb=" C ILE C 535 " ideal model delta sigma weight residual 112.96 108.77 4.19 1.00e+00 1.00e+00 1.76e+01 angle pdb=" CA LEU F 584 " pdb=" CB LEU F 584 " pdb=" CG LEU F 584 " ideal model delta sigma weight residual 116.30 127.65 -11.35 3.50e+00 8.16e-02 1.05e+01 ... (remaining 53239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 21644 17.46 - 34.92: 1626 34.92 - 52.38: 342 52.38 - 69.84: 66 69.84 - 87.30: 19 Dihedral angle restraints: 23697 sinusoidal: 9813 harmonic: 13884 Sorted by residual: dihedral pdb=" CB CYS F 57 " pdb=" SG CYS F 57 " pdb=" SG CYS F 65 " pdb=" CB CYS F 65 " ideal model delta sinusoidal sigma weight residual -86.00 -43.03 -42.97 1 1.00e+01 1.00e-02 2.58e+01 dihedral pdb=" CB CYS D 57 " pdb=" SG CYS D 57 " pdb=" SG CYS D 65 " pdb=" CB CYS D 65 " ideal model delta sinusoidal sigma weight residual -86.00 -44.81 -41.19 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" CB CYS B 57 " pdb=" SG CYS B 57 " pdb=" SG CYS B 65 " pdb=" CB CYS B 65 " ideal model delta sinusoidal sigma weight residual -86.00 -47.04 -38.96 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 23694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3191 0.027 - 0.053: 1851 0.053 - 0.080: 709 0.080 - 0.106: 234 0.106 - 0.133: 111 Chirality restraints: 6096 Sorted by residual: chirality pdb=" CA ILE B 677 " pdb=" N ILE B 677 " pdb=" C ILE B 677 " pdb=" CB ILE B 677 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE C 677 " pdb=" N ILE C 677 " pdb=" C ILE C 677 " pdb=" CB ILE C 677 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE E 677 " pdb=" N ILE E 677 " pdb=" C ILE E 677 " pdb=" CB ILE E 677 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 6093 not shown) Planarity restraints: 6615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 724 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO C 725 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 725 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 725 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 724 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO E 725 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 725 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 725 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 395 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.36e+00 pdb=" C SER D 395 " 0.020 2.00e-02 2.50e+03 pdb=" O SER D 395 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU D 396 " -0.007 2.00e-02 2.50e+03 ... (remaining 6612 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 939 2.68 - 3.24: 40166 3.24 - 3.79: 64404 3.79 - 4.35: 84709 4.35 - 4.90: 136453 Nonbonded interactions: 326671 Sorted by model distance: nonbonded pdb=" OE1 GLN G 39 " pdb=" OH TYR G 95 " model vdw 2.130 2.440 nonbonded pdb=" OD2 ASP E 102 " pdb=" OH TYR F 106 " model vdw 2.154 2.440 nonbonded pdb=" OH TYR B 351 " pdb=" OD2 ASP B 380 " model vdw 2.161 2.440 nonbonded pdb=" OD1 ASN C 554 " pdb=" OG1 THR C 579 " model vdw 2.164 2.440 nonbonded pdb=" OD2 ASP A 102 " pdb=" OH TYR B 106 " model vdw 2.167 2.440 ... (remaining 326666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 9.370 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 94.610 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 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 : 0.004 0.030 39273 Z= 0.253 Angle : 0.553 11.352 53244 Z= 0.307 Chirality : 0.040 0.133 6096 Planarity : 0.003 0.041 6615 Dihedral : 13.063 87.299 14628 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.44 % Allowed : 10.01 % Favored : 84.55 % 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: -0.45 (0.13), residues: 4638 helix: 0.12 (0.12), residues: 2034 sheet: -0.93 (0.19), residues: 768 loop : -0.26 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.005 0.001 HIS E 119 PHE 0.010 0.001 PHE D 324 TYR 0.017 0.001 TYR A 281 ARG 0.003 0.000 ARG A 731 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 623 time to evaluate : 4.620 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: A 35 MET cc_start: 0.7960 (mtm) cc_final: 0.7587 (mtp) REVERT: A 274 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.6949 (mmtt) REVERT: A 590 MET cc_start: 0.6499 (mpp) cc_final: 0.5796 (mmp) REVERT: A 598 LEU cc_start: 0.6151 (mt) cc_final: 0.5924 (mm) REVERT: A 663 ASN cc_start: 0.5374 (m110) cc_final: 0.4551 (t0) REVERT: B 17 TYR cc_start: 0.6294 (OUTLIER) cc_final: 0.5041 (m-80) REVERT: B 36 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7793 (tp) REVERT: B 104 HIS cc_start: 0.8845 (OUTLIER) cc_final: 0.8509 (t70) REVERT: B 165 ASP cc_start: 0.6267 (OUTLIER) cc_final: 0.5903 (p0) REVERT: B 265 MET cc_start: 0.6938 (mmm) cc_final: 0.6734 (mmm) REVERT: B 343 MET cc_start: 0.8332 (ttm) cc_final: 0.7710 (ttm) REVERT: B 375 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7111 (ttm) REVERT: B 434 MET cc_start: 0.7632 (mtp) cc_final: 0.7123 (ptm) REVERT: B 592 ASN cc_start: 0.8048 (m-40) cc_final: 0.7581 (t0) REVERT: B 623 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6295 (t0) REVERT: B 650 HIS cc_start: 0.6857 (m90) cc_final: 0.6274 (t70) REVERT: B 668 TYR cc_start: 0.5959 (m-80) cc_final: 0.4498 (m-10) REVERT: B 699 PHE cc_start: 0.4843 (p90) cc_final: 0.4457 (p90) REVERT: B 738 LEU cc_start: 0.8279 (mt) cc_final: 0.8006 (mt) REVERT: B 791 PHE cc_start: 0.1603 (t80) cc_final: 0.0943 (t80) REVERT: C 35 MET cc_start: 0.7819 (mtm) cc_final: 0.7505 (mtp) REVERT: C 103 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6936 (tmm-80) REVERT: C 154 GLU cc_start: 0.7677 (pt0) cc_final: 0.7384 (tp30) REVERT: C 294 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: C 323 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7541 (m) REVERT: C 332 TYR cc_start: 0.7930 (t80) cc_final: 0.7704 (t80) REVERT: C 340 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7997 (tp) REVERT: C 374 PHE cc_start: 0.7926 (t80) cc_final: 0.7678 (t80) REVERT: C 513 TYR cc_start: 0.4062 (m-80) cc_final: 0.3840 (m-10) REVERT: C 590 MET cc_start: 0.5662 (mpp) cc_final: 0.5440 (mmt) REVERT: C 720 ILE cc_start: 0.4853 (mp) cc_final: 0.4199 (tt) REVERT: C 749 ARG cc_start: 0.4435 (mtp180) cc_final: 0.3803 (mtm180) REVERT: D 17 TYR cc_start: 0.6207 (OUTLIER) cc_final: 0.5238 (m-80) REVERT: D 36 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8089 (tp) REVERT: D 155 HIS cc_start: 0.6198 (OUTLIER) cc_final: 0.5957 (m170) REVERT: D 157 VAL cc_start: 0.8073 (t) cc_final: 0.7831 (p) REVERT: D 236 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6535 (tm-30) REVERT: D 275 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.6716 (t80) REVERT: D 338 TYR cc_start: 0.7162 (t80) cc_final: 0.6837 (t80) REVERT: D 343 MET cc_start: 0.8425 (ttm) cc_final: 0.7969 (mtp) REVERT: D 350 LYS cc_start: 0.6117 (tppt) cc_final: 0.5174 (mmtm) REVERT: D 353 PHE cc_start: 0.5065 (OUTLIER) cc_final: 0.3204 (t80) REVERT: D 401 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7375 (mtpp) REVERT: D 520 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: D 542 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: D 629 ILE cc_start: 0.5301 (pt) cc_final: 0.4961 (mm) REVERT: D 648 TYR cc_start: 0.4788 (m-80) cc_final: 0.3507 (m-80) REVERT: D 650 HIS cc_start: 0.6427 (m-70) cc_final: 0.6022 (t-170) REVERT: D 699 PHE cc_start: 0.3801 (p90) cc_final: 0.3241 (p90) REVERT: D 726 GLU cc_start: 0.7283 (tt0) cc_final: 0.6721 (tp30) REVERT: D 743 LEU cc_start: 0.3425 (OUTLIER) cc_final: 0.3173 (mp) REVERT: D 765 ARG cc_start: 0.4818 (OUTLIER) cc_final: 0.3710 (mpp-170) REVERT: E 35 MET cc_start: 0.8033 (mtm) cc_final: 0.7653 (mtp) REVERT: E 104 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.8451 (t70) REVERT: E 274 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6998 (tppt) REVERT: E 340 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8128 (tp) REVERT: E 341 TRP cc_start: 0.5581 (t60) cc_final: 0.4769 (t60) REVERT: E 358 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.5850 (tt0) REVERT: E 445 LEU cc_start: 0.4335 (OUTLIER) cc_final: 0.4107 (mp) REVERT: E 451 LEU cc_start: 0.6327 (tp) cc_final: 0.6038 (tp) REVERT: E 637 HIS cc_start: 0.6536 (m170) cc_final: 0.6105 (m90) REVERT: E 676 LYS cc_start: 0.3918 (tppt) cc_final: 0.3389 (mttp) REVERT: E 692 LEU cc_start: 0.7271 (mt) cc_final: 0.7008 (mt) REVERT: E 720 ILE cc_start: 0.4939 (mm) cc_final: 0.4244 (mm) REVERT: E 728 PHE cc_start: 0.2461 (m-80) cc_final: 0.1643 (m-80) REVERT: F 17 TYR cc_start: 0.6091 (OUTLIER) cc_final: 0.5086 (m-80) REVERT: F 36 LEU cc_start: 0.8417 (mt) cc_final: 0.8068 (tp) REVERT: F 234 LYS cc_start: 0.6392 (mmtt) cc_final: 0.6066 (ptpp) REVERT: F 388 LYS cc_start: 0.7678 (tptt) cc_final: 0.7319 (ttmt) REVERT: F 434 MET cc_start: 0.7948 (mtp) cc_final: 0.7538 (ptm) REVERT: F 483 ILE cc_start: 0.6556 (tt) cc_final: 0.6146 (tt) REVERT: F 527 LEU cc_start: 0.6157 (pp) cc_final: 0.5830 (tp) REVERT: F 554 ASN cc_start: 0.6229 (m110) cc_final: 0.5669 (m-40) REVERT: F 568 HIS cc_start: 0.6075 (OUTLIER) cc_final: 0.5445 (p-80) REVERT: F 570 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.5950 (pp30) REVERT: F 596 LEU cc_start: 0.7084 (tp) cc_final: 0.6356 (pp) REVERT: F 603 LEU cc_start: 0.7141 (mm) cc_final: 0.6836 (mm) REVERT: F 616 LEU cc_start: 0.6041 (tp) cc_final: 0.5618 (tp) REVERT: F 629 ILE cc_start: 0.5867 (pt) cc_final: 0.5508 (mm) REVERT: F 648 TYR cc_start: 0.4806 (m-80) cc_final: 0.4454 (m-80) REVERT: F 679 THR cc_start: 0.5361 (t) cc_final: 0.5059 (p) REVERT: F 699 PHE cc_start: 0.3622 (p90) cc_final: 0.3393 (p90) REVERT: G 20 LEU cc_start: 0.4968 (mt) cc_final: 0.4746 (tp) REVERT: I 38 ARG cc_start: 0.6564 (ptt180) cc_final: 0.6263 (ptp-170) REVERT: I 83 MET cc_start: 0.2892 (OUTLIER) cc_final: 0.2637 (mpp) REVERT: I 90 ASP cc_start: 0.1713 (OUTLIER) cc_final: 0.1464 (m-30) REVERT: H 25 SER cc_start: 0.5498 (p) cc_final: 0.4848 (m) REVERT: H 32 GLU cc_start: 0.6722 (tp30) cc_final: 0.5470 (tt0) REVERT: H 83 MET cc_start: 0.4448 (OUTLIER) cc_final: 0.3424 (mpp) outliers start: 233 outliers final: 60 residues processed: 825 average time/residue: 0.5445 time to fit residues: 713.0190 Evaluate side-chains 370 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 277 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 520 GLU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 765 ARG Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 570 GLN Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 83 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 5.9990 chunk 350 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 236 optimal weight: 0.6980 chunk 187 optimal weight: 8.9990 chunk 362 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 269 optimal weight: 0.0060 chunk 419 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 ASN A 637 HIS A 709 ASN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 HIS ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 ASN C 637 HIS ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN D 478 HIS D 637 HIS ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 ASN ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 GLN F 467 GLN ** F 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 592 ASN F 650 HIS G 30 GLN I 82 GLN I 84 ASN H 3 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39273 Z= 0.180 Angle : 0.596 13.216 53244 Z= 0.303 Chirality : 0.042 0.172 6096 Planarity : 0.004 0.079 6615 Dihedral : 6.772 73.182 5300 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.04 % Allowed : 14.24 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.12), residues: 4638 helix: 0.05 (0.11), residues: 2118 sheet: -0.69 (0.19), residues: 765 loop : -0.42 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 54 HIS 0.015 0.001 HIS A 637 PHE 0.019 0.001 PHE E 699 TYR 0.020 0.001 TYR H 80 ARG 0.009 0.000 ARG B 762 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 332 time to evaluate : 4.331 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 49 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7463 (pm20) REVERT: A 274 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7101 (mmtt) REVERT: A 278 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.7059 (mt) REVERT: A 340 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7926 (tp) REVERT: A 358 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6049 (pp20) REVERT: A 516 LYS cc_start: 0.6107 (tptt) cc_final: 0.5501 (mtpp) REVERT: A 590 MET cc_start: 0.6531 (mpp) cc_final: 0.5818 (mmp) REVERT: A 598 LEU cc_start: 0.6234 (mt) cc_final: 0.5979 (mm) REVERT: A 663 ASN cc_start: 0.5072 (m110) cc_final: 0.4494 (t0) REVERT: B 17 TYR cc_start: 0.6232 (OUTLIER) cc_final: 0.4943 (m-80) REVERT: B 36 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7827 (tp) REVERT: B 104 HIS cc_start: 0.8782 (OUTLIER) cc_final: 0.8359 (t70) REVERT: B 353 PHE cc_start: 0.4469 (OUTLIER) cc_final: 0.2376 (t80) REVERT: B 434 MET cc_start: 0.7580 (mtp) cc_final: 0.7071 (ptm) REVERT: B 592 ASN cc_start: 0.7954 (m-40) cc_final: 0.7641 (t0) REVERT: B 623 ASP cc_start: 0.6751 (OUTLIER) cc_final: 0.6167 (t0) REVERT: B 650 HIS cc_start: 0.6797 (m90) cc_final: 0.6285 (t-170) REVERT: B 668 TYR cc_start: 0.5749 (m-80) cc_final: 0.4760 (m-10) REVERT: C 154 GLU cc_start: 0.7630 (pt0) cc_final: 0.7344 (tp30) REVERT: C 294 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8127 (m-30) REVERT: C 340 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8198 (tp) REVERT: C 451 LEU cc_start: 0.6553 (tp) cc_final: 0.6339 (tp) REVERT: C 590 MET cc_start: 0.6098 (mpp) cc_final: 0.5809 (mmt) REVERT: C 686 LYS cc_start: 0.6086 (tppt) cc_final: 0.5660 (mtmt) REVERT: D 17 TYR cc_start: 0.6177 (OUTLIER) cc_final: 0.5120 (m-80) REVERT: D 36 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7878 (tp) REVERT: D 338 TYR cc_start: 0.7208 (t80) cc_final: 0.6843 (t80) REVERT: D 343 MET cc_start: 0.8219 (ttm) cc_final: 0.7916 (mtp) REVERT: D 353 PHE cc_start: 0.4882 (OUTLIER) cc_final: 0.2886 (t80) REVERT: D 390 PHE cc_start: 0.7016 (t80) cc_final: 0.6389 (t80) REVERT: D 401 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7414 (mtpp) REVERT: D 441 THR cc_start: 0.5324 (OUTLIER) cc_final: 0.5117 (m) REVERT: D 542 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6583 (mp0) REVERT: D 625 ASN cc_start: 0.5812 (OUTLIER) cc_final: 0.5532 (m-40) REVERT: D 629 ILE cc_start: 0.5323 (pt) cc_final: 0.4750 (mm) REVERT: D 650 HIS cc_start: 0.6272 (m-70) cc_final: 0.6015 (t-170) REVERT: D 726 GLU cc_start: 0.7069 (tt0) cc_final: 0.6604 (tp30) REVERT: D 743 LEU cc_start: 0.3387 (OUTLIER) cc_final: 0.3177 (mp) REVERT: D 756 LEU cc_start: 0.7095 (tp) cc_final: 0.6521 (mt) REVERT: D 765 ARG cc_start: 0.4992 (OUTLIER) cc_final: 0.4023 (mpp-170) REVERT: D 794 LEU cc_start: 0.4365 (mt) cc_final: 0.4008 (pp) REVERT: E 35 MET cc_start: 0.7888 (mtm) cc_final: 0.7657 (mtp) REVERT: E 104 HIS cc_start: 0.9038 (OUTLIER) cc_final: 0.8365 (t70) REVERT: E 160 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7042 (mt) REVERT: E 274 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6703 (mmtt) REVERT: E 292 ASP cc_start: 0.8804 (p0) cc_final: 0.8051 (p0) REVERT: E 341 TRP cc_start: 0.5475 (t60) cc_final: 0.4995 (t60) REVERT: E 354 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: E 358 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.5858 (pt0) REVERT: E 402 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5698 (mp) REVERT: E 676 LYS cc_start: 0.4289 (tppt) cc_final: 0.3446 (mttp) REVERT: E 692 LEU cc_start: 0.7524 (mt) cc_final: 0.7304 (mt) REVERT: E 720 ILE cc_start: 0.5104 (mm) cc_final: 0.4689 (mm) REVERT: E 738 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6252 (pp) REVERT: F 17 TYR cc_start: 0.5941 (OUTLIER) cc_final: 0.4915 (m-80) REVERT: F 36 LEU cc_start: 0.8477 (mt) cc_final: 0.8178 (tp) REVERT: F 234 LYS cc_start: 0.6068 (mmtt) cc_final: 0.5750 (ptpp) REVERT: F 350 LYS cc_start: 0.6488 (tptt) cc_final: 0.5725 (mmtm) REVERT: F 353 PHE cc_start: 0.4836 (OUTLIER) cc_final: 0.2155 (t80) REVERT: F 434 MET cc_start: 0.7864 (mtp) cc_final: 0.7513 (ptm) REVERT: F 527 LEU cc_start: 0.5989 (OUTLIER) cc_final: 0.5649 (tp) REVERT: F 554 ASN cc_start: 0.5957 (m110) cc_final: 0.5373 (m-40) REVERT: F 568 HIS cc_start: 0.6483 (OUTLIER) cc_final: 0.5878 (p-80) REVERT: F 589 LYS cc_start: 0.5270 (mttm) cc_final: 0.4762 (tppt) REVERT: F 592 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7595 (t0) REVERT: F 603 LEU cc_start: 0.7070 (mm) cc_final: 0.6858 (mm) REVERT: F 629 ILE cc_start: 0.5763 (pt) cc_final: 0.5540 (mm) REVERT: F 756 LEU cc_start: 0.6486 (tp) cc_final: 0.6014 (mt) REVERT: F 767 GLU cc_start: 0.6177 (mp0) cc_final: 0.5682 (pm20) REVERT: G 18 LEU cc_start: 0.2884 (tp) cc_final: 0.2680 (tp) REVERT: I 90 ASP cc_start: 0.2064 (OUTLIER) cc_final: 0.1665 (m-30) REVERT: H 25 SER cc_start: 0.5346 (p) cc_final: 0.4983 (m) REVERT: H 81 LEU cc_start: 0.6406 (tp) cc_final: 0.6092 (tp) outliers start: 173 outliers final: 75 residues processed: 475 average time/residue: 0.5252 time to fit residues: 410.0664 Evaluate side-chains 361 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 252 time to evaluate : 4.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 637 HIS Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 765 ARG Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 592 ASN Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 349 optimal weight: 5.9990 chunk 285 optimal weight: 0.9980 chunk 115 optimal weight: 0.0070 chunk 420 optimal weight: 5.9990 chunk 454 optimal weight: 8.9990 chunk 374 optimal weight: 2.9990 chunk 416 optimal weight: 0.0270 chunk 143 optimal weight: 0.8980 chunk 337 optimal weight: 4.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 ASN A 592 ASN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS D 637 HIS ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 672 ASN ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 39273 Z= 0.147 Angle : 0.529 11.061 53244 Z= 0.270 Chirality : 0.040 0.174 6096 Planarity : 0.003 0.034 6615 Dihedral : 6.095 72.486 5250 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.97 % Allowed : 15.22 % Favored : 80.81 % 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: -0.41 (0.12), residues: 4638 helix: 0.11 (0.11), residues: 2121 sheet: -0.58 (0.19), residues: 762 loop : -0.38 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 143 HIS 0.010 0.001 HIS B 637 PHE 0.014 0.001 PHE E 699 TYR 0.015 0.001 TYR E 281 ARG 0.007 0.000 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 299 time to evaluate : 4.699 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 49 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: A 274 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7209 (mmtt) REVERT: A 278 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.7102 (mt) REVERT: A 340 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8036 (tp) REVERT: A 344 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7672 (tp) REVERT: A 358 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6063 (pp20) REVERT: A 590 MET cc_start: 0.6536 (mpp) cc_final: 0.5813 (mmp) REVERT: A 598 LEU cc_start: 0.6226 (mt) cc_final: 0.5978 (mm) REVERT: A 663 ASN cc_start: 0.5090 (m110) cc_final: 0.4619 (t0) REVERT: B 17 TYR cc_start: 0.6129 (OUTLIER) cc_final: 0.4762 (m-80) REVERT: B 36 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7842 (tp) REVERT: B 104 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.8290 (t70) REVERT: B 343 MET cc_start: 0.8305 (ttp) cc_final: 0.7943 (mtp) REVERT: B 353 PHE cc_start: 0.4332 (OUTLIER) cc_final: 0.2182 (t80) REVERT: B 434 MET cc_start: 0.7560 (mtp) cc_final: 0.7040 (ptm) REVERT: B 592 ASN cc_start: 0.7883 (m-40) cc_final: 0.7380 (t0) REVERT: B 623 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6261 (t0) REVERT: B 650 HIS cc_start: 0.6775 (m90) cc_final: 0.6257 (t-170) REVERT: C 35 MET cc_start: 0.7665 (mtp) cc_final: 0.7380 (mtp) REVERT: C 154 GLU cc_start: 0.7557 (pt0) cc_final: 0.7252 (tp30) REVERT: C 294 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: C 340 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8099 (tp) REVERT: C 358 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.5756 (pp20) REVERT: C 451 LEU cc_start: 0.6540 (tp) cc_final: 0.6318 (tp) REVERT: C 516 LYS cc_start: 0.6053 (tptt) cc_final: 0.4436 (mttm) REVERT: C 555 LEU cc_start: 0.3945 (OUTLIER) cc_final: 0.3355 (mt) REVERT: C 590 MET cc_start: 0.6050 (mpp) cc_final: 0.5780 (mmt) REVERT: C 686 LYS cc_start: 0.5733 (tppt) cc_final: 0.5516 (mtmt) REVERT: C 720 ILE cc_start: 0.5213 (mp) cc_final: 0.4672 (tt) REVERT: D 36 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8033 (tp) REVERT: D 173 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6314 (mm) REVERT: D 338 TYR cc_start: 0.7066 (t80) cc_final: 0.6799 (t80) REVERT: D 343 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8016 (mtp) REVERT: D 353 PHE cc_start: 0.4794 (OUTLIER) cc_final: 0.2871 (t80) REVERT: D 390 PHE cc_start: 0.6965 (t80) cc_final: 0.6359 (t80) REVERT: D 401 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7497 (mtpp) REVERT: D 625 ASN cc_start: 0.5853 (OUTLIER) cc_final: 0.5581 (m-40) REVERT: D 629 ILE cc_start: 0.5038 (pt) cc_final: 0.4522 (mm) REVERT: D 756 LEU cc_start: 0.7050 (tp) cc_final: 0.6456 (mt) REVERT: D 765 ARG cc_start: 0.4952 (OUTLIER) cc_final: 0.3976 (mpp-170) REVERT: E 35 MET cc_start: 0.7865 (mtm) cc_final: 0.7503 (mtp) REVERT: E 104 HIS cc_start: 0.9066 (OUTLIER) cc_final: 0.8408 (t70) REVERT: E 160 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7105 (mt) REVERT: E 274 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6652 (mmtt) REVERT: E 292 ASP cc_start: 0.8685 (p0) cc_final: 0.8103 (p0) REVERT: E 341 TRP cc_start: 0.5487 (t60) cc_final: 0.4976 (t60) REVERT: E 354 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: E 358 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.5771 (pt0) REVERT: E 639 HIS cc_start: 0.6364 (p90) cc_final: 0.5997 (p-80) REVERT: E 676 LYS cc_start: 0.4323 (tppt) cc_final: 0.3480 (mttp) REVERT: E 720 ILE cc_start: 0.5188 (mm) cc_final: 0.4804 (mm) REVERT: E 738 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6232 (pp) REVERT: F 17 TYR cc_start: 0.5883 (OUTLIER) cc_final: 0.4863 (m-80) REVERT: F 36 LEU cc_start: 0.8387 (mt) cc_final: 0.8067 (tp) REVERT: F 350 LYS cc_start: 0.6384 (tptt) cc_final: 0.5580 (mmtm) REVERT: F 353 PHE cc_start: 0.4517 (OUTLIER) cc_final: 0.1978 (t80) REVERT: F 434 MET cc_start: 0.7827 (mtp) cc_final: 0.7501 (ptm) REVERT: F 527 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.5592 (tp) REVERT: F 554 ASN cc_start: 0.5927 (m110) cc_final: 0.5346 (m-40) REVERT: F 568 HIS cc_start: 0.6110 (OUTLIER) cc_final: 0.5400 (p-80) REVERT: F 589 LYS cc_start: 0.5013 (mttm) cc_final: 0.4791 (tppt) REVERT: F 603 LEU cc_start: 0.6910 (mm) cc_final: 0.6597 (mm) REVERT: F 736 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7274 (pp) REVERT: F 756 LEU cc_start: 0.6386 (tp) cc_final: 0.5893 (mt) REVERT: I 30 GLN cc_start: 0.5640 (OUTLIER) cc_final: 0.5286 (pp30) REVERT: I 90 ASP cc_start: 0.1873 (OUTLIER) cc_final: 0.0496 (t0) REVERT: H 19 ARG cc_start: 0.6106 (tpp80) cc_final: 0.5866 (tpp80) REVERT: H 25 SER cc_start: 0.5467 (p) cc_final: 0.5103 (m) REVERT: H 32 GLU cc_start: 0.7450 (tt0) cc_final: 0.6369 (tp30) REVERT: H 54 TRP cc_start: 0.4767 (p90) cc_final: 0.3694 (p90) REVERT: H 74 ASN cc_start: 0.6467 (OUTLIER) cc_final: 0.5787 (t0) outliers start: 170 outliers final: 76 residues processed: 444 average time/residue: 0.5202 time to fit residues: 389.2806 Evaluate side-chains 364 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 252 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 699 PHE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 622 LYS Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 637 HIS Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 765 ARG Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 685 ARG Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 4.9990 chunk 316 optimal weight: 5.9990 chunk 218 optimal weight: 0.3980 chunk 46 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 421 optimal weight: 2.9990 chunk 446 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 399 optimal weight: 0.0040 chunk 120 optimal weight: 0.8980 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN B 478 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN D 478 HIS D 592 ASN D 637 HIS E 105 GLN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 ASN ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 GLN G 30 GLN H 30 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39273 Z= 0.184 Angle : 0.532 10.537 53244 Z= 0.272 Chirality : 0.041 0.149 6096 Planarity : 0.003 0.038 6615 Dihedral : 5.921 72.365 5232 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.60 % Allowed : 15.64 % Favored : 79.76 % 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: -0.41 (0.12), residues: 4638 helix: 0.10 (0.11), residues: 2124 sheet: -0.46 (0.20), residues: 732 loop : -0.42 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 143 HIS 0.011 0.001 HIS A 499 PHE 0.014 0.001 PHE D 611 TYR 0.017 0.001 TYR E 653 ARG 0.005 0.000 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 265 time to evaluate : 4.005 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 49 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7567 (pm20) REVERT: A 274 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7200 (mmtt) REVERT: A 340 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8074 (tp) REVERT: A 344 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7640 (tp) REVERT: A 358 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6046 (pp20) REVERT: A 590 MET cc_start: 0.6595 (mpp) cc_final: 0.5839 (mmp) REVERT: A 663 ASN cc_start: 0.5072 (m110) cc_final: 0.4608 (t0) REVERT: A 720 ILE cc_start: 0.4795 (OUTLIER) cc_final: 0.4365 (tp) REVERT: B 17 TYR cc_start: 0.6125 (OUTLIER) cc_final: 0.4740 (m-80) REVERT: B 36 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7899 (tp) REVERT: B 104 HIS cc_start: 0.8791 (OUTLIER) cc_final: 0.8301 (t70) REVERT: B 353 PHE cc_start: 0.4333 (OUTLIER) cc_final: 0.1966 (t80) REVERT: B 434 MET cc_start: 0.7489 (mtp) cc_final: 0.7170 (ptm) REVERT: B 592 ASN cc_start: 0.8087 (m-40) cc_final: 0.7367 (t0) REVERT: B 623 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6406 (t0) REVERT: B 650 HIS cc_start: 0.6895 (m90) cc_final: 0.6354 (t-170) REVERT: C 35 MET cc_start: 0.7456 (mtp) cc_final: 0.7047 (mtp) REVERT: C 103 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6553 (tmm-80) REVERT: C 154 GLU cc_start: 0.7559 (pt0) cc_final: 0.7249 (tp30) REVERT: C 294 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: C 340 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8146 (tp) REVERT: C 358 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.5821 (pp20) REVERT: C 590 MET cc_start: 0.6259 (mpp) cc_final: 0.5985 (mmt) REVERT: C 720 ILE cc_start: 0.5324 (OUTLIER) cc_final: 0.4734 (tt) REVERT: D 17 TYR cc_start: 0.6231 (OUTLIER) cc_final: 0.5176 (m-80) REVERT: D 36 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8045 (tp) REVERT: D 173 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6402 (mm) REVERT: D 232 LEU cc_start: 0.5200 (OUTLIER) cc_final: 0.4969 (pp) REVERT: D 343 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7922 (mtp) REVERT: D 353 PHE cc_start: 0.4858 (OUTLIER) cc_final: 0.2895 (t80) REVERT: D 401 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7606 (mtpp) REVERT: D 542 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6474 (mp0) REVERT: D 756 LEU cc_start: 0.7092 (tp) cc_final: 0.6536 (mt) REVERT: D 765 ARG cc_start: 0.4849 (OUTLIER) cc_final: 0.3816 (mpp-170) REVERT: E 35 MET cc_start: 0.7880 (mtm) cc_final: 0.7566 (mtp) REVERT: E 104 HIS cc_start: 0.9071 (OUTLIER) cc_final: 0.8429 (t70) REVERT: E 160 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7111 (mt) REVERT: E 274 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6778 (mmtt) REVERT: E 341 TRP cc_start: 0.5690 (t60) cc_final: 0.5062 (t60) REVERT: E 354 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: E 358 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.5794 (pt0) REVERT: E 516 LYS cc_start: 0.6324 (tptt) cc_final: 0.4867 (mttm) REVERT: E 623 ASP cc_start: 0.8544 (t0) cc_final: 0.8066 (t70) REVERT: E 639 HIS cc_start: 0.6370 (p90) cc_final: 0.6014 (p-80) REVERT: E 676 LYS cc_start: 0.4225 (tppt) cc_final: 0.3323 (mttp) REVERT: E 720 ILE cc_start: 0.5262 (mm) cc_final: 0.4889 (mm) REVERT: E 738 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6251 (pp) REVERT: F 17 TYR cc_start: 0.5966 (OUTLIER) cc_final: 0.4843 (m-80) REVERT: F 36 LEU cc_start: 0.8372 (mt) cc_final: 0.8068 (tp) REVERT: F 350 LYS cc_start: 0.6404 (tptt) cc_final: 0.5546 (mmtm) REVERT: F 353 PHE cc_start: 0.4014 (OUTLIER) cc_final: 0.1310 (t80) REVERT: F 434 MET cc_start: 0.7885 (mtp) cc_final: 0.7561 (ptm) REVERT: F 527 LEU cc_start: 0.5833 (OUTLIER) cc_final: 0.5470 (tp) REVERT: F 554 ASN cc_start: 0.5845 (m110) cc_final: 0.5367 (m-40) REVERT: F 568 HIS cc_start: 0.6155 (OUTLIER) cc_final: 0.5415 (p-80) REVERT: F 575 ASN cc_start: 0.5105 (OUTLIER) cc_final: 0.4678 (t0) REVERT: F 589 LYS cc_start: 0.5217 (mttm) cc_final: 0.4951 (tppt) REVERT: F 603 LEU cc_start: 0.7004 (mm) cc_final: 0.6772 (mm) REVERT: F 645 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7122 (pttm) REVERT: F 736 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7350 (pp) REVERT: F 756 LEU cc_start: 0.6477 (tp) cc_final: 0.6032 (mt) REVERT: F 767 GLU cc_start: 0.6252 (mp0) cc_final: 0.5703 (pm20) REVERT: I 90 ASP cc_start: 0.1984 (OUTLIER) cc_final: 0.0855 (t0) REVERT: H 25 SER cc_start: 0.5540 (p) cc_final: 0.5183 (m) REVERT: H 30 GLN cc_start: 0.4480 (OUTLIER) cc_final: 0.4271 (pp30) REVERT: H 32 GLU cc_start: 0.7505 (tt0) cc_final: 0.7146 (tt0) REVERT: H 54 TRP cc_start: 0.5067 (p90) cc_final: 0.4075 (p90) REVERT: H 74 ASN cc_start: 0.6467 (OUTLIER) cc_final: 0.5815 (t0) outliers start: 197 outliers final: 103 residues processed: 434 average time/residue: 0.4860 time to fit residues: 353.9119 Evaluate side-chains 381 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 237 time to evaluate : 4.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 699 PHE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 637 HIS Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 761 LEU Chi-restraints excluded: chain D residue 765 ARG Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 685 ARG Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 575 ASN Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 645 LYS Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 6.9990 chunk 253 optimal weight: 7.9990 chunk 6 optimal weight: 0.0070 chunk 332 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 381 optimal weight: 3.9990 chunk 308 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 400 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 HIS ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 ASN C 650 HIS ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS D 649 ASN D 650 HIS D 663 ASN E 253 HIS E 312 HIS ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 592 ASN ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN F 467 GLN F 614 HIS F 663 ASN I 30 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 39273 Z= 0.538 Angle : 0.853 11.649 53244 Z= 0.440 Chirality : 0.052 0.253 6096 Planarity : 0.006 0.068 6615 Dihedral : 7.233 75.587 5229 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 6.40 % Allowed : 16.95 % Favored : 76.66 % Cbeta Deviations : 0.02 % 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: -1.52 (0.12), residues: 4638 helix: -0.84 (0.11), residues: 2109 sheet: -0.82 (0.20), residues: 744 loop : -1.06 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP B 143 HIS 0.034 0.002 HIS D 637 PHE 0.033 0.003 PHE C 146 TYR 0.031 0.003 TYR E 668 ARG 0.008 0.001 ARG D 545 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 257 time to evaluate : 4.529 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: A 35 MET cc_start: 0.7983 (mtp) cc_final: 0.7435 (mtp) REVERT: A 49 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7877 (pm20) REVERT: A 274 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7094 (ttmm) REVERT: A 337 MET cc_start: 0.7739 (mtm) cc_final: 0.7478 (ptp) REVERT: A 358 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6134 (pp20) REVERT: A 419 ARG cc_start: 0.5640 (OUTLIER) cc_final: 0.5192 (ttm110) REVERT: A 590 MET cc_start: 0.6926 (mpp) cc_final: 0.6276 (mmp) REVERT: A 720 ILE cc_start: 0.5149 (OUTLIER) cc_final: 0.4628 (tt) REVERT: B 17 TYR cc_start: 0.6482 (OUTLIER) cc_final: 0.5110 (m-80) REVERT: B 104 HIS cc_start: 0.8965 (OUTLIER) cc_final: 0.8688 (t70) REVERT: B 115 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7641 (tm-30) REVERT: B 353 PHE cc_start: 0.4350 (OUTLIER) cc_final: 0.2109 (t80) REVERT: B 377 HIS cc_start: 0.6976 (OUTLIER) cc_final: 0.5597 (m90) REVERT: B 434 MET cc_start: 0.7777 (mtp) cc_final: 0.7420 (ptm) REVERT: B 561 VAL cc_start: 0.3943 (OUTLIER) cc_final: 0.3497 (m) REVERT: B 623 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.6893 (t0) REVERT: B 650 HIS cc_start: 0.7199 (m90) cc_final: 0.6312 (t-170) REVERT: C 35 MET cc_start: 0.7861 (mtp) cc_final: 0.7540 (mtp) REVERT: C 103 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6922 (tmm-80) REVERT: C 301 SER cc_start: 0.8660 (p) cc_final: 0.8368 (t) REVERT: C 358 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.5770 (pp20) REVERT: C 516 LYS cc_start: 0.5648 (tptt) cc_final: 0.5399 (tptt) REVERT: C 590 MET cc_start: 0.6764 (mpp) cc_final: 0.6444 (mmt) REVERT: C 614 HIS cc_start: 0.6002 (m90) cc_final: 0.5465 (m-70) REVERT: C 686 LYS cc_start: 0.6092 (tppt) cc_final: 0.5634 (mttm) REVERT: D 343 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7718 (mtp) REVERT: D 353 PHE cc_start: 0.4810 (OUTLIER) cc_final: 0.2554 (t80) REVERT: D 401 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7505 (mtpp) REVERT: D 519 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6249 (mm-30) REVERT: D 689 TYR cc_start: 0.6397 (m-80) cc_final: 0.5943 (t80) REVERT: D 765 ARG cc_start: 0.4152 (OUTLIER) cc_final: 0.3360 (mpp-170) REVERT: E 341 TRP cc_start: 0.6406 (t60) cc_final: 0.5729 (t-100) REVERT: E 354 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6076 (mp0) REVERT: E 358 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.5960 (pt0) REVERT: E 370 ASN cc_start: 0.6751 (OUTLIER) cc_final: 0.6443 (p0) REVERT: E 623 ASP cc_start: 0.8512 (t0) cc_final: 0.8044 (t0) REVERT: E 720 ILE cc_start: 0.5946 (mm) cc_final: 0.5682 (mm) REVERT: E 738 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6494 (pp) REVERT: F 17 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.4650 (m-80) REVERT: F 37 MET cc_start: 0.7350 (mmp) cc_final: 0.7137 (mmp) REVERT: F 234 LYS cc_start: 0.6197 (mmtt) cc_final: 0.5601 (ptpp) REVERT: F 350 LYS cc_start: 0.6951 (tptt) cc_final: 0.5594 (mmtm) REVERT: F 353 PHE cc_start: 0.3676 (OUTLIER) cc_final: 0.1194 (t80) REVERT: F 434 MET cc_start: 0.8013 (mtp) cc_final: 0.7562 (ptm) REVERT: F 527 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5144 (tp) REVERT: F 568 HIS cc_start: 0.6103 (OUTLIER) cc_final: 0.5864 (p-80) REVERT: F 645 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7207 (pttm) REVERT: F 736 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6929 (pp) REVERT: I 25 SER cc_start: 0.6724 (p) cc_final: 0.6379 (m) REVERT: I 32 GLU cc_start: 0.6514 (tp30) cc_final: 0.6067 (pt0) outliers start: 274 outliers final: 163 residues processed: 501 average time/residue: 0.4939 time to fit residues: 412.6180 Evaluate side-chains 395 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 204 time to evaluate : 4.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 698 THR Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 482 LYS Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 622 LYS Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 719 ARG Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 761 LEU Chi-restraints excluded: chain D residue 765 ARG Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 598 LEU Chi-restraints excluded: chain E residue 685 ARG Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 438 ILE Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 645 LYS Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 0.8980 chunk 402 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 262 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 447 optimal weight: 10.0000 chunk 371 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN A 431 HIS ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 HIS A 657 GLN A 660 ASN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS D 636 GLN D 650 HIS ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 GLN F 650 HIS ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 ASN H 84 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39273 Z= 0.183 Angle : 0.572 9.796 53244 Z= 0.293 Chirality : 0.042 0.293 6096 Planarity : 0.004 0.043 6615 Dihedral : 6.075 72.606 5210 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.41 % Allowed : 19.30 % Favored : 76.28 % 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: -0.96 (0.12), residues: 4638 helix: -0.29 (0.11), residues: 2106 sheet: -0.66 (0.20), residues: 744 loop : -0.85 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 143 HIS 0.012 0.001 HIS A 637 PHE 0.022 0.001 PHE D 611 TYR 0.027 0.001 TYR B 264 ARG 0.005 0.000 ARG F 309 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 239 time to evaluate : 4.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: A 274 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6891 (mmtt) REVERT: A 292 ASP cc_start: 0.8761 (p0) cc_final: 0.7967 (p0) REVERT: A 340 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8003 (tp) REVERT: A 344 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7902 (tp) REVERT: A 358 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6012 (pp20) REVERT: A 434 MET cc_start: 0.6845 (mmm) cc_final: 0.6464 (mmm) REVERT: A 590 MET cc_start: 0.6424 (mpp) cc_final: 0.5748 (mmp) REVERT: A 720 ILE cc_start: 0.4950 (OUTLIER) cc_final: 0.4422 (tt) REVERT: A 756 LEU cc_start: 0.4399 (OUTLIER) cc_final: 0.3339 (tp) REVERT: B 17 TYR cc_start: 0.5880 (OUTLIER) cc_final: 0.4864 (m-80) REVERT: B 104 HIS cc_start: 0.8863 (OUTLIER) cc_final: 0.8182 (t70) REVERT: B 353 PHE cc_start: 0.4496 (OUTLIER) cc_final: 0.2229 (t80) REVERT: B 377 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.5606 (m90) REVERT: B 434 MET cc_start: 0.7717 (mtp) cc_final: 0.7356 (ptm) REVERT: B 623 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7044 (t0) REVERT: B 650 HIS cc_start: 0.7299 (m90) cc_final: 0.6649 (t-170) REVERT: C 35 MET cc_start: 0.7517 (mtp) cc_final: 0.7189 (mtp) REVERT: C 294 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8171 (m-30) REVERT: C 301 SER cc_start: 0.8430 (p) cc_final: 0.7949 (t) REVERT: C 340 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8111 (tp) REVERT: C 358 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.5738 (pp20) REVERT: C 370 ASN cc_start: 0.6649 (OUTLIER) cc_final: 0.6399 (p0) REVERT: C 590 MET cc_start: 0.6655 (mpp) cc_final: 0.6425 (mmt) REVERT: C 663 ASN cc_start: 0.5095 (OUTLIER) cc_final: 0.4619 (t0) REVERT: D 17 TYR cc_start: 0.6185 (OUTLIER) cc_final: 0.5711 (m-80) REVERT: D 173 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7065 (mm) REVERT: D 279 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7607 (tt) REVERT: D 343 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7731 (mtp) REVERT: D 353 PHE cc_start: 0.4813 (OUTLIER) cc_final: 0.2156 (t80) REVERT: D 401 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7339 (mtpp) REVERT: D 689 TYR cc_start: 0.6349 (m-80) cc_final: 0.6033 (t80) REVERT: D 723 LEU cc_start: 0.5775 (tp) cc_final: 0.5370 (mp) REVERT: D 765 ARG cc_start: 0.4188 (OUTLIER) cc_final: 0.3422 (mpp-170) REVERT: E 341 TRP cc_start: 0.6444 (t60) cc_final: 0.5721 (t-100) REVERT: E 354 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.5980 (mp0) REVERT: E 358 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.5948 (pt0) REVERT: E 370 ASN cc_start: 0.6551 (OUTLIER) cc_final: 0.6259 (p0) REVERT: E 516 LYS cc_start: 0.5701 (tptt) cc_final: 0.4086 (mttm) REVERT: E 623 ASP cc_start: 0.8509 (t0) cc_final: 0.8051 (t0) REVERT: E 653 TYR cc_start: 0.4620 (p90) cc_final: 0.4304 (p90) REVERT: E 720 ILE cc_start: 0.5533 (mm) cc_final: 0.5189 (mm) REVERT: E 738 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6356 (pp) REVERT: F 17 TYR cc_start: 0.6030 (OUTLIER) cc_final: 0.4601 (m-80) REVERT: F 350 LYS cc_start: 0.6753 (tptt) cc_final: 0.5551 (mmtm) REVERT: F 353 PHE cc_start: 0.4485 (OUTLIER) cc_final: 0.1528 (t80) REVERT: F 434 MET cc_start: 0.7941 (mtp) cc_final: 0.7258 (ptm) REVERT: F 527 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.4842 (tp) REVERT: F 554 ASN cc_start: 0.5503 (m110) cc_final: 0.5236 (m-40) REVERT: F 568 HIS cc_start: 0.6075 (OUTLIER) cc_final: 0.5246 (p-80) REVERT: F 645 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7446 (pttm) REVERT: F 736 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7391 (pp) REVERT: I 32 GLU cc_start: 0.6502 (tp30) cc_final: 0.6223 (tp30) REVERT: H 74 ASN cc_start: 0.6455 (OUTLIER) cc_final: 0.5843 (t0) outliers start: 189 outliers final: 112 residues processed: 408 average time/residue: 0.4823 time to fit residues: 333.4565 Evaluate side-chains 360 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 213 time to evaluate : 4.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 663 ASN Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 699 PHE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 482 LYS Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 622 LYS Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 761 LEU Chi-restraints excluded: chain D residue 765 ARG Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 598 LEU Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 685 ARG Chi-restraints excluded: chain E residue 699 PHE Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 645 LYS Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 326 optimal weight: 9.9990 chunk 252 optimal weight: 4.9990 chunk 376 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 445 optimal weight: 0.9980 chunk 278 optimal weight: 20.0000 chunk 271 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 GLN ** F 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN ** F 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 39273 Z= 0.456 Angle : 0.750 13.560 53244 Z= 0.384 Chirality : 0.048 0.196 6096 Planarity : 0.005 0.049 6615 Dihedral : 6.614 74.690 5203 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.18 % Allowed : 19.63 % Favored : 75.19 % 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: -1.50 (0.12), residues: 4638 helix: -0.71 (0.11), residues: 2106 sheet: -0.89 (0.20), residues: 732 loop : -1.18 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 143 HIS 0.012 0.002 HIS F 104 PHE 0.025 0.002 PHE C 146 TYR 0.031 0.003 TYR F 264 ARG 0.008 0.001 ARG D 496 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 219 time to evaluate : 4.554 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: A 35 MET cc_start: 0.7900 (mtp) cc_final: 0.7361 (mtp) REVERT: A 49 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: A 274 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7424 (tptt) REVERT: A 337 MET cc_start: 0.7732 (mtm) cc_final: 0.7466 (ptp) REVERT: A 358 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6622 (mm-30) REVERT: A 419 ARG cc_start: 0.5832 (OUTLIER) cc_final: 0.5264 (ttm110) REVERT: A 720 ILE cc_start: 0.5047 (OUTLIER) cc_final: 0.4516 (tt) REVERT: B 17 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.4898 (m-80) REVERT: B 353 PHE cc_start: 0.4458 (OUTLIER) cc_final: 0.2102 (t80) REVERT: B 377 HIS cc_start: 0.6995 (OUTLIER) cc_final: 0.5803 (m90) REVERT: B 434 MET cc_start: 0.7774 (mtp) cc_final: 0.7441 (ptm) REVERT: B 622 LYS cc_start: 0.3335 (OUTLIER) cc_final: 0.2852 (mmtm) REVERT: B 623 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7142 (t0) REVERT: B 650 HIS cc_start: 0.7349 (m90) cc_final: 0.6420 (t-170) REVERT: C 35 MET cc_start: 0.7775 (mtp) cc_final: 0.7452 (mtp) REVERT: C 103 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6767 (tmm-80) REVERT: C 358 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6105 (pp20) REVERT: C 516 LYS cc_start: 0.5432 (tptt) cc_final: 0.5137 (tptt) REVERT: C 614 HIS cc_start: 0.6040 (m90) cc_final: 0.5521 (m170) REVERT: C 663 ASN cc_start: 0.4943 (OUTLIER) cc_final: 0.4444 (t0) REVERT: C 699 PHE cc_start: 0.5886 (OUTLIER) cc_final: 0.4897 (t80) REVERT: D 173 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7131 (mm) REVERT: D 343 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7802 (mtp) REVERT: D 353 PHE cc_start: 0.5004 (OUTLIER) cc_final: 0.2732 (t80) REVERT: D 401 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7402 (mtpp) REVERT: D 571 LYS cc_start: 0.7010 (tttm) cc_final: 0.6797 (ttmt) REVERT: D 689 TYR cc_start: 0.6381 (m-80) cc_final: 0.5869 (t80) REVERT: E 341 TRP cc_start: 0.6568 (t60) cc_final: 0.5795 (t-100) REVERT: E 354 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6117 (mp0) REVERT: E 358 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.5831 (pt0) REVERT: E 370 ASN cc_start: 0.6634 (OUTLIER) cc_final: 0.6376 (p0) REVERT: E 516 LYS cc_start: 0.5734 (tptt) cc_final: 0.3788 (mttm) REVERT: E 623 ASP cc_start: 0.8478 (t0) cc_final: 0.8061 (t0) REVERT: E 738 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6420 (pp) REVERT: F 17 TYR cc_start: 0.6155 (OUTLIER) cc_final: 0.4610 (m-80) REVERT: F 343 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7550 (mtp) REVERT: F 353 PHE cc_start: 0.4234 (OUTLIER) cc_final: 0.1318 (t80) REVERT: F 434 MET cc_start: 0.7981 (mtp) cc_final: 0.7506 (ptm) REVERT: F 527 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.4577 (tt) REVERT: F 568 HIS cc_start: 0.5966 (OUTLIER) cc_final: 0.5098 (p-80) REVERT: F 736 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7155 (pp) REVERT: I 25 SER cc_start: 0.6386 (p) cc_final: 0.6009 (m) REVERT: I 32 GLU cc_start: 0.6475 (tp30) cc_final: 0.6003 (pt0) REVERT: H 70 VAL cc_start: 0.1709 (OUTLIER) cc_final: 0.1310 (t) REVERT: H 74 ASN cc_start: 0.6566 (OUTLIER) cc_final: 0.5881 (t0) outliers start: 222 outliers final: 158 residues processed: 419 average time/residue: 0.4821 time to fit residues: 342.7332 Evaluate side-chains 386 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 198 time to evaluate : 4.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 663 ASN Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 699 PHE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 482 LYS Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 622 LYS Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 719 ARG Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 761 LEU Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 598 LEU Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 685 ARG Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 343 MET Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 562 VAL Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 chunk 265 optimal weight: 0.9980 chunk 134 optimal weight: 0.0970 chunk 87 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 283 optimal weight: 5.9990 chunk 303 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 350 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS D 650 HIS ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 GLN ** F 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39273 Z= 0.190 Angle : 0.579 9.693 53244 Z= 0.295 Chirality : 0.042 0.241 6096 Planarity : 0.004 0.044 6615 Dihedral : 5.983 71.904 5197 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.39 % Allowed : 20.59 % Favored : 75.02 % 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: -1.09 (0.12), residues: 4638 helix: -0.36 (0.11), residues: 2103 sheet: -0.75 (0.20), residues: 729 loop : -0.94 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 143 HIS 0.016 0.001 HIS D 650 PHE 0.021 0.001 PHE E 374 TYR 0.028 0.001 TYR F 264 ARG 0.003 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 223 time to evaluate : 4.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: A 274 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.6979 (mmtt) REVERT: A 292 ASP cc_start: 0.8672 (p0) cc_final: 0.7859 (p0) REVERT: A 337 MET cc_start: 0.7680 (mtm) cc_final: 0.7263 (ptm) REVERT: A 340 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8048 (tp) REVERT: A 344 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7868 (tp) REVERT: A 358 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6587 (mm-30) REVERT: A 419 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.5455 (ttm110) REVERT: A 516 LYS cc_start: 0.6161 (tptt) cc_final: 0.5049 (mttm) REVERT: A 590 MET cc_start: 0.5183 (mmp) cc_final: 0.4514 (mmp) REVERT: A 720 ILE cc_start: 0.4970 (OUTLIER) cc_final: 0.4459 (tt) REVERT: A 756 LEU cc_start: 0.4369 (OUTLIER) cc_final: 0.3242 (tp) REVERT: B 17 TYR cc_start: 0.6284 (OUTLIER) cc_final: 0.4824 (m-80) REVERT: B 353 PHE cc_start: 0.4455 (OUTLIER) cc_final: 0.2173 (t80) REVERT: B 377 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.5846 (m90) REVERT: B 434 MET cc_start: 0.7775 (mtp) cc_final: 0.7449 (ptm) REVERT: B 623 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7219 (t0) REVERT: B 650 HIS cc_start: 0.7085 (m90) cc_final: 0.6375 (t-170) REVERT: B 753 LEU cc_start: 0.3654 (mt) cc_final: 0.3332 (mt) REVERT: C 35 MET cc_start: 0.7530 (mtp) cc_final: 0.7230 (mtp) REVERT: C 301 SER cc_start: 0.8494 (p) cc_final: 0.8015 (t) REVERT: C 340 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8117 (tp) REVERT: C 358 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.5982 (pp20) REVERT: C 370 ASN cc_start: 0.6570 (OUTLIER) cc_final: 0.6291 (p0) REVERT: C 663 ASN cc_start: 0.5091 (OUTLIER) cc_final: 0.4632 (t0) REVERT: C 699 PHE cc_start: 0.5956 (OUTLIER) cc_final: 0.5337 (t80) REVERT: C 731 ARG cc_start: 0.4056 (mmm160) cc_final: 0.3588 (mmm160) REVERT: D 17 TYR cc_start: 0.6195 (OUTLIER) cc_final: 0.5430 (m-80) REVERT: D 173 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7107 (mm) REVERT: D 343 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7746 (mtp) REVERT: D 353 PHE cc_start: 0.4900 (OUTLIER) cc_final: 0.2364 (t80) REVERT: D 401 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7375 (mtpp) REVERT: D 571 LYS cc_start: 0.6936 (tttm) cc_final: 0.6699 (ttmt) REVERT: E 104 HIS cc_start: 0.9060 (OUTLIER) cc_final: 0.8445 (t70) REVERT: E 337 MET cc_start: 0.7602 (mtm) cc_final: 0.7247 (ptm) REVERT: E 341 TRP cc_start: 0.6458 (t60) cc_final: 0.5732 (t-100) REVERT: E 354 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5974 (mp0) REVERT: E 358 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.5734 (tt0) REVERT: E 370 ASN cc_start: 0.6569 (OUTLIER) cc_final: 0.6232 (p0) REVERT: E 516 LYS cc_start: 0.5884 (tptt) cc_final: 0.4126 (mttm) REVERT: E 738 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6368 (pp) REVERT: F 17 TYR cc_start: 0.5961 (OUTLIER) cc_final: 0.4559 (m-80) REVERT: F 343 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7286 (mtp) REVERT: F 353 PHE cc_start: 0.4133 (OUTLIER) cc_final: 0.0890 (t80) REVERT: F 375 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7462 (ttm) REVERT: F 434 MET cc_start: 0.7990 (mtp) cc_final: 0.7270 (ptm) REVERT: F 527 LEU cc_start: 0.5892 (OUTLIER) cc_final: 0.4797 (tt) REVERT: F 568 HIS cc_start: 0.6024 (OUTLIER) cc_final: 0.5147 (p-80) REVERT: F 648 TYR cc_start: 0.5141 (m-80) cc_final: 0.4741 (m-80) REVERT: F 723 LEU cc_start: 0.5811 (tp) cc_final: 0.5201 (mp) REVERT: F 736 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7226 (pp) REVERT: I 25 SER cc_start: 0.6265 (p) cc_final: 0.5890 (m) REVERT: I 74 ASN cc_start: 0.6491 (OUTLIER) cc_final: 0.6144 (t0) REVERT: H 74 ASN cc_start: 0.6489 (OUTLIER) cc_final: 0.5938 (t0) outliers start: 188 outliers final: 120 residues processed: 388 average time/residue: 0.4796 time to fit residues: 315.6811 Evaluate side-chains 361 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 205 time to evaluate : 4.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 663 ASN Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 699 PHE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 622 LYS Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 719 ARG Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 761 LEU Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 454 GLU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 598 LEU Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 685 ARG Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 343 MET Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 375 MET Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 595 GLU Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 726 GLU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 8.9990 chunk 426 optimal weight: 7.9990 chunk 389 optimal weight: 0.0010 chunk 414 optimal weight: 0.0570 chunk 249 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 325 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 374 optimal weight: 2.9990 chunk 392 optimal weight: 0.0980 chunk 413 optimal weight: 6.9990 overall best weight: 0.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS D 650 HIS ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN F 467 GLN ** F 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 ASN ** F 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39273 Z= 0.171 Angle : 0.555 9.627 53244 Z= 0.281 Chirality : 0.041 0.280 6096 Planarity : 0.004 0.047 6615 Dihedral : 5.668 72.408 5197 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.78 % Allowed : 21.41 % Favored : 74.81 % 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: -0.82 (0.12), residues: 4638 helix: -0.10 (0.11), residues: 2085 sheet: -0.63 (0.20), residues: 726 loop : -0.84 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP E 647 HIS 0.016 0.001 HIS D 650 PHE 0.020 0.001 PHE E 374 TYR 0.021 0.001 TYR D 264 ARG 0.003 0.000 ARG F 309 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 223 time to evaluate : 4.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8084 (pm20) REVERT: A 274 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6941 (mmtt) REVERT: A 292 ASP cc_start: 0.8581 (p0) cc_final: 0.7788 (p0) REVERT: A 337 MET cc_start: 0.7672 (mtm) cc_final: 0.7267 (ptm) REVERT: A 340 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7990 (tp) REVERT: A 344 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7799 (tp) REVERT: A 358 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6609 (mm-30) REVERT: A 419 ARG cc_start: 0.6017 (OUTLIER) cc_final: 0.5306 (ttm110) REVERT: A 434 MET cc_start: 0.6966 (mmm) cc_final: 0.6638 (mmm) REVERT: A 590 MET cc_start: 0.5149 (mmp) cc_final: 0.4511 (mmp) REVERT: A 625 ASN cc_start: 0.7309 (t0) cc_final: 0.7076 (t0) REVERT: A 720 ILE cc_start: 0.4960 (OUTLIER) cc_final: 0.4443 (tt) REVERT: A 756 LEU cc_start: 0.4358 (OUTLIER) cc_final: 0.3220 (tp) REVERT: B 17 TYR cc_start: 0.6201 (OUTLIER) cc_final: 0.4772 (m-80) REVERT: B 171 ARG cc_start: 0.7047 (ptm160) cc_final: 0.6260 (ptm-80) REVERT: B 353 PHE cc_start: 0.4417 (OUTLIER) cc_final: 0.2103 (t80) REVERT: B 377 HIS cc_start: 0.6691 (OUTLIER) cc_final: 0.5821 (m90) REVERT: B 434 MET cc_start: 0.7749 (mtp) cc_final: 0.7428 (ptm) REVERT: B 623 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7277 (t0) REVERT: B 650 HIS cc_start: 0.7087 (m90) cc_final: 0.6527 (t-170) REVERT: B 753 LEU cc_start: 0.3506 (mt) cc_final: 0.3194 (mt) REVERT: C 35 MET cc_start: 0.7642 (mtp) cc_final: 0.7380 (mtp) REVERT: C 294 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8169 (m-30) REVERT: C 340 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8150 (tp) REVERT: C 358 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.5992 (pp20) REVERT: C 370 ASN cc_start: 0.6624 (OUTLIER) cc_final: 0.6388 (p0) REVERT: C 516 LYS cc_start: 0.5681 (tptt) cc_final: 0.4515 (mttm) REVERT: C 663 ASN cc_start: 0.5361 (OUTLIER) cc_final: 0.4909 (t0) REVERT: C 699 PHE cc_start: 0.5813 (OUTLIER) cc_final: 0.5205 (t80) REVERT: D 17 TYR cc_start: 0.6123 (OUTLIER) cc_final: 0.5200 (m-80) REVERT: D 173 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6966 (mm) REVERT: D 343 MET cc_start: 0.8514 (ttm) cc_final: 0.7859 (mtp) REVERT: D 353 PHE cc_start: 0.4643 (OUTLIER) cc_final: 0.2375 (t80) REVERT: D 401 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7345 (mtpp) REVERT: D 571 LYS cc_start: 0.6890 (tttm) cc_final: 0.6396 (tttt) REVERT: D 622 LYS cc_start: 0.4534 (OUTLIER) cc_final: 0.3869 (tptt) REVERT: D 723 LEU cc_start: 0.5847 (tp) cc_final: 0.5149 (mp) REVERT: E 104 HIS cc_start: 0.9061 (OUTLIER) cc_final: 0.8418 (t70) REVERT: E 341 TRP cc_start: 0.6483 (t60) cc_final: 0.5786 (t-100) REVERT: E 354 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5980 (mp0) REVERT: E 358 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.5727 (tt0) REVERT: E 370 ASN cc_start: 0.6661 (OUTLIER) cc_final: 0.6275 (p0) REVERT: E 516 LYS cc_start: 0.5990 (tptt) cc_final: 0.4186 (mttm) REVERT: E 738 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6342 (pp) REVERT: F 17 TYR cc_start: 0.5902 (OUTLIER) cc_final: 0.4555 (m-80) REVERT: F 353 PHE cc_start: 0.4202 (OUTLIER) cc_final: 0.1094 (t80) REVERT: F 434 MET cc_start: 0.7969 (mtp) cc_final: 0.7241 (ptm) REVERT: F 527 LEU cc_start: 0.5976 (OUTLIER) cc_final: 0.4915 (tt) REVERT: F 568 HIS cc_start: 0.5992 (OUTLIER) cc_final: 0.5100 (p-80) REVERT: F 648 TYR cc_start: 0.5096 (m-80) cc_final: 0.4579 (m-80) REVERT: I 59 TYR cc_start: 0.6717 (t80) cc_final: 0.6467 (t80) REVERT: I 74 ASN cc_start: 0.6354 (OUTLIER) cc_final: 0.5991 (t0) REVERT: H 74 ASN cc_start: 0.6374 (p0) cc_final: 0.5932 (t0) outliers start: 162 outliers final: 111 residues processed: 368 average time/residue: 0.4936 time to fit residues: 310.2450 Evaluate side-chains 346 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 202 time to evaluate : 4.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 663 ASN Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 699 PHE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 622 LYS Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 719 ARG Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 761 LEU Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 454 GLU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 685 ARG Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 595 GLU Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain F residue 726 GLU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 305 optimal weight: 0.9980 chunk 460 optimal weight: 0.6980 chunk 423 optimal weight: 5.9990 chunk 366 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 283 optimal weight: 0.0030 chunk 224 optimal weight: 0.8980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS D 650 HIS ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 39273 Z= 0.161 Angle : 0.548 10.578 53244 Z= 0.277 Chirality : 0.041 0.270 6096 Planarity : 0.003 0.043 6615 Dihedral : 5.452 70.670 5190 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.57 % Allowed : 21.80 % Favored : 74.63 % 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: -0.74 (0.12), residues: 4638 helix: -0.09 (0.11), residues: 2106 sheet: -0.53 (0.20), residues: 726 loop : -0.78 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP E 647 HIS 0.017 0.001 HIS D 650 PHE 0.030 0.001 PHE A 374 TYR 0.020 0.001 TYR B 264 ARG 0.005 0.000 ARG B 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 216 time to evaluate : 4.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.6919 (mmtt) REVERT: A 292 ASP cc_start: 0.8413 (p0) cc_final: 0.7576 (p0) REVERT: A 337 MET cc_start: 0.7744 (mtm) cc_final: 0.7305 (ptm) REVERT: A 340 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8100 (tp) REVERT: A 344 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7694 (tp) REVERT: A 358 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6622 (mm-30) REVERT: A 419 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5436 (ttm110) REVERT: A 434 MET cc_start: 0.6966 (mmm) cc_final: 0.6646 (mmm) REVERT: A 516 LYS cc_start: 0.6145 (tptt) cc_final: 0.5217 (mttm) REVERT: A 720 ILE cc_start: 0.4926 (OUTLIER) cc_final: 0.4408 (tt) REVERT: A 756 LEU cc_start: 0.4287 (OUTLIER) cc_final: 0.3158 (tp) REVERT: B 17 TYR cc_start: 0.6154 (OUTLIER) cc_final: 0.4723 (m-80) REVERT: B 171 ARG cc_start: 0.7116 (ptm160) cc_final: 0.6136 (ptm-80) REVERT: B 353 PHE cc_start: 0.4386 (OUTLIER) cc_final: 0.2082 (t80) REVERT: B 377 HIS cc_start: 0.6578 (OUTLIER) cc_final: 0.5652 (m90) REVERT: B 434 MET cc_start: 0.7700 (mtp) cc_final: 0.7305 (ptm) REVERT: B 438 ILE cc_start: 0.8507 (pt) cc_final: 0.8246 (mt) REVERT: B 623 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7312 (t0) REVERT: B 648 TYR cc_start: 0.4655 (m-10) cc_final: 0.4364 (m-10) REVERT: B 650 HIS cc_start: 0.7045 (m90) cc_final: 0.6459 (t-170) REVERT: B 753 LEU cc_start: 0.3339 (mt) cc_final: 0.3018 (mt) REVERT: C 294 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8226 (m-30) REVERT: C 340 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8235 (tp) REVERT: C 358 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.5852 (pp20) REVERT: C 370 ASN cc_start: 0.6626 (OUTLIER) cc_final: 0.6394 (p0) REVERT: C 663 ASN cc_start: 0.5255 (OUTLIER) cc_final: 0.4812 (t0) REVERT: C 699 PHE cc_start: 0.5792 (OUTLIER) cc_final: 0.5155 (t80) REVERT: D 17 TYR cc_start: 0.6093 (OUTLIER) cc_final: 0.5139 (m-80) REVERT: D 173 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7034 (mm) REVERT: D 343 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7852 (mtp) REVERT: D 353 PHE cc_start: 0.4618 (OUTLIER) cc_final: 0.2351 (t80) REVERT: D 401 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7537 (mtpp) REVERT: D 723 LEU cc_start: 0.5891 (tp) cc_final: 0.5302 (mp) REVERT: E 104 HIS cc_start: 0.9060 (OUTLIER) cc_final: 0.8422 (t70) REVERT: E 341 TRP cc_start: 0.6465 (t60) cc_final: 0.5767 (t60) REVERT: E 354 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6184 (mp0) REVERT: E 358 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.5853 (tt0) REVERT: E 370 ASN cc_start: 0.6530 (OUTLIER) cc_final: 0.6091 (p0) REVERT: E 516 LYS cc_start: 0.5961 (tptt) cc_final: 0.4177 (mttm) REVERT: F 17 TYR cc_start: 0.5919 (OUTLIER) cc_final: 0.4610 (m-80) REVERT: F 353 PHE cc_start: 0.3629 (OUTLIER) cc_final: 0.0730 (t80) REVERT: F 434 MET cc_start: 0.7947 (mtp) cc_final: 0.7225 (ptm) REVERT: F 527 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.4921 (tt) REVERT: F 568 HIS cc_start: 0.5973 (OUTLIER) cc_final: 0.5482 (p-80) REVERT: F 648 TYR cc_start: 0.5052 (m-80) cc_final: 0.4530 (m-80) REVERT: G 74 ASN cc_start: 0.6406 (OUTLIER) cc_final: 0.6073 (t0) REVERT: I 74 ASN cc_start: 0.6825 (OUTLIER) cc_final: 0.6600 (t0) REVERT: H 74 ASN cc_start: 0.6515 (p0) cc_final: 0.6170 (t0) outliers start: 153 outliers final: 105 residues processed: 352 average time/residue: 0.5084 time to fit residues: 305.3412 Evaluate side-chains 339 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 202 time to evaluate : 4.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 663 ASN Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 699 PHE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 761 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 454 GLU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 685 ARG Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 595 GLU Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 726 GLU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 100 TYR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 0.7980 chunk 390 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 337 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 367 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 376 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS ** D 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN ** F 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.113941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.095658 restraints weight = 115458.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.096372 restraints weight = 182361.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.096734 restraints weight = 126689.461| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 39273 Z= 0.248 Angle : 0.592 9.825 53244 Z= 0.301 Chirality : 0.043 0.272 6096 Planarity : 0.004 0.045 6615 Dihedral : 5.582 72.160 5187 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.76 % Allowed : 21.64 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4638 helix: -0.22 (0.11), residues: 2109 sheet: -0.52 (0.20), residues: 723 loop : -0.83 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP E 647 HIS 0.016 0.001 HIS D 650 PHE 0.015 0.002 PHE F 682 TYR 0.028 0.002 TYR B 264 ARG 0.005 0.000 ARG C 731 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7534.39 seconds wall clock time: 140 minutes 16.93 seconds (8416.93 seconds total)