Starting phenix.real_space_refine on Sat Mar 23 00:02:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zsu_6952/03_2024/5zsu_6952.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zsu_6952/03_2024/5zsu_6952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zsu_6952/03_2024/5zsu_6952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zsu_6952/03_2024/5zsu_6952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zsu_6952/03_2024/5zsu_6952.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zsu_6952/03_2024/5zsu_6952.pdb" } resolution = 4.25 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= 0.001 sd= 0.008 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 144 5.16 5 C 22779 2.51 5 N 5889 2.21 5 O 6147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 389": "NH1" <-> "NH2" Residue "C PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 389": "NH1" <-> "NH2" Residue "D PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E ARG 266": "NH1" <-> "NH2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 389": "NH1" <-> "NH2" Residue "E PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F ARG 266": "NH1" <-> "NH2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 389": "NH1" <-> "NH2" Residue "F PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34959 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5843 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 27, 'TRANS': 679} Chain breaks: 2 Chain: "B" Number of atoms: 5810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5810 Classifications: {'peptide': 702} Link IDs: {'PTRANS': 27, 'TRANS': 674} Chain breaks: 2 Chain: "C" Number of atoms: 5843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5843 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 27, 'TRANS': 679} Chain breaks: 2 Chain: "D" Number of atoms: 5810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5810 Classifications: {'peptide': 702} Link IDs: {'PTRANS': 27, 'TRANS': 674} Chain breaks: 2 Chain: "E" Number of atoms: 5843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5843 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 27, 'TRANS': 679} Chain breaks: 2 Chain: "F" Number of atoms: 5810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5810 Classifications: {'peptide': 702} Link IDs: {'PTRANS': 27, 'TRANS': 674} Chain breaks: 2 Time building chain proxies: 16.48, per 1000 atoms: 0.47 Number of scatterers: 34959 At special positions: 0 Unit cell: (150.49, 144.53, 193.7, 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 144 16.00 O 6147 8.00 N 5889 7.00 C 22779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.04 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: 12.87 Conformation dependent library (CDL) restraints added in 6.3 seconds 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8196 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 12 sheets defined 52.9% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 124 through 145 Processing helix chain 'A' and resid 146 through 166 Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 234 through 255 removed outlier: 3.627A pdb=" N GLU A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 287 removed outlier: 4.774A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 346 Processing helix chain 'A' and resid 350 through 363 Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.555A pdb=" N LEU A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 395 Processing helix chain 'A' and resid 395 through 410 Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.506A pdb=" N LEU A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.510A pdb=" N ALA A 466 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 493 removed outlier: 3.789A pdb=" N PHE A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 536 removed outlier: 3.503A pdb=" N ILE A 535 " --> pdb=" O ASN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.510A pdb=" N LEU A 540 " --> pdb=" O ILE A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 removed outlier: 3.508A pdb=" N VAL A 565 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 566 " --> pdb=" O THR A 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 562 through 566' Processing helix chain 'A' and resid 583 through 590 removed outlier: 3.738A pdb=" N LEU A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.503A pdb=" N ILE A 610 " --> pdb=" O PRO A 607 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 611 " --> pdb=" O HIS A 608 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 612 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.509A pdb=" N PHE A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 638 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 removed outlier: 3.505A pdb=" N ILE A 658 " --> pdb=" O PRO A 655 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 659 " --> pdb=" O ILE A 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 655 through 659' Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.507A pdb=" N LEU A 681 " --> pdb=" O PRO A 678 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 682 " --> pdb=" O THR A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 705 removed outlier: 3.502A pdb=" N ILE A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.507A pdb=" N LEU A 727 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 728 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS A 730 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.509A pdb=" N VAL A 750 " --> pdb=" O PRO A 747 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 753 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 775 removed outlier: 3.503A pdb=" N LEU A 773 " --> pdb=" O PRO A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 786 removed outlier: 3.511A pdb=" N VAL A 786 " --> pdb=" O GLY A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 794 through 806 Processing helix chain 'B' and resid 22 through 50 removed outlier: 3.681A pdb=" N ASP B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 145 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 146 through 166 Processing helix chain 'B' and resid 166 through 175 Processing helix chain 'B' and resid 233 through 254 removed outlier: 3.685A pdb=" N GLY B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 286 removed outlier: 3.683A pdb=" N TYR B 261 " --> pdb=" O GLY B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 346 Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 383 through 395 removed outlier: 3.516A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 441 through 445 Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.504A pdb=" N ALA B 466 " --> pdb=" O PRO B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 493 removed outlier: 3.677A pdb=" N PHE B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.505A pdb=" N LEU B 540 " --> pdb=" O ILE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 566 removed outlier: 3.507A pdb=" N ASP B 564 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 565 " --> pdb=" O VAL B 562 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 566 " --> pdb=" O THR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 607 through 613 removed outlier: 3.503A pdb=" N ILE B 610 " --> pdb=" O PRO B 607 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 611 " --> pdb=" O HIS B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 removed outlier: 3.505A pdb=" N PHE B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 removed outlier: 3.504A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.503A pdb=" N LEU B 681 " --> pdb=" O PRO B 678 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 682 " --> pdb=" O THR B 679 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 683 " --> pdb=" O GLN B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 removed outlier: 3.506A pdb=" N ILE B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.510A pdb=" N LEU B 727 " --> pdb=" O PRO B 724 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 728 " --> pdb=" O PRO B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.506A pdb=" N VAL B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 775 removed outlier: 3.508A pdb=" N LEU B 773 " --> pdb=" O PRO B 770 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 775 " --> pdb=" O GLU B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 786 Processing helix chain 'B' and resid 787 through 793 Processing helix chain 'B' and resid 794 through 806 Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 124 through 145 Processing helix chain 'C' and resid 146 through 166 Processing helix chain 'C' and resid 166 through 175 Processing helix chain 'C' and resid 234 through 255 removed outlier: 3.626A pdb=" N GLU C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 287 removed outlier: 4.775A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 346 Processing helix chain 'C' and resid 350 through 363 Processing helix chain 'C' and resid 372 through 383 removed outlier: 3.556A pdb=" N LEU C 376 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 395 Processing helix chain 'C' and resid 395 through 410 Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'C' and resid 441 through 445 removed outlier: 3.506A pdb=" N LEU C 445 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 removed outlier: 3.510A pdb=" N ALA C 466 " --> pdb=" O PRO C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 493 removed outlier: 3.788A pdb=" N PHE C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 493 " --> pdb=" O ALA C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 536 removed outlier: 3.503A pdb=" N ILE C 535 " --> pdb=" O ASN C 531 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C 536 " --> pdb=" O ASN C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 541 removed outlier: 3.511A pdb=" N LEU C 540 " --> pdb=" O ILE C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 566 removed outlier: 3.509A pdb=" N VAL C 565 " --> pdb=" O VAL C 562 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 566 " --> pdb=" O THR C 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 562 through 566' Processing helix chain 'C' and resid 583 through 590 removed outlier: 3.739A pdb=" N LEU C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET C 590 " --> pdb=" O SER C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 613 removed outlier: 3.504A pdb=" N ILE C 610 " --> pdb=" O PRO C 607 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 611 " --> pdb=" O HIS C 608 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 612 " --> pdb=" O SER C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 removed outlier: 3.508A pdb=" N PHE C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS C 637 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 638 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 659 removed outlier: 3.505A pdb=" N ILE C 658 " --> pdb=" O PRO C 655 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY C 659 " --> pdb=" O ILE C 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 655 through 659' Processing helix chain 'C' and resid 678 through 684 removed outlier: 3.506A pdb=" N LEU C 681 " --> pdb=" O PRO C 678 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 682 " --> pdb=" O THR C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 705 removed outlier: 3.503A pdb=" N ILE C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 removed outlier: 3.508A pdb=" N LEU C 727 " --> pdb=" O PRO C 724 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 728 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS C 730 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.509A pdb=" N VAL C 750 " --> pdb=" O PRO C 747 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 753 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 775 removed outlier: 3.502A pdb=" N LEU C 773 " --> pdb=" O PRO C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 786 removed outlier: 3.511A pdb=" N VAL C 786 " --> pdb=" O GLY C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 793 Processing helix chain 'C' and resid 794 through 806 Processing helix chain 'D' and resid 22 through 50 removed outlier: 3.681A pdb=" N ASP D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 145 Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 146 through 166 Processing helix chain 'D' and resid 166 through 175 Processing helix chain 'D' and resid 233 through 254 removed outlier: 3.686A pdb=" N GLY D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 286 removed outlier: 3.685A pdb=" N TYR D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 346 Processing helix chain 'D' and resid 350 through 364 Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 383 through 395 removed outlier: 3.516A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 410 Processing helix chain 'D' and resid 412 through 419 Processing helix chain 'D' and resid 441 through 445 Processing helix chain 'D' and resid 462 through 468 removed outlier: 3.504A pdb=" N ALA D 466 " --> pdb=" O PRO D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 493 removed outlier: 3.678A pdb=" N PHE D 490 " --> pdb=" O PRO D 486 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 493 " --> pdb=" O ALA D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.501A pdb=" N TYR D 534 " --> pdb=" O GLU D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.505A pdb=" N LEU D 540 " --> pdb=" O ILE D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 566 removed outlier: 3.507A pdb=" N ASP D 564 " --> pdb=" O VAL D 561 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 565 " --> pdb=" O VAL D 562 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 566 " --> pdb=" O THR D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 588 Processing helix chain 'D' and resid 607 through 613 removed outlier: 3.503A pdb=" N ILE D 610 " --> pdb=" O PRO D 607 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE D 611 " --> pdb=" O HIS D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 638 removed outlier: 3.507A pdb=" N PHE D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 638 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 659 removed outlier: 3.505A pdb=" N ILE D 658 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 removed outlier: 3.503A pdb=" N LEU D 681 " --> pdb=" O PRO D 678 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE D 682 " --> pdb=" O THR D 679 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 683 " --> pdb=" O GLN D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 705 removed outlier: 3.504A pdb=" N ILE D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 730 removed outlier: 3.510A pdb=" N LEU D 727 " --> pdb=" O PRO D 724 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE D 728 " --> pdb=" O PRO D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 752 removed outlier: 3.506A pdb=" N VAL D 750 " --> pdb=" O PRO D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 775 removed outlier: 3.508A pdb=" N LEU D 773 " --> pdb=" O PRO D 770 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 775 " --> pdb=" O GLU D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 786 Processing helix chain 'D' and resid 787 through 793 Processing helix chain 'D' and resid 794 through 806 Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 116 Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 124 through 145 Processing helix chain 'E' and resid 146 through 166 Processing helix chain 'E' and resid 166 through 175 Processing helix chain 'E' and resid 234 through 255 removed outlier: 3.627A pdb=" N GLU E 255 " --> pdb=" O ARG E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 287 removed outlier: 4.774A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 346 Processing helix chain 'E' and resid 350 through 363 Processing helix chain 'E' and resid 372 through 383 removed outlier: 3.556A pdb=" N LEU E 376 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 395 Processing helix chain 'E' and resid 395 through 410 Processing helix chain 'E' and resid 412 through 418 Processing helix chain 'E' and resid 441 through 445 removed outlier: 3.506A pdb=" N LEU E 445 " --> pdb=" O VAL E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 removed outlier: 3.509A pdb=" N ALA E 466 " --> pdb=" O PRO E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 493 removed outlier: 3.788A pdb=" N PHE E 490 " --> pdb=" O PRO E 486 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU E 493 " --> pdb=" O ALA E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 536 removed outlier: 3.503A pdb=" N ILE E 535 " --> pdb=" O ASN E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 541 removed outlier: 3.511A pdb=" N LEU E 540 " --> pdb=" O ILE E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 566 removed outlier: 3.509A pdb=" N VAL E 565 " --> pdb=" O VAL E 562 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY E 566 " --> pdb=" O THR E 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 562 through 566' Processing helix chain 'E' and resid 583 through 590 removed outlier: 3.739A pdb=" N LEU E 587 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET E 590 " --> pdb=" O SER E 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 613 removed outlier: 3.503A pdb=" N ILE E 610 " --> pdb=" O PRO E 607 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE E 611 " --> pdb=" O HIS E 608 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER E 612 " --> pdb=" O SER E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 638 removed outlier: 3.508A pdb=" N PHE E 635 " --> pdb=" O GLU E 631 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS E 637 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 638 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 659 removed outlier: 3.505A pdb=" N ILE E 658 " --> pdb=" O PRO E 655 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY E 659 " --> pdb=" O ILE E 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 655 through 659' Processing helix chain 'E' and resid 678 through 684 removed outlier: 3.506A pdb=" N LEU E 681 " --> pdb=" O PRO E 678 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE E 682 " --> pdb=" O THR E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 705 removed outlier: 3.502A pdb=" N ILE E 704 " --> pdb=" O PRO E 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 730 removed outlier: 3.508A pdb=" N LEU E 727 " --> pdb=" O PRO E 724 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE E 728 " --> pdb=" O PRO E 725 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS E 730 " --> pdb=" O LEU E 727 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 753 removed outlier: 3.509A pdb=" N VAL E 750 " --> pdb=" O PRO E 747 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 753 " --> pdb=" O VAL E 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 775 removed outlier: 3.502A pdb=" N LEU E 773 " --> pdb=" O PRO E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 782 through 786 removed outlier: 3.512A pdb=" N VAL E 786 " --> pdb=" O GLY E 783 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 793 Processing helix chain 'E' and resid 794 through 806 Processing helix chain 'F' and resid 22 through 50 removed outlier: 3.681A pdb=" N ASP F 50 " --> pdb=" O GLN F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 117 Processing helix chain 'F' and resid 119 through 145 Proline residue: F 126 - end of helix Processing helix chain 'F' and resid 146 through 166 Processing helix chain 'F' and resid 166 through 175 Processing helix chain 'F' and resid 233 through 254 removed outlier: 3.685A pdb=" N GLY F 237 " --> pdb=" O ASP F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 286 removed outlier: 3.685A pdb=" N TYR F 261 " --> pdb=" O GLY F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 346 Processing helix chain 'F' and resid 350 through 364 Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 383 through 395 removed outlier: 3.516A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 410 Processing helix chain 'F' and resid 412 through 419 Processing helix chain 'F' and resid 441 through 445 Processing helix chain 'F' and resid 462 through 468 removed outlier: 3.504A pdb=" N ALA F 466 " --> pdb=" O PRO F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 493 removed outlier: 3.677A pdb=" N PHE F 490 " --> pdb=" O PRO F 486 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU F 493 " --> pdb=" O ALA F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.501A pdb=" N TYR F 534 " --> pdb=" O GLU F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.505A pdb=" N LEU F 540 " --> pdb=" O ILE F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 566 removed outlier: 3.507A pdb=" N ASP F 564 " --> pdb=" O VAL F 561 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL F 565 " --> pdb=" O VAL F 562 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY F 566 " --> pdb=" O THR F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 588 Processing helix chain 'F' and resid 607 through 613 removed outlier: 3.502A pdb=" N ILE F 610 " --> pdb=" O PRO F 607 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE F 611 " --> pdb=" O HIS F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 638 removed outlier: 3.506A pdb=" N PHE F 635 " --> pdb=" O GLU F 631 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU F 638 " --> pdb=" O SER F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 659 removed outlier: 3.505A pdb=" N ILE F 658 " --> pdb=" O PRO F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 684 removed outlier: 3.503A pdb=" N LEU F 681 " --> pdb=" O PRO F 678 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE F 682 " --> pdb=" O THR F 679 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR F 683 " --> pdb=" O GLN F 680 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 705 removed outlier: 3.505A pdb=" N ILE F 704 " --> pdb=" O PRO F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 730 removed outlier: 3.509A pdb=" N LEU F 727 " --> pdb=" O PRO F 724 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE F 728 " --> pdb=" O PRO F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 removed outlier: 3.506A pdb=" N VAL F 750 " --> pdb=" O PRO F 747 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 775 removed outlier: 3.508A pdb=" N LEU F 773 " --> pdb=" O PRO F 770 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU F 775 " --> pdb=" O GLU F 772 " (cutoff:3.500A) Processing helix chain 'F' and resid 782 through 786 Processing helix chain 'F' and resid 787 through 793 Processing helix chain 'F' and resid 794 through 806 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 57 removed outlier: 4.644A pdb=" N THR A 307 " --> pdb=" O CYS A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.412A pdb=" N LEU A 451 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 596 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 690 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 427 through 429 removed outlier: 6.536A pdb=" N LEU B 428 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 596 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 690 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 57 removed outlier: 4.643A pdb=" N THR C 307 " --> pdb=" O CYS C 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 427 through 429 removed outlier: 6.412A pdb=" N LEU C 451 " --> pdb=" O TRP C 475 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU C 596 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 690 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 57 removed outlier: 4.820A pdb=" N THR D 307 " --> pdb=" O CYS D 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 427 through 429 removed outlier: 6.537A pdb=" N LEU D 428 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU D 451 " --> pdb=" O TRP D 475 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU D 596 " --> pdb=" O ASP D 620 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU D 690 " --> pdb=" O ALA D 714 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 57 removed outlier: 4.643A pdb=" N THR E 307 " --> pdb=" O CYS E 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 427 through 429 removed outlier: 6.413A pdb=" N LEU E 451 " --> pdb=" O TRP E 475 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU E 596 " --> pdb=" O ASP E 620 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU E 690 " --> pdb=" O ALA E 714 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 57 removed outlier: 4.820A pdb=" N THR F 307 " --> pdb=" O CYS F 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 427 through 429 removed outlier: 6.537A pdb=" N LEU F 428 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU F 451 " --> pdb=" O TRP F 475 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU F 596 " --> pdb=" O ASP F 620 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU F 690 " --> pdb=" O ALA F 714 " (cutoff:3.500A) 1550 hydrogen bonds defined for protein. 4308 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: 13.56 Time building geometry restraints manager: 13.91 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: 10810 1.34 - 1.46: 7908 1.46 - 1.58: 16829 1.58 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 35745 Sorted by residual: bond pdb=" C HIS D 312 " pdb=" N PRO D 313 " ideal model delta sigma weight residual 1.334 1.310 0.023 8.40e-03 1.42e+04 7.79e+00 bond pdb=" C HIS C 312 " pdb=" N PRO C 313 " ideal model delta sigma weight residual 1.334 1.310 0.023 8.40e-03 1.42e+04 7.59e+00 bond pdb=" C HIS F 312 " pdb=" N PRO F 313 " ideal model delta sigma weight residual 1.334 1.311 0.023 8.40e-03 1.42e+04 7.37e+00 bond pdb=" C HIS A 312 " pdb=" N PRO A 313 " ideal model delta sigma weight residual 1.334 1.311 0.023 8.40e-03 1.42e+04 7.26e+00 bond pdb=" C HIS B 312 " pdb=" N PRO B 313 " ideal model delta sigma weight residual 1.334 1.311 0.023 8.40e-03 1.42e+04 7.22e+00 ... (remaining 35740 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.16: 767 106.16 - 113.27: 19970 113.27 - 120.39: 14426 120.39 - 127.50: 12903 127.50 - 134.62: 387 Bond angle restraints: 48453 Sorted by residual: angle pdb=" CA TYR E 477 " pdb=" CB TYR E 477 " pdb=" CG TYR E 477 " ideal model delta sigma weight residual 113.90 122.54 -8.64 1.80e+00 3.09e-01 2.31e+01 angle pdb=" CA TYR A 477 " pdb=" CB TYR A 477 " pdb=" CG TYR A 477 " ideal model delta sigma weight residual 113.90 122.53 -8.63 1.80e+00 3.09e-01 2.30e+01 angle pdb=" CA TYR C 477 " pdb=" CB TYR C 477 " pdb=" CG TYR C 477 " ideal model delta sigma weight residual 113.90 122.51 -8.61 1.80e+00 3.09e-01 2.29e+01 angle pdb=" C LEU D 430 " pdb=" N HIS D 431 " pdb=" CA HIS D 431 " ideal model delta sigma weight residual 121.97 129.44 -7.47 1.73e+00 3.34e-01 1.87e+01 angle pdb=" C LEU B 430 " pdb=" N HIS B 431 " pdb=" CA HIS B 431 " ideal model delta sigma weight residual 121.97 129.40 -7.43 1.73e+00 3.34e-01 1.85e+01 ... (remaining 48448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.85: 19952 14.85 - 29.71: 1303 29.71 - 44.56: 336 44.56 - 59.41: 27 59.41 - 74.27: 9 Dihedral angle restraints: 21627 sinusoidal: 9048 harmonic: 12579 Sorted by residual: dihedral pdb=" CA ASP C 371 " pdb=" C ASP C 371 " pdb=" N PHE C 372 " pdb=" CA PHE C 372 " ideal model delta harmonic sigma weight residual -180.00 -136.44 -43.56 0 5.00e+00 4.00e-02 7.59e+01 dihedral pdb=" CA ASP A 371 " pdb=" C ASP A 371 " pdb=" N PHE A 372 " pdb=" CA PHE A 372 " ideal model delta harmonic sigma weight residual 180.00 -136.44 -43.56 0 5.00e+00 4.00e-02 7.59e+01 dihedral pdb=" CA ASP E 371 " pdb=" C ASP E 371 " pdb=" N PHE E 372 " pdb=" CA PHE E 372 " ideal model delta harmonic sigma weight residual -180.00 -136.47 -43.53 0 5.00e+00 4.00e-02 7.58e+01 ... (remaining 21624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4072 0.059 - 0.119: 1199 0.119 - 0.178: 258 0.178 - 0.238: 54 0.238 - 0.297: 15 Chirality restraints: 5598 Sorted by residual: chirality pdb=" CB ILE D 715 " pdb=" CA ILE D 715 " pdb=" CG1 ILE D 715 " pdb=" CG2 ILE D 715 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE B 715 " pdb=" CA ILE B 715 " pdb=" CG1 ILE B 715 " pdb=" CG2 ILE B 715 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE F 715 " pdb=" CA ILE F 715 " pdb=" CG1 ILE F 715 " pdb=" CG2 ILE F 715 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 5595 not shown) Planarity restraints: 5994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 456 " -0.054 5.00e-02 4.00e+02 8.27e-02 1.10e+01 pdb=" N PRO E 457 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 457 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO E 457 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 456 " 0.054 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO A 457 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 457 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 457 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 456 " 0.054 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO C 457 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 457 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 457 " 0.045 5.00e-02 4.00e+02 ... (remaining 5991 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9287 2.81 - 3.33: 33307 3.33 - 3.85: 59074 3.85 - 4.38: 67959 4.38 - 4.90: 109594 Nonbonded interactions: 279221 Sorted by model distance: nonbonded pdb=" O LYS D 249 " pdb=" OG1 THR D 252 " model vdw 2.286 2.440 nonbonded pdb=" O LYS B 249 " pdb=" OG1 THR B 252 " model vdw 2.286 2.440 nonbonded pdb=" O LYS F 249 " pdb=" OG1 THR F 252 " model vdw 2.287 2.440 nonbonded pdb=" O PRO B 147 " pdb=" OG SER B 150 " model vdw 2.309 2.440 nonbonded pdb=" O PRO F 147 " pdb=" OG SER F 150 " model vdw 2.309 2.440 ... (remaining 279216 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' and (resid 18 through 175 or resid 232 through 806)) selection = chain 'B' selection = (chain 'C' and (resid 18 through 175 or resid 232 through 806)) selection = chain 'D' selection = (chain 'E' and (resid 18 through 175 or resid 232 through 806)) selection = chain 'F' } 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.400 Check model and map are aligned: 0.580 Set scattering table: 0.340 Process input model: 87.510 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.120 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 : 0.006 0.076 35745 Z= 0.402 Angle : 1.137 14.728 48453 Z= 0.591 Chirality : 0.060 0.297 5598 Planarity : 0.007 0.083 5994 Dihedral : 10.785 74.266 13395 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 0.76 % Allowed : 5.42 % Favored : 93.82 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -4.45 (0.10), residues: 4191 helix: -2.93 (0.08), residues: 1992 sheet: -2.48 (0.21), residues: 465 loop : -2.95 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP E 647 HIS 0.030 0.004 HIS F 499 PHE 0.025 0.003 PHE F 353 TYR 0.045 0.003 TYR C 477 ARG 0.012 0.001 ARG D 688 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 919 time to evaluate : 4.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8607 (mt) cc_final: 0.8351 (mm) REVERT: A 233 ASP cc_start: 0.8479 (m-30) cc_final: 0.7947 (t0) REVERT: A 402 LEU cc_start: 0.8619 (tm) cc_final: 0.8160 (tp) REVERT: A 473 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7636 (tt0) REVERT: A 476 LEU cc_start: 0.8988 (mt) cc_final: 0.8419 (pp) REVERT: A 518 LEU cc_start: 0.8942 (tp) cc_final: 0.8536 (tp) REVERT: A 592 ASN cc_start: 0.7953 (m-40) cc_final: 0.7670 (t0) REVERT: A 595 GLU cc_start: 0.8502 (tt0) cc_final: 0.7169 (tm-30) REVERT: A 654 ILE cc_start: 0.7705 (mt) cc_final: 0.7451 (mm) REVERT: A 707 LEU cc_start: 0.8852 (mt) cc_final: 0.8385 (tp) REVERT: A 758 GLN cc_start: 0.8719 (mt0) cc_final: 0.8502 (pp30) REVERT: B 35 MET cc_start: 0.8004 (ttm) cc_final: 0.7680 (ttm) REVERT: B 255 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7753 (mp0) REVERT: B 280 CYS cc_start: 0.8698 (m) cc_final: 0.8197 (t) REVERT: B 321 LEU cc_start: 0.8911 (pp) cc_final: 0.8315 (mp) REVERT: B 367 ASP cc_start: 0.7169 (m-30) cc_final: 0.6338 (t0) REVERT: B 473 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7122 (mp0) REVERT: B 482 LYS cc_start: 0.8188 (mttt) cc_final: 0.7715 (tppt) REVERT: B 492 ARG cc_start: 0.8821 (mtt180) cc_final: 0.8533 (mtm110) REVERT: B 622 LYS cc_start: 0.8181 (mttt) cc_final: 0.7894 (mttp) REVERT: B 623 ASP cc_start: 0.8361 (m-30) cc_final: 0.8090 (t0) REVERT: B 629 ILE cc_start: 0.6050 (OUTLIER) cc_final: 0.5504 (mt) REVERT: B 689 TYR cc_start: 0.6608 (t80) cc_final: 0.6228 (t80) REVERT: B 694 HIS cc_start: 0.7858 (t-90) cc_final: 0.7467 (t-90) REVERT: B 707 LEU cc_start: 0.8384 (mt) cc_final: 0.7954 (tp) REVERT: B 716 THR cc_start: 0.7590 (t) cc_final: 0.5898 (m) REVERT: C 101 LEU cc_start: 0.8728 (mt) cc_final: 0.8414 (mm) REVERT: C 128 LEU cc_start: 0.9304 (mt) cc_final: 0.8991 (tt) REVERT: C 402 LEU cc_start: 0.8413 (tm) cc_final: 0.8020 (tp) REVERT: C 414 ASP cc_start: 0.8388 (m-30) cc_final: 0.7946 (p0) REVERT: C 476 LEU cc_start: 0.9001 (mt) cc_final: 0.8616 (pp) REVERT: C 495 LEU cc_start: 0.9135 (pp) cc_final: 0.8795 (mp) REVERT: C 498 LEU cc_start: 0.9127 (tp) cc_final: 0.8562 (tp) REVERT: C 515 LEU cc_start: 0.8989 (pt) cc_final: 0.8694 (pp) REVERT: C 518 LEU cc_start: 0.8674 (tp) cc_final: 0.8354 (tp) REVERT: C 543 LEU cc_start: 0.7940 (mp) cc_final: 0.7537 (mp) REVERT: C 658 ILE cc_start: 0.8864 (tt) cc_final: 0.8658 (pt) REVERT: D 102 ASP cc_start: 0.8210 (t0) cc_final: 0.7957 (t0) REVERT: D 124 TYR cc_start: 0.8744 (m-80) cc_final: 0.8036 (m-80) REVERT: D 367 ASP cc_start: 0.7110 (m-30) cc_final: 0.6679 (t70) REVERT: D 455 LEU cc_start: 0.8421 (mt) cc_final: 0.8021 (mt) REVERT: D 473 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7186 (mp0) REVERT: D 474 LEU cc_start: 0.8898 (tp) cc_final: 0.8645 (tp) REVERT: D 482 LYS cc_start: 0.7915 (mttt) cc_final: 0.7381 (tppt) REVERT: D 500 ILE cc_start: 0.8944 (mp) cc_final: 0.8741 (mm) REVERT: D 571 LYS cc_start: 0.8473 (mttt) cc_final: 0.7797 (mtmm) REVERT: D 623 ASP cc_start: 0.8165 (m-30) cc_final: 0.7723 (t0) REVERT: D 629 ILE cc_start: 0.6149 (OUTLIER) cc_final: 0.5724 (mt) REVERT: D 635 PHE cc_start: 0.7992 (m-80) cc_final: 0.7687 (m-80) REVERT: D 668 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7657 (m-10) REVERT: D 689 TYR cc_start: 0.6538 (t80) cc_final: 0.6233 (t80) REVERT: D 707 LEU cc_start: 0.8603 (mt) cc_final: 0.8166 (tp) REVERT: D 788 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7965 (tp30) REVERT: E 337 MET cc_start: 0.8453 (tmm) cc_final: 0.8170 (tmm) REVERT: E 402 LEU cc_start: 0.8286 (tm) cc_final: 0.7779 (tp) REVERT: E 448 LEU cc_start: 0.9087 (tp) cc_final: 0.8883 (tp) REVERT: E 473 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7580 (mp0) REVERT: E 476 LEU cc_start: 0.8995 (mt) cc_final: 0.8544 (pp) REVERT: E 482 LYS cc_start: 0.8715 (mttt) cc_final: 0.8418 (tptp) REVERT: E 498 LEU cc_start: 0.9109 (tp) cc_final: 0.8737 (tp) REVERT: E 518 LEU cc_start: 0.8888 (tp) cc_final: 0.8207 (tp) REVERT: E 543 LEU cc_start: 0.8164 (mp) cc_final: 0.7932 (mp) REVERT: E 592 ASN cc_start: 0.7972 (m-40) cc_final: 0.7769 (m-40) REVERT: F 35 MET cc_start: 0.8296 (ttm) cc_final: 0.7957 (ttp) REVERT: F 153 LEU cc_start: 0.8902 (mt) cc_final: 0.8699 (tt) REVERT: F 336 CYS cc_start: 0.8139 (m) cc_final: 0.7750 (m) REVERT: F 343 MET cc_start: 0.8001 (mmp) cc_final: 0.7639 (tpp) REVERT: F 473 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7223 (mp0) REVERT: F 476 LEU cc_start: 0.9060 (mt) cc_final: 0.8781 (pp) REVERT: F 482 LYS cc_start: 0.7608 (mttt) cc_final: 0.7007 (tppt) REVERT: F 492 ARG cc_start: 0.8619 (mtt180) cc_final: 0.8365 (ttp-110) REVERT: F 623 ASP cc_start: 0.8571 (m-30) cc_final: 0.8201 (t0) REVERT: F 629 ILE cc_start: 0.6425 (OUTLIER) cc_final: 0.6093 (mt) REVERT: F 689 TYR cc_start: 0.6926 (t80) cc_final: 0.6594 (t80) REVERT: F 707 LEU cc_start: 0.8498 (mt) cc_final: 0.8055 (tp) REVERT: F 788 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8083 (tp30) outliers start: 30 outliers final: 1 residues processed: 940 average time/residue: 0.5027 time to fit residues: 735.0513 Evaluate side-chains 525 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 520 time to evaluate : 4.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 0.0060 chunk 318 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 170 optimal weight: 10.0000 chunk 329 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 200 optimal weight: 0.5980 chunk 245 optimal weight: 8.9990 chunk 381 optimal weight: 5.9990 overall best weight: 1.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 287 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN A 744 GLN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN B 526 ASN ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS B 709 ASN B 718 ASN C 104 HIS ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN C 494 ASN C 615 ASN C 695 ASN C 709 ASN C 718 ASN C 744 GLN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 ASN D 526 ASN ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS D 709 ASN D 718 ASN D 737 HIS ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 ASN E 494 ASN ** E 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 615 ASN ** E 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 718 ASN E 744 GLN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 ASN F 526 ASN F 708 GLN F 709 ASN F 718 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35745 Z= 0.244 Angle : 0.802 10.638 48453 Z= 0.420 Chirality : 0.046 0.179 5598 Planarity : 0.006 0.065 5994 Dihedral : 6.658 39.608 4617 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.12), residues: 4191 helix: -1.69 (0.10), residues: 2115 sheet: -1.75 (0.22), residues: 468 loop : -2.54 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 168 HIS 0.030 0.002 HIS D 155 PHE 0.037 0.002 PHE D 502 TYR 0.031 0.002 TYR C 477 ARG 0.009 0.001 ARG D 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 649 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 52 MET cc_start: 0.8816 (ttp) cc_final: 0.8531 (ttm) REVERT: A 105 GLN cc_start: 0.9350 (mt0) cc_final: 0.9095 (mp10) REVERT: A 168 TRP cc_start: 0.8491 (t60) cc_final: 0.8221 (t-100) REVERT: A 170 THR cc_start: 0.8388 (m) cc_final: 0.8175 (m) REVERT: A 246 LYS cc_start: 0.8291 (mttt) cc_final: 0.7987 (mmtm) REVERT: A 332 TYR cc_start: 0.8716 (t80) cc_final: 0.8379 (t80) REVERT: A 402 LEU cc_start: 0.8570 (tt) cc_final: 0.8299 (tp) REVERT: A 471 LEU cc_start: 0.8850 (tt) cc_final: 0.8532 (mt) REVERT: A 473 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7957 (tt0) REVERT: A 498 LEU cc_start: 0.9120 (tp) cc_final: 0.8875 (tp) REVERT: A 518 LEU cc_start: 0.8767 (tp) cc_final: 0.8484 (tp) REVERT: A 520 GLU cc_start: 0.8204 (pt0) cc_final: 0.7873 (pt0) REVERT: A 653 TYR cc_start: 0.6939 (t80) cc_final: 0.6667 (t80) REVERT: A 654 ILE cc_start: 0.7826 (mt) cc_final: 0.7427 (mm) REVERT: A 673 LYS cc_start: 0.9195 (tmtt) cc_final: 0.8982 (tptp) REVERT: A 707 LEU cc_start: 0.8889 (mt) cc_final: 0.8368 (tp) REVERT: A 758 GLN cc_start: 0.8911 (mt0) cc_final: 0.8670 (pp30) REVERT: B 35 MET cc_start: 0.8067 (ttm) cc_final: 0.7606 (ttm) REVERT: B 52 MET cc_start: 0.7986 (mtp) cc_final: 0.7752 (mtp) REVERT: B 154 GLU cc_start: 0.8430 (tt0) cc_final: 0.8083 (tp30) REVERT: B 280 CYS cc_start: 0.8767 (m) cc_final: 0.8387 (t) REVERT: B 367 ASP cc_start: 0.6945 (m-30) cc_final: 0.6409 (t0) REVERT: B 433 PHE cc_start: 0.7330 (m-80) cc_final: 0.7073 (m-10) REVERT: B 473 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7232 (mp0) REVERT: B 482 LYS cc_start: 0.8203 (mttt) cc_final: 0.7538 (tppt) REVERT: B 501 LYS cc_start: 0.8305 (mtmt) cc_final: 0.7923 (mtmt) REVERT: B 623 ASP cc_start: 0.8284 (m-30) cc_final: 0.7948 (t0) REVERT: B 694 HIS cc_start: 0.7929 (t-90) cc_final: 0.7611 (t-90) REVERT: B 707 LEU cc_start: 0.8561 (mt) cc_final: 0.7969 (tp) REVERT: C 105 GLN cc_start: 0.9357 (mt0) cc_final: 0.9068 (mt0) REVERT: C 332 TYR cc_start: 0.8492 (t80) cc_final: 0.8136 (t80) REVERT: C 402 LEU cc_start: 0.8320 (tt) cc_final: 0.8096 (tt) REVERT: C 414 ASP cc_start: 0.8557 (m-30) cc_final: 0.7982 (p0) REVERT: C 454 GLU cc_start: 0.6703 (pt0) cc_final: 0.6154 (pt0) REVERT: C 498 LEU cc_start: 0.9197 (tp) cc_final: 0.8830 (tp) REVERT: C 518 LEU cc_start: 0.8567 (tp) cc_final: 0.8184 (tp) REVERT: C 543 LEU cc_start: 0.8229 (mp) cc_final: 0.7959 (mp) REVERT: C 546 LEU cc_start: 0.8559 (mm) cc_final: 0.8125 (mm) REVERT: C 653 TYR cc_start: 0.7049 (t80) cc_final: 0.6802 (t80) REVERT: D 115 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8227 (tm-30) REVERT: D 154 GLU cc_start: 0.8669 (tt0) cc_final: 0.8392 (tp30) REVERT: D 161 LEU cc_start: 0.8550 (tp) cc_final: 0.8338 (pp) REVERT: D 367 ASP cc_start: 0.6918 (m-30) cc_final: 0.6667 (t70) REVERT: D 374 PHE cc_start: 0.6207 (t80) cc_final: 0.5865 (t80) REVERT: D 473 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7065 (mp0) REVERT: D 482 LYS cc_start: 0.7764 (mttt) cc_final: 0.7303 (tppt) REVERT: D 576 ASN cc_start: 0.7759 (m-40) cc_final: 0.7549 (t0) REVERT: D 623 ASP cc_start: 0.8035 (m-30) cc_final: 0.7428 (t0) REVERT: D 631 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7736 (pm20) REVERT: D 635 PHE cc_start: 0.7819 (m-80) cc_final: 0.7559 (m-80) REVERT: D 707 LEU cc_start: 0.8690 (mt) cc_final: 0.8166 (tp) REVERT: D 788 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7836 (tp30) REVERT: E 25 ASP cc_start: 0.7292 (m-30) cc_final: 0.7089 (t0) REVERT: E 49 GLN cc_start: 0.8634 (tp-100) cc_final: 0.8365 (tp-100) REVERT: E 168 TRP cc_start: 0.7860 (t60) cc_final: 0.7638 (t-100) REVERT: E 337 MET cc_start: 0.8409 (tmm) cc_final: 0.7923 (tmm) REVERT: E 434 MET cc_start: 0.8224 (tpp) cc_final: 0.7883 (tpp) REVERT: E 476 LEU cc_start: 0.8877 (mt) cc_final: 0.8674 (tt) REVERT: E 498 LEU cc_start: 0.9140 (tp) cc_final: 0.8835 (tp) REVERT: E 518 LEU cc_start: 0.8712 (tp) cc_final: 0.8300 (tp) REVERT: E 590 MET cc_start: 0.7863 (ppp) cc_final: 0.7492 (ppp) REVERT: E 592 ASN cc_start: 0.8461 (m-40) cc_final: 0.7976 (m-40) REVERT: F 154 GLU cc_start: 0.8777 (tt0) cc_final: 0.8307 (tp30) REVERT: F 161 LEU cc_start: 0.8537 (tp) cc_final: 0.8080 (pp) REVERT: F 292 ASP cc_start: 0.8502 (p0) cc_final: 0.8292 (p0) REVERT: F 332 TYR cc_start: 0.8598 (t80) cc_final: 0.7841 (t80) REVERT: F 336 CYS cc_start: 0.8052 (m) cc_final: 0.7376 (m) REVERT: F 374 PHE cc_start: 0.7022 (t80) cc_final: 0.6694 (t80) REVERT: F 420 LEU cc_start: 0.7491 (mt) cc_final: 0.7248 (mt) REVERT: F 428 LEU cc_start: 0.8063 (mm) cc_final: 0.7656 (mm) REVERT: F 433 PHE cc_start: 0.8072 (m-10) cc_final: 0.7776 (m-10) REVERT: F 434 MET cc_start: 0.8312 (mtp) cc_final: 0.8025 (mmm) REVERT: F 448 LEU cc_start: 0.8631 (tt) cc_final: 0.8405 (tt) REVERT: F 471 LEU cc_start: 0.9353 (tp) cc_final: 0.9119 (mm) REVERT: F 473 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7033 (mp0) REVERT: F 482 LYS cc_start: 0.7556 (mttt) cc_final: 0.6967 (tppt) REVERT: F 501 LYS cc_start: 0.8724 (mtpp) cc_final: 0.8491 (mtpp) REVERT: F 534 TYR cc_start: 0.8251 (m-10) cc_final: 0.7805 (m-10) REVERT: F 788 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8065 (tp30) outliers start: 1 outliers final: 1 residues processed: 650 average time/residue: 0.4893 time to fit residues: 512.8551 Evaluate side-chains 428 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 427 time to evaluate : 4.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 211 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 317 optimal weight: 4.9990 chunk 259 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 382 optimal weight: 0.9980 chunk 412 optimal weight: 0.5980 chunk 340 optimal weight: 1.9990 chunk 378 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 306 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 HIS B 708 GLN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 GLN D 132 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 614 HIS D 695 ASN D 708 GLN E 104 HIS E 132 HIS ** E 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 650 HIS E 695 ASN E 709 ASN F 132 HIS F 253 HIS ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 HIS F 740 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35745 Z= 0.190 Angle : 0.729 9.794 48453 Z= 0.373 Chirality : 0.045 0.173 5598 Planarity : 0.005 0.066 5994 Dihedral : 6.103 38.010 4617 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.15 % Allowed : 4.20 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.46 (0.12), residues: 4191 helix: -1.07 (0.11), residues: 2073 sheet: -1.29 (0.24), residues: 468 loop : -2.37 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 647 HIS 0.018 0.001 HIS D 155 PHE 0.028 0.002 PHE E 490 TYR 0.027 0.002 TYR A 477 ARG 0.008 0.000 ARG C 666 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 600 time to evaluate : 4.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8227 (mttt) cc_final: 0.7914 (mmtm) REVERT: A 265 MET cc_start: 0.7731 (mmp) cc_final: 0.7320 (tpp) REVERT: A 332 TYR cc_start: 0.8510 (t80) cc_final: 0.7602 (t80) REVERT: A 402 LEU cc_start: 0.8481 (tt) cc_final: 0.8126 (tp) REVERT: A 454 GLU cc_start: 0.5414 (pt0) cc_final: 0.4969 (pt0) REVERT: A 473 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8063 (tt0) REVERT: A 498 LEU cc_start: 0.9204 (tp) cc_final: 0.8928 (tp) REVERT: A 518 LEU cc_start: 0.8689 (tp) cc_final: 0.8394 (tp) REVERT: A 520 GLU cc_start: 0.8227 (pt0) cc_final: 0.7896 (pt0) REVERT: A 653 TYR cc_start: 0.6743 (t80) cc_final: 0.6458 (t80) REVERT: A 654 ILE cc_start: 0.7846 (mt) cc_final: 0.7418 (mm) REVERT: A 707 LEU cc_start: 0.8906 (mt) cc_final: 0.8376 (tp) REVERT: B 35 MET cc_start: 0.8407 (ttm) cc_final: 0.8138 (ttm) REVERT: B 154 GLU cc_start: 0.8459 (tt0) cc_final: 0.8184 (tp30) REVERT: B 280 CYS cc_start: 0.8640 (m) cc_final: 0.8309 (t) REVERT: B 473 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7024 (mp0) REVERT: B 482 LYS cc_start: 0.8173 (mttt) cc_final: 0.7568 (tppt) REVERT: B 501 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7634 (mtmt) REVERT: B 576 ASN cc_start: 0.6949 (m-40) cc_final: 0.6741 (m-40) REVERT: B 590 MET cc_start: 0.6440 (mmt) cc_final: 0.6115 (tpp) REVERT: B 707 LEU cc_start: 0.8649 (mt) cc_final: 0.8011 (tp) REVERT: B 803 TRP cc_start: 0.6796 (m100) cc_final: 0.5900 (t60) REVERT: C 402 LEU cc_start: 0.8548 (tt) cc_final: 0.7898 (tt) REVERT: C 454 GLU cc_start: 0.6205 (pt0) cc_final: 0.5655 (pt0) REVERT: C 518 LEU cc_start: 0.8540 (tp) cc_final: 0.8296 (tp) REVERT: C 653 TYR cc_start: 0.7101 (t80) cc_final: 0.6501 (t80) REVERT: D 25 ASP cc_start: 0.8321 (m-30) cc_final: 0.7877 (t70) REVERT: D 115 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8192 (tm-30) REVERT: D 124 TYR cc_start: 0.8528 (m-80) cc_final: 0.8214 (m-10) REVERT: D 154 GLU cc_start: 0.8837 (tt0) cc_final: 0.8473 (tp30) REVERT: D 161 LEU cc_start: 0.8571 (tp) cc_final: 0.8344 (pp) REVERT: D 367 ASP cc_start: 0.7124 (m-30) cc_final: 0.6385 (t0) REVERT: D 473 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7071 (mp0) REVERT: D 482 LYS cc_start: 0.7542 (mttt) cc_final: 0.7244 (tppt) REVERT: D 576 ASN cc_start: 0.7459 (m-40) cc_final: 0.7064 (t0) REVERT: D 590 MET cc_start: 0.5829 (mmp) cc_final: 0.4946 (tpp) REVERT: D 622 LYS cc_start: 0.8015 (mttt) cc_final: 0.7780 (mttp) REVERT: D 623 ASP cc_start: 0.7645 (m-30) cc_final: 0.7358 (t0) REVERT: D 635 PHE cc_start: 0.7845 (m-80) cc_final: 0.7542 (m-80) REVERT: D 707 LEU cc_start: 0.8749 (mt) cc_final: 0.8096 (tp) REVERT: D 788 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7952 (tp30) REVERT: E 337 MET cc_start: 0.8435 (tmm) cc_final: 0.7892 (tmm) REVERT: E 498 LEU cc_start: 0.9205 (tp) cc_final: 0.8986 (tp) REVERT: E 518 LEU cc_start: 0.8760 (tp) cc_final: 0.8382 (tp) REVERT: E 590 MET cc_start: 0.8093 (ppp) cc_final: 0.7692 (ppp) REVERT: E 654 ILE cc_start: 0.7825 (mm) cc_final: 0.7324 (mm) REVERT: F 25 ASP cc_start: 0.8429 (m-30) cc_final: 0.8057 (t70) REVERT: F 154 GLU cc_start: 0.8711 (tt0) cc_final: 0.8217 (tp30) REVERT: F 161 LEU cc_start: 0.8498 (tp) cc_final: 0.8091 (pp) REVERT: F 292 ASP cc_start: 0.8679 (p0) cc_final: 0.8377 (p0) REVERT: F 332 TYR cc_start: 0.8562 (t80) cc_final: 0.7693 (t80) REVERT: F 336 CYS cc_start: 0.8195 (m) cc_final: 0.7436 (m) REVERT: F 374 PHE cc_start: 0.6606 (t80) cc_final: 0.6389 (t80) REVERT: F 428 LEU cc_start: 0.7831 (mm) cc_final: 0.7358 (mm) REVERT: F 433 PHE cc_start: 0.7980 (m-10) cc_final: 0.7699 (m-10) REVERT: F 434 MET cc_start: 0.8237 (mtp) cc_final: 0.8000 (mmm) REVERT: F 448 LEU cc_start: 0.8761 (tt) cc_final: 0.8489 (tp) REVERT: F 455 LEU cc_start: 0.8727 (mt) cc_final: 0.8486 (mt) REVERT: F 473 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7144 (mp0) REVERT: F 482 LYS cc_start: 0.7614 (mttt) cc_final: 0.7011 (tppt) REVERT: F 501 LYS cc_start: 0.8777 (mtpp) cc_final: 0.8557 (mtpp) REVERT: F 590 MET cc_start: 0.5585 (mmp) cc_final: 0.4905 (tpp) REVERT: F 623 ASP cc_start: 0.7710 (t0) cc_final: 0.7173 (t0) REVERT: F 707 LEU cc_start: 0.8792 (mp) cc_final: 0.8148 (tp) REVERT: F 762 ARG cc_start: 0.8376 (tpm170) cc_final: 0.7997 (tpm170) REVERT: F 788 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8125 (tp30) outliers start: 6 outliers final: 2 residues processed: 603 average time/residue: 0.4241 time to fit residues: 425.7464 Evaluate side-chains 430 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 428 time to evaluate : 4.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 377 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 256 optimal weight: 20.0000 chunk 383 optimal weight: 3.9990 chunk 405 optimal weight: 0.0070 chunk 200 optimal weight: 0.8980 chunk 363 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 HIS ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 HIS ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 35745 Z= 0.207 Angle : 0.708 10.139 48453 Z= 0.363 Chirality : 0.045 0.175 5598 Planarity : 0.004 0.085 5994 Dihedral : 5.831 36.056 4617 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.03 % Allowed : 3.33 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.13 (0.13), residues: 4191 helix: -0.80 (0.11), residues: 2079 sheet: -1.04 (0.24), residues: 468 loop : -2.23 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 647 HIS 0.013 0.001 HIS A 104 PHE 0.028 0.002 PHE C 136 TYR 0.029 0.002 TYR F 477 ARG 0.018 0.000 ARG E 666 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 544 time to evaluate : 3.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8221 (mttt) cc_final: 0.7972 (mmtp) REVERT: A 332 TYR cc_start: 0.8394 (t80) cc_final: 0.7909 (t80) REVERT: A 402 LEU cc_start: 0.8638 (tt) cc_final: 0.7801 (tp) REVERT: A 414 ASP cc_start: 0.8637 (m-30) cc_final: 0.8432 (m-30) REVERT: A 454 GLU cc_start: 0.5225 (pt0) cc_final: 0.4696 (pt0) REVERT: A 473 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7872 (tt0) REVERT: A 498 LEU cc_start: 0.9163 (tp) cc_final: 0.8847 (tp) REVERT: A 518 LEU cc_start: 0.8601 (tp) cc_final: 0.8334 (tp) REVERT: A 520 GLU cc_start: 0.8260 (pt0) cc_final: 0.7895 (pt0) REVERT: A 590 MET cc_start: 0.7896 (ppp) cc_final: 0.7549 (ppp) REVERT: A 653 TYR cc_start: 0.6827 (t80) cc_final: 0.6387 (t80) REVERT: A 654 ILE cc_start: 0.7811 (mt) cc_final: 0.7363 (mm) REVERT: A 673 LYS cc_start: 0.9097 (tmtt) cc_final: 0.8872 (tptp) REVERT: A 707 LEU cc_start: 0.8928 (mt) cc_final: 0.8400 (tp) REVERT: A 758 GLN cc_start: 0.8933 (mt0) cc_final: 0.8662 (pp30) REVERT: B 25 ASP cc_start: 0.8693 (m-30) cc_final: 0.7758 (t70) REVERT: B 35 MET cc_start: 0.8557 (ttm) cc_final: 0.8205 (ttm) REVERT: B 115 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8244 (tm-30) REVERT: B 154 GLU cc_start: 0.8492 (tt0) cc_final: 0.8264 (tp30) REVERT: B 280 CYS cc_start: 0.8572 (m) cc_final: 0.8350 (t) REVERT: B 448 LEU cc_start: 0.8417 (mm) cc_final: 0.8180 (tp) REVERT: B 473 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7080 (mp0) REVERT: B 482 LYS cc_start: 0.8124 (mttt) cc_final: 0.7491 (tppt) REVERT: B 501 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7717 (mtmt) REVERT: B 623 ASP cc_start: 0.7101 (t0) cc_final: 0.6803 (t0) REVERT: B 694 HIS cc_start: 0.7876 (t-90) cc_final: 0.7569 (t-90) REVERT: B 707 LEU cc_start: 0.8725 (mt) cc_final: 0.8507 (mt) REVERT: C 332 TYR cc_start: 0.8327 (t80) cc_final: 0.7947 (t80) REVERT: C 402 LEU cc_start: 0.8614 (tt) cc_final: 0.7815 (tt) REVERT: C 454 GLU cc_start: 0.6214 (pt0) cc_final: 0.5614 (pt0) REVERT: C 498 LEU cc_start: 0.9139 (tp) cc_final: 0.8833 (tp) REVERT: C 518 LEU cc_start: 0.8517 (tp) cc_final: 0.8275 (tp) REVERT: C 653 TYR cc_start: 0.7023 (t80) cc_final: 0.6419 (t80) REVERT: C 654 ILE cc_start: 0.7977 (mm) cc_final: 0.7767 (mm) REVERT: D 25 ASP cc_start: 0.8476 (m-30) cc_final: 0.7963 (t70) REVERT: D 115 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8138 (tm-30) REVERT: D 154 GLU cc_start: 0.8848 (tt0) cc_final: 0.8469 (tp30) REVERT: D 161 LEU cc_start: 0.8419 (tp) cc_final: 0.8191 (pp) REVERT: D 367 ASP cc_start: 0.6718 (m-30) cc_final: 0.6358 (t0) REVERT: D 428 LEU cc_start: 0.7644 (mm) cc_final: 0.7140 (mm) REVERT: D 473 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7048 (mp0) REVERT: D 482 LYS cc_start: 0.7572 (mttt) cc_final: 0.7277 (tppt) REVERT: D 590 MET cc_start: 0.5539 (mmp) cc_final: 0.4923 (tpp) REVERT: D 623 ASP cc_start: 0.7661 (m-30) cc_final: 0.7420 (t0) REVERT: D 635 PHE cc_start: 0.7733 (m-80) cc_final: 0.7464 (m-80) REVERT: D 707 LEU cc_start: 0.8739 (mt) cc_final: 0.7958 (tp) REVERT: D 788 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7839 (tp30) REVERT: E 246 LYS cc_start: 0.8274 (mppt) cc_final: 0.7988 (mmtt) REVERT: E 337 MET cc_start: 0.8440 (tmm) cc_final: 0.7940 (tmm) REVERT: E 402 LEU cc_start: 0.8368 (tp) cc_final: 0.8062 (tp) REVERT: E 434 MET cc_start: 0.8087 (tpp) cc_final: 0.7869 (tpp) REVERT: E 476 LEU cc_start: 0.8891 (mt) cc_final: 0.8542 (tt) REVERT: E 498 LEU cc_start: 0.9256 (tp) cc_final: 0.9037 (tp) REVERT: E 518 LEU cc_start: 0.8735 (tp) cc_final: 0.8431 (tp) REVERT: E 654 ILE cc_start: 0.7835 (mm) cc_final: 0.7341 (mm) REVERT: F 25 ASP cc_start: 0.8513 (m-30) cc_final: 0.8112 (t70) REVERT: F 154 GLU cc_start: 0.8731 (tt0) cc_final: 0.8226 (tp30) REVERT: F 161 LEU cc_start: 0.8492 (tp) cc_final: 0.8118 (pp) REVERT: F 292 ASP cc_start: 0.8651 (p0) cc_final: 0.8346 (p0) REVERT: F 332 TYR cc_start: 0.8574 (t80) cc_final: 0.8206 (t80) REVERT: F 411 TRP cc_start: 0.6448 (m100) cc_final: 0.6210 (m100) REVERT: F 428 LEU cc_start: 0.7785 (mm) cc_final: 0.7031 (mm) REVERT: F 433 PHE cc_start: 0.8066 (m-10) cc_final: 0.7779 (m-10) REVERT: F 434 MET cc_start: 0.8370 (mtp) cc_final: 0.8135 (mmm) REVERT: F 448 LEU cc_start: 0.8244 (tt) cc_final: 0.8005 (tp) REVERT: F 473 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7047 (mp0) REVERT: F 482 LYS cc_start: 0.7601 (mttt) cc_final: 0.6995 (tppt) REVERT: F 501 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8457 (mtpp) REVERT: F 590 MET cc_start: 0.5692 (mmp) cc_final: 0.5150 (tpp) REVERT: F 623 ASP cc_start: 0.7769 (t0) cc_final: 0.7287 (t0) REVERT: F 707 LEU cc_start: 0.8856 (mp) cc_final: 0.8182 (tp) REVERT: F 762 ARG cc_start: 0.8628 (tpm170) cc_final: 0.8249 (tpm170) REVERT: F 788 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8032 (tp30) outliers start: 1 outliers final: 0 residues processed: 545 average time/residue: 0.4222 time to fit residues: 381.5892 Evaluate side-chains 419 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 4.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 338 optimal weight: 8.9990 chunk 230 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 302 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 346 optimal weight: 0.0670 chunk 280 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 364 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 ASN A 744 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 HIS E 744 GLN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35745 Z= 0.180 Angle : 0.687 10.122 48453 Z= 0.347 Chirality : 0.044 0.172 5598 Planarity : 0.004 0.053 5994 Dihedral : 5.575 35.600 4617 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.03 % Allowed : 3.33 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.88 (0.13), residues: 4191 helix: -0.62 (0.11), residues: 2085 sheet: -0.90 (0.25), residues: 492 loop : -2.09 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 647 HIS 0.012 0.001 HIS A 104 PHE 0.017 0.001 PHE F 324 TYR 0.024 0.002 TYR B 477 ARG 0.005 0.000 ARG F 417 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 551 time to evaluate : 4.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.7236 (mmp) cc_final: 0.6986 (tpp) REVERT: A 332 TYR cc_start: 0.8398 (t80) cc_final: 0.7712 (t80) REVERT: A 402 LEU cc_start: 0.8507 (tt) cc_final: 0.7927 (tp) REVERT: A 448 LEU cc_start: 0.8875 (mp) cc_final: 0.8673 (mp) REVERT: A 473 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7902 (tt0) REVERT: A 498 LEU cc_start: 0.9167 (tp) cc_final: 0.8866 (tp) REVERT: A 518 LEU cc_start: 0.8527 (tp) cc_final: 0.8298 (tp) REVERT: A 520 GLU cc_start: 0.8264 (pt0) cc_final: 0.7858 (pt0) REVERT: A 590 MET cc_start: 0.7692 (ppp) cc_final: 0.7366 (ppp) REVERT: A 653 TYR cc_start: 0.6875 (t80) cc_final: 0.6393 (t80) REVERT: A 654 ILE cc_start: 0.7823 (mt) cc_final: 0.7553 (mm) REVERT: A 673 LYS cc_start: 0.9075 (tmtt) cc_final: 0.8846 (tptp) REVERT: A 707 LEU cc_start: 0.8891 (mt) cc_final: 0.8361 (tp) REVERT: B 25 ASP cc_start: 0.8661 (m-30) cc_final: 0.7817 (t70) REVERT: B 35 MET cc_start: 0.8606 (ttm) cc_final: 0.8259 (ttm) REVERT: B 115 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8307 (tm-30) REVERT: B 128 LEU cc_start: 0.9290 (tt) cc_final: 0.8972 (tt) REVERT: B 154 GLU cc_start: 0.8651 (tt0) cc_final: 0.8291 (tp30) REVERT: B 337 MET cc_start: 0.8447 (ttt) cc_final: 0.7828 (tmm) REVERT: B 448 LEU cc_start: 0.8499 (mm) cc_final: 0.8182 (tp) REVERT: B 473 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7074 (mp0) REVERT: B 482 LYS cc_start: 0.8171 (mttt) cc_final: 0.7560 (tppt) REVERT: B 501 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7644 (mtmt) REVERT: B 576 ASN cc_start: 0.7072 (m-40) cc_final: 0.6748 (m-40) REVERT: B 590 MET cc_start: 0.5736 (tpt) cc_final: 0.4864 (tpp) REVERT: B 623 ASP cc_start: 0.7258 (t0) cc_final: 0.6959 (t0) REVERT: B 635 PHE cc_start: 0.7856 (m-80) cc_final: 0.7479 (m-80) REVERT: B 683 TYR cc_start: 0.7567 (t80) cc_final: 0.7310 (t80) REVERT: B 689 TYR cc_start: 0.6594 (t80) cc_final: 0.6218 (t80) REVERT: C 134 LEU cc_start: 0.8726 (tp) cc_final: 0.8461 (tt) REVERT: C 402 LEU cc_start: 0.8541 (tt) cc_final: 0.7718 (tt) REVERT: C 498 LEU cc_start: 0.9196 (tp) cc_final: 0.8917 (tp) REVERT: C 518 LEU cc_start: 0.8470 (tp) cc_final: 0.8226 (tp) REVERT: C 653 TYR cc_start: 0.6893 (t80) cc_final: 0.6359 (t80) REVERT: C 654 ILE cc_start: 0.7990 (mm) cc_final: 0.7491 (mm) REVERT: D 25 ASP cc_start: 0.8459 (m-30) cc_final: 0.7995 (t70) REVERT: D 115 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8155 (tm-30) REVERT: D 154 GLU cc_start: 0.8835 (tt0) cc_final: 0.8394 (tp30) REVERT: D 337 MET cc_start: 0.8392 (ttp) cc_final: 0.7979 (tmm) REVERT: D 367 ASP cc_start: 0.7154 (m-30) cc_final: 0.6283 (t0) REVERT: D 374 PHE cc_start: 0.7009 (t80) cc_final: 0.6522 (t80) REVERT: D 473 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7294 (mp0) REVERT: D 482 LYS cc_start: 0.7550 (mttt) cc_final: 0.7238 (tppt) REVERT: D 590 MET cc_start: 0.5965 (mmp) cc_final: 0.5472 (tpp) REVERT: D 623 ASP cc_start: 0.7728 (m-30) cc_final: 0.7512 (t0) REVERT: D 707 LEU cc_start: 0.8719 (mt) cc_final: 0.8071 (tp) REVERT: D 788 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7629 (tp30) REVERT: E 337 MET cc_start: 0.8430 (tmm) cc_final: 0.7917 (tmm) REVERT: E 498 LEU cc_start: 0.9154 (tp) cc_final: 0.8875 (tp) REVERT: E 518 LEU cc_start: 0.8718 (tp) cc_final: 0.8347 (tp) REVERT: E 653 TYR cc_start: 0.7108 (t80) cc_final: 0.6849 (t80) REVERT: E 654 ILE cc_start: 0.7856 (mm) cc_final: 0.7358 (mm) REVERT: F 25 ASP cc_start: 0.8367 (m-30) cc_final: 0.7982 (t70) REVERT: F 154 GLU cc_start: 0.8759 (tt0) cc_final: 0.8232 (tp30) REVERT: F 161 LEU cc_start: 0.8484 (tp) cc_final: 0.8124 (pp) REVERT: F 292 ASP cc_start: 0.8679 (p0) cc_final: 0.8428 (p0) REVERT: F 332 TYR cc_start: 0.8817 (t80) cc_final: 0.8220 (t80) REVERT: F 337 MET cc_start: 0.8343 (tmm) cc_final: 0.7923 (tmm) REVERT: F 343 MET cc_start: 0.7960 (mmp) cc_final: 0.7348 (tpp) REVERT: F 374 PHE cc_start: 0.6571 (t80) cc_final: 0.6304 (t80) REVERT: F 428 LEU cc_start: 0.8019 (mm) cc_final: 0.7530 (mm) REVERT: F 433 PHE cc_start: 0.8014 (m-10) cc_final: 0.7746 (m-10) REVERT: F 434 MET cc_start: 0.8297 (mtp) cc_final: 0.8095 (mmm) REVERT: F 473 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7067 (mp0) REVERT: F 482 LYS cc_start: 0.7621 (mttt) cc_final: 0.7029 (tppt) REVERT: F 501 LYS cc_start: 0.8766 (mtpp) cc_final: 0.8532 (mtpp) REVERT: F 623 ASP cc_start: 0.7751 (t0) cc_final: 0.7293 (t0) REVERT: F 707 LEU cc_start: 0.8842 (mp) cc_final: 0.8149 (tp) REVERT: F 762 ARG cc_start: 0.8758 (tpm170) cc_final: 0.8378 (tpm170) REVERT: F 788 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8116 (tp30) outliers start: 1 outliers final: 0 residues processed: 552 average time/residue: 0.4185 time to fit residues: 388.6791 Evaluate side-chains 421 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 4.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 136 optimal weight: 30.0000 chunk 365 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 406 optimal weight: 10.0000 chunk 337 optimal weight: 20.0000 chunk 188 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 213 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN C 132 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS D 624 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 HIS E 406 ASN E 624 ASN F 104 HIS ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 HIS ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 526 ASN F 649 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 35745 Z= 0.389 Angle : 0.845 12.111 48453 Z= 0.433 Chirality : 0.050 0.202 5598 Planarity : 0.005 0.058 5994 Dihedral : 5.918 38.159 4617 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.13 (0.13), residues: 4191 helix: -0.87 (0.11), residues: 2091 sheet: -0.97 (0.24), residues: 507 loop : -2.18 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 647 HIS 0.026 0.002 HIS A 104 PHE 0.027 0.003 PHE B 318 TYR 0.047 0.003 TYR B 106 ARG 0.017 0.001 ARG B 671 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 479 time to evaluate : 4.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 PHE cc_start: 0.8539 (m-80) cc_final: 0.8243 (m-80) REVERT: A 265 MET cc_start: 0.8266 (mmp) cc_final: 0.7816 (tpp) REVERT: A 283 VAL cc_start: 0.9160 (t) cc_final: 0.8910 (p) REVERT: A 308 TYR cc_start: 0.8374 (m-80) cc_final: 0.8131 (m-80) REVERT: A 332 TYR cc_start: 0.8503 (t80) cc_final: 0.7598 (t80) REVERT: A 374 PHE cc_start: 0.7894 (t80) cc_final: 0.7358 (t80) REVERT: A 402 LEU cc_start: 0.8709 (tt) cc_final: 0.7888 (tt) REVERT: A 414 ASP cc_start: 0.8818 (m-30) cc_final: 0.8588 (m-30) REVERT: A 427 LYS cc_start: 0.6866 (mttt) cc_final: 0.6628 (mptt) REVERT: A 473 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7802 (tt0) REVERT: A 498 LEU cc_start: 0.9166 (tp) cc_final: 0.8878 (tp) REVERT: A 520 GLU cc_start: 0.8367 (pt0) cc_final: 0.8032 (pt0) REVERT: A 590 MET cc_start: 0.7787 (ppp) cc_final: 0.7538 (ppp) REVERT: A 653 TYR cc_start: 0.7001 (t80) cc_final: 0.6489 (t80) REVERT: A 654 ILE cc_start: 0.7974 (mt) cc_final: 0.7335 (mm) REVERT: A 707 LEU cc_start: 0.9021 (mt) cc_final: 0.8540 (tp) REVERT: B 25 ASP cc_start: 0.8976 (m-30) cc_final: 0.8200 (t70) REVERT: B 35 MET cc_start: 0.8891 (ttm) cc_final: 0.8213 (ttp) REVERT: B 37 MET cc_start: 0.8592 (tmm) cc_final: 0.7911 (tmm) REVERT: B 115 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8368 (tm-30) REVERT: B 154 GLU cc_start: 0.8705 (tt0) cc_final: 0.8353 (tp30) REVERT: B 337 MET cc_start: 0.8571 (ttt) cc_final: 0.8039 (tmm) REVERT: B 473 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7041 (mp0) REVERT: B 482 LYS cc_start: 0.8418 (mttt) cc_final: 0.7861 (tppt) REVERT: B 501 LYS cc_start: 0.8338 (mtmt) cc_final: 0.7842 (mtmt) REVERT: B 590 MET cc_start: 0.5996 (tpt) cc_final: 0.4808 (tpp) REVERT: B 623 ASP cc_start: 0.7389 (t0) cc_final: 0.7180 (t0) REVERT: B 635 PHE cc_start: 0.7851 (m-80) cc_final: 0.7518 (m-80) REVERT: B 683 TYR cc_start: 0.7766 (t80) cc_final: 0.7449 (t80) REVERT: B 689 TYR cc_start: 0.6699 (t80) cc_final: 0.6315 (t80) REVERT: B 694 HIS cc_start: 0.8336 (t-90) cc_final: 0.8090 (t-90) REVERT: C 134 LEU cc_start: 0.8786 (tp) cc_final: 0.8544 (tt) REVERT: C 374 PHE cc_start: 0.7758 (t80) cc_final: 0.7406 (t80) REVERT: C 402 LEU cc_start: 0.8633 (tt) cc_final: 0.7837 (tt) REVERT: C 498 LEU cc_start: 0.9196 (tp) cc_final: 0.8793 (tp) REVERT: C 518 LEU cc_start: 0.8398 (tp) cc_final: 0.8169 (tp) REVERT: C 654 ILE cc_start: 0.8076 (mm) cc_final: 0.7813 (mm) REVERT: D 25 ASP cc_start: 0.8782 (m-30) cc_final: 0.8159 (t70) REVERT: D 35 MET cc_start: 0.8741 (ttm) cc_final: 0.8406 (ttm) REVERT: D 37 MET cc_start: 0.8749 (ttp) cc_final: 0.8432 (tmm) REVERT: D 115 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8261 (tm-30) REVERT: D 154 GLU cc_start: 0.8834 (tt0) cc_final: 0.8503 (tp30) REVERT: D 235 LYS cc_start: 0.9010 (mppt) cc_final: 0.8517 (ptmm) REVERT: D 367 ASP cc_start: 0.7272 (m-30) cc_final: 0.6492 (t0) REVERT: D 374 PHE cc_start: 0.7336 (t80) cc_final: 0.6793 (t80) REVERT: D 482 LYS cc_start: 0.7643 (mttt) cc_final: 0.6919 (mmmt) REVERT: D 590 MET cc_start: 0.6139 (mmp) cc_final: 0.5549 (tpt) REVERT: D 704 ILE cc_start: 0.7808 (pt) cc_final: 0.7577 (pt) REVERT: D 707 LEU cc_start: 0.8795 (mt) cc_final: 0.8230 (tp) REVERT: D 788 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7812 (tp30) REVERT: E 337 MET cc_start: 0.8525 (tmm) cc_final: 0.8058 (tmm) REVERT: E 374 PHE cc_start: 0.8013 (t80) cc_final: 0.7620 (t80) REVERT: E 402 LEU cc_start: 0.8194 (tp) cc_final: 0.7883 (mt) REVERT: E 414 ASP cc_start: 0.8515 (m-30) cc_final: 0.8248 (m-30) REVERT: E 448 LEU cc_start: 0.8992 (tp) cc_final: 0.8729 (mm) REVERT: E 476 LEU cc_start: 0.9199 (mt) cc_final: 0.8933 (tt) REVERT: E 571 LYS cc_start: 0.8076 (mttt) cc_final: 0.7630 (mtpp) REVERT: E 654 ILE cc_start: 0.8128 (mm) cc_final: 0.7649 (mm) REVERT: F 25 ASP cc_start: 0.8967 (m-30) cc_final: 0.8410 (t70) REVERT: F 52 MET cc_start: 0.8070 (mtp) cc_final: 0.7815 (mtp) REVERT: F 154 GLU cc_start: 0.8799 (tt0) cc_final: 0.8298 (tp30) REVERT: F 161 LEU cc_start: 0.8666 (tp) cc_final: 0.8270 (pp) REVERT: F 337 MET cc_start: 0.8235 (tmm) cc_final: 0.7883 (tmm) REVERT: F 343 MET cc_start: 0.8139 (mmp) cc_final: 0.7636 (tpp) REVERT: F 374 PHE cc_start: 0.7229 (t80) cc_final: 0.6861 (t80) REVERT: F 433 PHE cc_start: 0.8105 (m-10) cc_final: 0.7829 (m-10) REVERT: F 482 LYS cc_start: 0.7740 (mttt) cc_final: 0.7133 (tppt) REVERT: F 501 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8588 (mtpp) REVERT: F 590 MET cc_start: 0.6347 (tpt) cc_final: 0.6056 (tpp) REVERT: F 623 ASP cc_start: 0.8022 (t0) cc_final: 0.7799 (t0) REVERT: F 683 TYR cc_start: 0.7818 (t80) cc_final: 0.7564 (t80) REVERT: F 707 LEU cc_start: 0.8807 (mp) cc_final: 0.7997 (tp) REVERT: F 762 ARG cc_start: 0.8721 (tpm170) cc_final: 0.8290 (tpm170) REVERT: F 788 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8062 (tp30) outliers start: 1 outliers final: 0 residues processed: 480 average time/residue: 0.4202 time to fit residues: 337.4091 Evaluate side-chains 356 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 4.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 391 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 chunk 296 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 342 optimal weight: 10.0000 chunk 226 optimal weight: 0.9980 chunk 404 optimal weight: 10.0000 chunk 253 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 712 ASN ** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN E 312 HIS ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 HIS ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 HIS ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 35745 Z= 0.223 Angle : 0.729 10.585 48453 Z= 0.371 Chirality : 0.046 0.216 5598 Planarity : 0.004 0.055 5994 Dihedral : 5.679 33.962 4617 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.87 (0.13), residues: 4191 helix: -0.66 (0.11), residues: 2088 sheet: -1.02 (0.24), residues: 537 loop : -1.98 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 647 HIS 0.030 0.001 HIS F 155 PHE 0.034 0.002 PHE F 250 TYR 0.033 0.002 TYR E 477 ARG 0.011 0.000 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 4.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8205 (tm-30) REVERT: A 136 PHE cc_start: 0.8559 (m-80) cc_final: 0.8306 (m-80) REVERT: A 161 LEU cc_start: 0.7736 (mm) cc_final: 0.7439 (pp) REVERT: A 265 MET cc_start: 0.8061 (mmp) cc_final: 0.7479 (tpp) REVERT: A 283 VAL cc_start: 0.9205 (t) cc_final: 0.8985 (p) REVERT: A 308 TYR cc_start: 0.8282 (m-80) cc_final: 0.8047 (m-80) REVERT: A 414 ASP cc_start: 0.8820 (m-30) cc_final: 0.8589 (m-30) REVERT: A 473 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7850 (tt0) REVERT: A 498 LEU cc_start: 0.9214 (tp) cc_final: 0.8949 (tp) REVERT: A 518 LEU cc_start: 0.8438 (tp) cc_final: 0.8227 (tp) REVERT: A 520 GLU cc_start: 0.8292 (pt0) cc_final: 0.8010 (pt0) REVERT: A 590 MET cc_start: 0.7780 (ppp) cc_final: 0.7349 (ppp) REVERT: A 653 TYR cc_start: 0.7234 (t80) cc_final: 0.6713 (t80) REVERT: A 654 ILE cc_start: 0.8021 (mt) cc_final: 0.7323 (mm) REVERT: A 707 LEU cc_start: 0.8953 (mt) cc_final: 0.8492 (tp) REVERT: B 25 ASP cc_start: 0.8004 (m-30) cc_final: 0.7758 (t70) REVERT: B 35 MET cc_start: 0.8687 (ttm) cc_final: 0.8069 (ttp) REVERT: B 37 MET cc_start: 0.8508 (tmm) cc_final: 0.7838 (tmm) REVERT: B 128 LEU cc_start: 0.9268 (tt) cc_final: 0.8959 (tt) REVERT: B 154 GLU cc_start: 0.8668 (tt0) cc_final: 0.8317 (tp30) REVERT: B 337 MET cc_start: 0.8574 (ttt) cc_final: 0.7985 (tmm) REVERT: B 427 LYS cc_start: 0.7012 (mttt) cc_final: 0.6527 (mptt) REVERT: B 474 LEU cc_start: 0.9355 (tp) cc_final: 0.8523 (tp) REVERT: B 482 LYS cc_start: 0.8359 (mttt) cc_final: 0.7806 (tppt) REVERT: B 501 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7945 (mtmt) REVERT: B 576 ASN cc_start: 0.6939 (m-40) cc_final: 0.6666 (t0) REVERT: B 590 MET cc_start: 0.5725 (tpt) cc_final: 0.4572 (tpp) REVERT: B 623 ASP cc_start: 0.7327 (t0) cc_final: 0.7073 (t0) REVERT: B 635 PHE cc_start: 0.7979 (m-80) cc_final: 0.7726 (m-80) REVERT: B 683 TYR cc_start: 0.7822 (t80) cc_final: 0.7499 (t80) REVERT: B 689 TYR cc_start: 0.6722 (t80) cc_final: 0.6299 (t80) REVERT: B 694 HIS cc_start: 0.8187 (t-90) cc_final: 0.7907 (t-90) REVERT: C 35 MET cc_start: 0.8171 (ttm) cc_final: 0.7528 (ttt) REVERT: C 134 LEU cc_start: 0.8858 (tp) cc_final: 0.8637 (tt) REVERT: C 402 LEU cc_start: 0.8344 (tt) cc_final: 0.7503 (tt) REVERT: C 498 LEU cc_start: 0.9140 (tp) cc_final: 0.8891 (tp) REVERT: C 518 LEU cc_start: 0.8463 (tp) cc_final: 0.8235 (tp) REVERT: C 590 MET cc_start: 0.7711 (mmp) cc_final: 0.7274 (mmm) REVERT: C 654 ILE cc_start: 0.8089 (mm) cc_final: 0.7818 (mm) REVERT: D 25 ASP cc_start: 0.8591 (m-30) cc_final: 0.8217 (t70) REVERT: D 35 MET cc_start: 0.8760 (ttm) cc_final: 0.8380 (ttm) REVERT: D 37 MET cc_start: 0.8611 (ttp) cc_final: 0.8203 (tmm) REVERT: D 115 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8219 (tm-30) REVERT: D 154 GLU cc_start: 0.8813 (tt0) cc_final: 0.8414 (tp30) REVERT: D 367 ASP cc_start: 0.6877 (m-30) cc_final: 0.6387 (t0) REVERT: D 374 PHE cc_start: 0.7099 (t80) cc_final: 0.6775 (t80) REVERT: D 420 LEU cc_start: 0.7577 (mt) cc_final: 0.7370 (mt) REVERT: D 473 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7153 (mp0) REVERT: D 474 LEU cc_start: 0.8692 (tp) cc_final: 0.8212 (tp) REVERT: D 476 LEU cc_start: 0.8382 (mt) cc_final: 0.8103 (mt) REVERT: D 482 LYS cc_start: 0.7639 (mttt) cc_final: 0.7343 (tppt) REVERT: D 590 MET cc_start: 0.5967 (mmp) cc_final: 0.5514 (tpt) REVERT: D 623 ASP cc_start: 0.7263 (t0) cc_final: 0.6936 (t0) REVERT: D 704 ILE cc_start: 0.7782 (pt) cc_final: 0.7545 (pt) REVERT: D 707 LEU cc_start: 0.8744 (mt) cc_final: 0.8030 (tp) REVERT: D 788 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7830 (tp30) REVERT: E 265 MET cc_start: 0.7411 (mmp) cc_final: 0.7200 (tpp) REVERT: E 337 MET cc_start: 0.8377 (tmm) cc_final: 0.7943 (tmm) REVERT: E 374 PHE cc_start: 0.7769 (t80) cc_final: 0.7520 (t80) REVERT: E 402 LEU cc_start: 0.7683 (tp) cc_final: 0.7405 (tp) REVERT: E 414 ASP cc_start: 0.8526 (m-30) cc_final: 0.8258 (m-30) REVERT: E 447 GLU cc_start: 0.8319 (tt0) cc_final: 0.8090 (tt0) REVERT: E 448 LEU cc_start: 0.8945 (tp) cc_final: 0.8717 (mm) REVERT: E 654 ILE cc_start: 0.8134 (mm) cc_final: 0.7670 (mm) REVERT: F 25 ASP cc_start: 0.8546 (m-30) cc_final: 0.8084 (t70) REVERT: F 115 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8391 (tm-30) REVERT: F 154 GLU cc_start: 0.8874 (tt0) cc_final: 0.8147 (tp30) REVERT: F 337 MET cc_start: 0.8237 (tmm) cc_final: 0.7844 (tmm) REVERT: F 343 MET cc_start: 0.8134 (mmp) cc_final: 0.7419 (tpp) REVERT: F 374 PHE cc_start: 0.6959 (t80) cc_final: 0.6575 (t80) REVERT: F 428 LEU cc_start: 0.7263 (mm) cc_final: 0.6754 (mm) REVERT: F 453 LEU cc_start: 0.8091 (mt) cc_final: 0.7880 (mt) REVERT: F 474 LEU cc_start: 0.9060 (tp) cc_final: 0.8350 (tp) REVERT: F 482 LYS cc_start: 0.7813 (mttt) cc_final: 0.7231 (tppt) REVERT: F 501 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8443 (mtpp) REVERT: F 590 MET cc_start: 0.6196 (tpt) cc_final: 0.5786 (tpp) REVERT: F 623 ASP cc_start: 0.8110 (t0) cc_final: 0.7784 (t0) REVERT: F 645 LYS cc_start: 0.7975 (mmtm) cc_final: 0.7721 (mmtp) REVERT: F 707 LEU cc_start: 0.8722 (mp) cc_final: 0.7826 (tp) REVERT: F 762 ARG cc_start: 0.8636 (tpm170) cc_final: 0.8238 (tpm170) REVERT: F 788 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8072 (tp30) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.4245 time to fit residues: 353.1982 Evaluate side-chains 383 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 4.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 250 optimal weight: 0.0870 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 8.9990 chunk 121 optimal weight: 30.0000 chunk 79 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 257 optimal weight: 10.0000 chunk 275 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 318 optimal weight: 0.8980 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 ASN ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35745 Z= 0.181 Angle : 0.708 10.564 48453 Z= 0.356 Chirality : 0.045 0.182 5598 Planarity : 0.004 0.058 5994 Dihedral : 5.464 33.631 4617 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.03 % Allowed : 1.42 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.74 (0.13), residues: 4191 helix: -0.53 (0.11), residues: 2088 sheet: -0.96 (0.24), residues: 522 loop : -1.96 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 647 HIS 0.025 0.001 HIS F 155 PHE 0.045 0.002 PHE D 250 TYR 0.028 0.002 TYR E 477 ARG 0.004 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 518 time to evaluate : 4.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 136 PHE cc_start: 0.8195 (m-80) cc_final: 0.7909 (m-80) REVERT: A 160 LEU cc_start: 0.6879 (tp) cc_final: 0.6608 (tp) REVERT: A 161 LEU cc_start: 0.7745 (mm) cc_final: 0.7413 (pp) REVERT: A 265 MET cc_start: 0.7877 (mmp) cc_final: 0.7400 (tpp) REVERT: A 308 TYR cc_start: 0.8286 (m-80) cc_final: 0.8079 (m-80) REVERT: A 328 LEU cc_start: 0.8640 (tp) cc_final: 0.8436 (tp) REVERT: A 402 LEU cc_start: 0.8697 (tt) cc_final: 0.7506 (tt) REVERT: A 414 ASP cc_start: 0.8763 (m-30) cc_final: 0.8553 (m-30) REVERT: A 447 GLU cc_start: 0.8726 (tt0) cc_final: 0.8325 (tt0) REVERT: A 473 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7859 (tt0) REVERT: A 498 LEU cc_start: 0.9252 (tp) cc_final: 0.8966 (tp) REVERT: A 520 GLU cc_start: 0.8294 (pt0) cc_final: 0.7807 (pt0) REVERT: A 590 MET cc_start: 0.7820 (ppp) cc_final: 0.7393 (ppp) REVERT: A 653 TYR cc_start: 0.7174 (t80) cc_final: 0.6651 (t80) REVERT: A 654 ILE cc_start: 0.8027 (mt) cc_final: 0.7335 (mm) REVERT: A 707 LEU cc_start: 0.8955 (mt) cc_final: 0.8479 (tp) REVERT: B 35 MET cc_start: 0.8749 (ttm) cc_final: 0.8178 (ttp) REVERT: B 37 MET cc_start: 0.8489 (tmm) cc_final: 0.7799 (tmm) REVERT: B 128 LEU cc_start: 0.9047 (tt) cc_final: 0.8653 (tt) REVERT: B 154 GLU cc_start: 0.8615 (tt0) cc_final: 0.8179 (tp30) REVERT: B 337 MET cc_start: 0.8589 (ttt) cc_final: 0.8011 (tmm) REVERT: B 343 MET cc_start: 0.7988 (mmp) cc_final: 0.7515 (mmm) REVERT: B 482 LYS cc_start: 0.8308 (mttt) cc_final: 0.7779 (tppt) REVERT: B 576 ASN cc_start: 0.6406 (m-40) cc_final: 0.6194 (m-40) REVERT: B 590 MET cc_start: 0.5533 (tpt) cc_final: 0.4633 (tpp) REVERT: B 623 ASP cc_start: 0.7427 (t0) cc_final: 0.7103 (t0) REVERT: B 635 PHE cc_start: 0.7990 (m-80) cc_final: 0.7744 (m-80) REVERT: B 683 TYR cc_start: 0.7710 (t80) cc_final: 0.7397 (t80) REVERT: B 689 TYR cc_start: 0.6860 (t80) cc_final: 0.6511 (t80) REVERT: B 694 HIS cc_start: 0.8280 (t-90) cc_final: 0.7988 (t-90) REVERT: B 788 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7451 (tp30) REVERT: C 35 MET cc_start: 0.8124 (ttm) cc_final: 0.7884 (ttm) REVERT: C 52 MET cc_start: 0.8072 (ttp) cc_final: 0.6343 (ttm) REVERT: C 134 LEU cc_start: 0.8878 (tp) cc_final: 0.8673 (tt) REVERT: C 402 LEU cc_start: 0.8298 (tt) cc_final: 0.7564 (tt) REVERT: C 518 LEU cc_start: 0.8470 (tp) cc_final: 0.8268 (tp) REVERT: C 590 MET cc_start: 0.7668 (mmp) cc_final: 0.7290 (mmm) REVERT: C 654 ILE cc_start: 0.8052 (mm) cc_final: 0.7784 (mm) REVERT: D 25 ASP cc_start: 0.8407 (m-30) cc_final: 0.8130 (t70) REVERT: D 37 MET cc_start: 0.8550 (ttp) cc_final: 0.8039 (tmm) REVERT: D 102 ASP cc_start: 0.8243 (m-30) cc_final: 0.7785 (m-30) REVERT: D 115 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8150 (tm-30) REVERT: D 154 GLU cc_start: 0.8786 (tt0) cc_final: 0.8231 (tp30) REVERT: D 248 LYS cc_start: 0.9049 (tttt) cc_final: 0.8843 (tppt) REVERT: D 337 MET cc_start: 0.8698 (ttp) cc_final: 0.8086 (tmm) REVERT: D 367 ASP cc_start: 0.6992 (m-30) cc_final: 0.6417 (t0) REVERT: D 473 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7088 (mp0) REVERT: D 476 LEU cc_start: 0.8279 (mt) cc_final: 0.8031 (mt) REVERT: D 482 LYS cc_start: 0.7647 (mttt) cc_final: 0.7136 (mmmt) REVERT: D 590 MET cc_start: 0.5884 (mmp) cc_final: 0.5345 (tpt) REVERT: D 623 ASP cc_start: 0.7240 (t0) cc_final: 0.6899 (t0) REVERT: D 683 TYR cc_start: 0.7696 (t80) cc_final: 0.7336 (t80) REVERT: D 704 ILE cc_start: 0.7907 (pt) cc_final: 0.7658 (pt) REVERT: D 707 LEU cc_start: 0.8736 (mt) cc_final: 0.8052 (tp) REVERT: D 788 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7711 (tp30) REVERT: E 337 MET cc_start: 0.8374 (tmm) cc_final: 0.7953 (tmm) REVERT: E 402 LEU cc_start: 0.7631 (tp) cc_final: 0.7258 (tp) REVERT: E 414 ASP cc_start: 0.8504 (m-30) cc_final: 0.8245 (m-30) REVERT: E 447 GLU cc_start: 0.8624 (tt0) cc_final: 0.8409 (tt0) REVERT: E 653 TYR cc_start: 0.7147 (t80) cc_final: 0.6927 (t80) REVERT: E 654 ILE cc_start: 0.8178 (mm) cc_final: 0.7724 (mm) REVERT: F 25 ASP cc_start: 0.8343 (m-30) cc_final: 0.7966 (t70) REVERT: F 154 GLU cc_start: 0.8622 (tt0) cc_final: 0.7852 (tp30) REVERT: F 337 MET cc_start: 0.8214 (tmm) cc_final: 0.7709 (tmm) REVERT: F 343 MET cc_start: 0.8284 (mmp) cc_final: 0.7680 (tpp) REVERT: F 367 ASP cc_start: 0.7573 (t0) cc_final: 0.6622 (p0) REVERT: F 374 PHE cc_start: 0.6553 (t80) cc_final: 0.6306 (t80) REVERT: F 453 LEU cc_start: 0.8089 (mt) cc_final: 0.7790 (mt) REVERT: F 455 LEU cc_start: 0.8806 (mt) cc_final: 0.8388 (mt) REVERT: F 482 LYS cc_start: 0.7779 (mttt) cc_final: 0.7210 (tppt) REVERT: F 590 MET cc_start: 0.6232 (tpt) cc_final: 0.5792 (tpp) REVERT: F 707 LEU cc_start: 0.8664 (mp) cc_final: 0.7766 (tp) REVERT: F 762 ARG cc_start: 0.8659 (tpm170) cc_final: 0.8272 (tpm170) REVERT: F 788 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8048 (tp30) outliers start: 1 outliers final: 0 residues processed: 519 average time/residue: 0.4285 time to fit residues: 374.6252 Evaluate side-chains 376 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 368 optimal weight: 4.9990 chunk 387 optimal weight: 9.9990 chunk 353 optimal weight: 3.9990 chunk 377 optimal weight: 0.8980 chunk 227 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 296 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 340 optimal weight: 1.9990 chunk 356 optimal weight: 2.9990 chunk 375 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 ASN ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 ASN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 ASN F 119 HIS F 288 ASN ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 35745 Z= 0.234 Angle : 0.743 11.126 48453 Z= 0.376 Chirality : 0.046 0.296 5598 Planarity : 0.004 0.059 5994 Dihedral : 5.524 33.650 4617 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.76 (0.13), residues: 4191 helix: -0.56 (0.11), residues: 2091 sheet: -0.95 (0.24), residues: 522 loop : -1.93 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 511 HIS 0.017 0.001 HIS A 104 PHE 0.051 0.002 PHE F 250 TYR 0.046 0.002 TYR D 477 ARG 0.004 0.000 ARG B 417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 time to evaluate : 4.285 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: A 115 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8275 (tm-30) REVERT: A 265 MET cc_start: 0.8024 (mmp) cc_final: 0.7540 (tpp) REVERT: A 308 TYR cc_start: 0.8363 (m-80) cc_final: 0.8111 (m-80) REVERT: A 374 PHE cc_start: 0.7596 (t80) cc_final: 0.7330 (t80) REVERT: A 386 TYR cc_start: 0.7158 (m-10) cc_final: 0.6748 (m-10) REVERT: A 402 LEU cc_start: 0.8717 (tt) cc_final: 0.7518 (tt) REVERT: A 447 GLU cc_start: 0.8679 (tt0) cc_final: 0.8344 (tt0) REVERT: A 473 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7931 (tt0) REVERT: A 498 LEU cc_start: 0.9265 (tp) cc_final: 0.9000 (tp) REVERT: A 520 GLU cc_start: 0.8299 (pt0) cc_final: 0.7814 (pt0) REVERT: A 590 MET cc_start: 0.7926 (ppp) cc_final: 0.7402 (ppp) REVERT: A 653 TYR cc_start: 0.7181 (t80) cc_final: 0.6641 (t80) REVERT: A 654 ILE cc_start: 0.8055 (mt) cc_final: 0.7351 (mm) REVERT: A 707 LEU cc_start: 0.8968 (mt) cc_final: 0.8464 (tp) REVERT: B 35 MET cc_start: 0.8783 (ttm) cc_final: 0.8196 (ttp) REVERT: B 37 MET cc_start: 0.8476 (tmm) cc_final: 0.7719 (tmm) REVERT: B 128 LEU cc_start: 0.9094 (tt) cc_final: 0.8686 (tt) REVERT: B 154 GLU cc_start: 0.8626 (tt0) cc_final: 0.8182 (tp30) REVERT: B 337 MET cc_start: 0.8611 (ttt) cc_final: 0.8037 (tmm) REVERT: B 343 MET cc_start: 0.8115 (mmp) cc_final: 0.7684 (mmm) REVERT: B 451 LEU cc_start: 0.8789 (tp) cc_final: 0.8531 (tp) REVERT: B 474 LEU cc_start: 0.9230 (tp) cc_final: 0.8542 (tp) REVERT: B 482 LYS cc_start: 0.8208 (mttt) cc_final: 0.7432 (mmmt) REVERT: B 534 TYR cc_start: 0.8673 (m-10) cc_final: 0.8454 (m-10) REVERT: B 576 ASN cc_start: 0.6709 (m-40) cc_final: 0.6464 (m-40) REVERT: B 590 MET cc_start: 0.5613 (tpt) cc_final: 0.4717 (tpp) REVERT: B 623 ASP cc_start: 0.7482 (t0) cc_final: 0.7211 (t0) REVERT: B 635 PHE cc_start: 0.8001 (m-80) cc_final: 0.7763 (m-80) REVERT: B 683 TYR cc_start: 0.7758 (t80) cc_final: 0.7470 (t80) REVERT: B 689 TYR cc_start: 0.6873 (t80) cc_final: 0.6513 (t80) REVERT: B 694 HIS cc_start: 0.8196 (t-90) cc_final: 0.7905 (t-90) REVERT: B 788 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7444 (tp30) REVERT: C 35 MET cc_start: 0.7994 (ttm) cc_final: 0.7716 (ttm) REVERT: C 402 LEU cc_start: 0.8336 (tt) cc_final: 0.7491 (tt) REVERT: C 590 MET cc_start: 0.7779 (mmp) cc_final: 0.7415 (mmm) REVERT: C 654 ILE cc_start: 0.8022 (mm) cc_final: 0.7732 (mm) REVERT: D 25 ASP cc_start: 0.8638 (m-30) cc_final: 0.8252 (t70) REVERT: D 37 MET cc_start: 0.8702 (ttp) cc_final: 0.8168 (tmm) REVERT: D 115 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8237 (tm-30) REVERT: D 154 GLU cc_start: 0.8805 (tt0) cc_final: 0.8257 (tp30) REVERT: D 248 LYS cc_start: 0.9106 (tttt) cc_final: 0.8862 (tppt) REVERT: D 337 MET cc_start: 0.8709 (ttp) cc_final: 0.8142 (tmm) REVERT: D 367 ASP cc_start: 0.6836 (m-30) cc_final: 0.6497 (t0) REVERT: D 471 LEU cc_start: 0.9400 (tt) cc_final: 0.9193 (mp) REVERT: D 474 LEU cc_start: 0.8815 (tp) cc_final: 0.7939 (tp) REVERT: D 476 LEU cc_start: 0.8624 (mt) cc_final: 0.8381 (mt) REVERT: D 482 LYS cc_start: 0.7507 (mttt) cc_final: 0.7142 (tppt) REVERT: D 590 MET cc_start: 0.5909 (mmp) cc_final: 0.5606 (tpt) REVERT: D 623 ASP cc_start: 0.7351 (t0) cc_final: 0.6989 (t0) REVERT: D 683 TYR cc_start: 0.7656 (t80) cc_final: 0.7288 (t80) REVERT: D 704 ILE cc_start: 0.7801 (pt) cc_final: 0.7600 (pt) REVERT: D 707 LEU cc_start: 0.8689 (mt) cc_final: 0.7997 (tp) REVERT: D 788 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7622 (tp30) REVERT: E 337 MET cc_start: 0.8393 (tmm) cc_final: 0.7860 (tmm) REVERT: E 374 PHE cc_start: 0.8059 (t80) cc_final: 0.7568 (t80) REVERT: E 402 LEU cc_start: 0.7794 (tp) cc_final: 0.7434 (tp) REVERT: E 414 ASP cc_start: 0.8554 (m-30) cc_final: 0.8295 (m-30) REVERT: E 447 GLU cc_start: 0.8592 (tt0) cc_final: 0.8310 (tt0) REVERT: E 654 ILE cc_start: 0.8263 (mm) cc_final: 0.7810 (mm) REVERT: F 25 ASP cc_start: 0.8556 (m-30) cc_final: 0.8136 (t70) REVERT: F 37 MET cc_start: 0.8241 (ttp) cc_final: 0.8009 (tmm) REVERT: F 154 GLU cc_start: 0.8642 (tt0) cc_final: 0.7806 (tp30) REVERT: F 332 TYR cc_start: 0.8738 (t80) cc_final: 0.8520 (t80) REVERT: F 337 MET cc_start: 0.8291 (tmm) cc_final: 0.7882 (tmm) REVERT: F 343 MET cc_start: 0.8376 (mmp) cc_final: 0.7792 (tpp) REVERT: F 367 ASP cc_start: 0.7578 (t0) cc_final: 0.6710 (p0) REVERT: F 374 PHE cc_start: 0.6436 (t80) cc_final: 0.6180 (t80) REVERT: F 453 LEU cc_start: 0.7968 (mt) cc_final: 0.7724 (mt) REVERT: F 482 LYS cc_start: 0.7641 (mttt) cc_final: 0.6874 (tppt) REVERT: F 590 MET cc_start: 0.6195 (tpt) cc_final: 0.5648 (tpp) REVERT: F 623 ASP cc_start: 0.7881 (t0) cc_final: 0.7568 (t0) REVERT: F 707 LEU cc_start: 0.8721 (mp) cc_final: 0.7812 (tp) REVERT: F 762 ARG cc_start: 0.8688 (tpm170) cc_final: 0.8295 (tpm170) REVERT: F 788 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8006 (tp30) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.4254 time to fit residues: 346.4366 Evaluate side-chains 365 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 4.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 247 optimal weight: 1.9990 chunk 398 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 189 optimal weight: 8.9990 chunk 277 optimal weight: 5.9990 chunk 418 optimal weight: 7.9990 chunk 385 optimal weight: 0.0970 chunk 333 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 257 optimal weight: 0.0570 chunk 204 optimal weight: 20.0000 overall best weight: 2.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 ASN F 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35745 Z= 0.227 Angle : 0.741 13.307 48453 Z= 0.371 Chirality : 0.046 0.209 5598 Planarity : 0.004 0.057 5994 Dihedral : 5.490 33.527 4617 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.77 (0.13), residues: 4191 helix: -0.56 (0.11), residues: 2088 sheet: -0.92 (0.25), residues: 507 loop : -1.96 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 647 HIS 0.023 0.002 HIS F 155 PHE 0.035 0.002 PHE F 433 TYR 0.035 0.002 TYR F 477 ARG 0.005 0.000 ARG B 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 471 time to evaluate : 4.281 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: A 52 MET cc_start: 0.7544 (ttm) cc_final: 0.7204 (ttp) REVERT: A 115 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8216 (tm-30) REVERT: A 265 MET cc_start: 0.8030 (mmp) cc_final: 0.7549 (tpp) REVERT: A 308 TYR cc_start: 0.8390 (m-80) cc_final: 0.8134 (m-80) REVERT: A 374 PHE cc_start: 0.7813 (t80) cc_final: 0.7538 (t80) REVERT: A 402 LEU cc_start: 0.8706 (tt) cc_final: 0.7469 (tt) REVERT: A 447 GLU cc_start: 0.8720 (tt0) cc_final: 0.8196 (tt0) REVERT: A 473 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7916 (tt0) REVERT: A 498 LEU cc_start: 0.9263 (tp) cc_final: 0.8996 (tp) REVERT: A 520 GLU cc_start: 0.8308 (pt0) cc_final: 0.7817 (pt0) REVERT: A 590 MET cc_start: 0.7982 (ppp) cc_final: 0.7436 (ppp) REVERT: A 653 TYR cc_start: 0.7191 (t80) cc_final: 0.6644 (t80) REVERT: A 654 ILE cc_start: 0.7989 (mt) cc_final: 0.7271 (mm) REVERT: A 707 LEU cc_start: 0.8972 (mt) cc_final: 0.8461 (tp) REVERT: B 35 MET cc_start: 0.8772 (ttm) cc_final: 0.8196 (ttp) REVERT: B 37 MET cc_start: 0.8452 (tmm) cc_final: 0.7704 (tmm) REVERT: B 128 LEU cc_start: 0.9089 (tt) cc_final: 0.8652 (tt) REVERT: B 154 GLU cc_start: 0.8643 (tt0) cc_final: 0.8160 (tp30) REVERT: B 337 MET cc_start: 0.8669 (ttt) cc_final: 0.7991 (tmm) REVERT: B 343 MET cc_start: 0.8125 (mmp) cc_final: 0.7713 (mmm) REVERT: B 427 LYS cc_start: 0.6590 (mttt) cc_final: 0.5959 (mppt) REVERT: B 482 LYS cc_start: 0.8194 (mttt) cc_final: 0.7441 (mmmt) REVERT: B 534 TYR cc_start: 0.8669 (m-10) cc_final: 0.8382 (m-10) REVERT: B 576 ASN cc_start: 0.6741 (m-40) cc_final: 0.6491 (m-40) REVERT: B 590 MET cc_start: 0.5550 (tpt) cc_final: 0.4754 (tpp) REVERT: B 635 PHE cc_start: 0.7954 (m-80) cc_final: 0.7684 (m-80) REVERT: B 683 TYR cc_start: 0.7737 (t80) cc_final: 0.7448 (t80) REVERT: B 689 TYR cc_start: 0.6883 (t80) cc_final: 0.6508 (t80) REVERT: B 694 HIS cc_start: 0.8187 (t-90) cc_final: 0.7861 (t-90) REVERT: B 788 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7443 (tp30) REVERT: C 35 MET cc_start: 0.8049 (ttm) cc_final: 0.7774 (ttm) REVERT: C 402 LEU cc_start: 0.8396 (tt) cc_final: 0.7697 (tt) REVERT: C 590 MET cc_start: 0.7806 (mmp) cc_final: 0.7468 (mmm) REVERT: C 654 ILE cc_start: 0.8005 (mm) cc_final: 0.7717 (mm) REVERT: D 25 ASP cc_start: 0.8556 (m-30) cc_final: 0.8213 (t70) REVERT: D 37 MET cc_start: 0.8650 (ttp) cc_final: 0.8156 (tmm) REVERT: D 115 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8210 (tm-30) REVERT: D 154 GLU cc_start: 0.8778 (tt0) cc_final: 0.8157 (tp30) REVERT: D 248 LYS cc_start: 0.9060 (tttt) cc_final: 0.8806 (tppt) REVERT: D 337 MET cc_start: 0.8696 (ttp) cc_final: 0.8059 (tmm) REVERT: D 367 ASP cc_start: 0.6996 (m-30) cc_final: 0.6425 (t0) REVERT: D 476 LEU cc_start: 0.8367 (mt) cc_final: 0.8104 (mt) REVERT: D 482 LYS cc_start: 0.7506 (mttt) cc_final: 0.7017 (mmmt) REVERT: D 590 MET cc_start: 0.6023 (mmp) cc_final: 0.5491 (tpt) REVERT: D 623 ASP cc_start: 0.7389 (t0) cc_final: 0.7002 (t0) REVERT: D 683 TYR cc_start: 0.7618 (t80) cc_final: 0.7241 (t80) REVERT: D 704 ILE cc_start: 0.8158 (pt) cc_final: 0.7956 (pt) REVERT: D 707 LEU cc_start: 0.8699 (mt) cc_final: 0.8003 (tp) REVERT: D 788 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7625 (tp30) REVERT: E 52 MET cc_start: 0.7803 (ttm) cc_final: 0.7329 (ttp) REVERT: E 265 MET cc_start: 0.7462 (mmp) cc_final: 0.6329 (ttt) REVERT: E 337 MET cc_start: 0.8391 (tmm) cc_final: 0.7895 (tmm) REVERT: E 374 PHE cc_start: 0.8025 (t80) cc_final: 0.7574 (t80) REVERT: E 402 LEU cc_start: 0.7774 (tp) cc_final: 0.7385 (tp) REVERT: E 654 ILE cc_start: 0.8239 (mm) cc_final: 0.7763 (mm) REVERT: F 25 ASP cc_start: 0.8483 (m-30) cc_final: 0.8061 (t70) REVERT: F 37 MET cc_start: 0.8255 (ttp) cc_final: 0.8036 (tmm) REVERT: F 52 MET cc_start: 0.8395 (mtp) cc_final: 0.8167 (mtp) REVERT: F 154 GLU cc_start: 0.8475 (tt0) cc_final: 0.7648 (tp30) REVERT: F 337 MET cc_start: 0.8300 (tmm) cc_final: 0.7881 (tmm) REVERT: F 343 MET cc_start: 0.8410 (mmp) cc_final: 0.7797 (tpp) REVERT: F 367 ASP cc_start: 0.7552 (t0) cc_final: 0.6694 (p0) REVERT: F 374 PHE cc_start: 0.6450 (t80) cc_final: 0.6182 (t80) REVERT: F 453 LEU cc_start: 0.8330 (mt) cc_final: 0.8075 (mt) REVERT: F 482 LYS cc_start: 0.7664 (mttt) cc_final: 0.7150 (mmmt) REVERT: F 590 MET cc_start: 0.6142 (tpt) cc_final: 0.5613 (tpp) REVERT: F 623 ASP cc_start: 0.7878 (t0) cc_final: 0.7570 (t0) REVERT: F 707 LEU cc_start: 0.8736 (mp) cc_final: 0.8020 (tp) REVERT: F 762 ARG cc_start: 0.8658 (tpm170) cc_final: 0.8318 (tpm170) REVERT: F 788 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8013 (tp30) outliers start: 0 outliers final: 0 residues processed: 471 average time/residue: 0.4221 time to fit residues: 335.2204 Evaluate side-chains 360 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 4.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 264 optimal weight: 0.3980 chunk 354 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 307 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 333 optimal weight: 5.9990 chunk 139 optimal weight: 0.4980 chunk 342 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN F 712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.111125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.086607 restraints weight = 103257.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.087580 restraints weight = 63147.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.087366 restraints weight = 38106.009| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35745 Z= 0.178 Angle : 0.722 13.159 48453 Z= 0.357 Chirality : 0.045 0.191 5598 Planarity : 0.004 0.057 5994 Dihedral : 5.340 33.221 4617 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 4191 helix: -0.42 (0.11), residues: 2058 sheet: -0.84 (0.25), residues: 507 loop : -1.89 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 411 HIS 0.011 0.001 HIS A 104 PHE 0.047 0.002 PHE A 502 TYR 0.038 0.002 TYR E 325 ARG 0.004 0.000 ARG B 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7516.70 seconds wall clock time: 136 minutes 53.13 seconds (8213.13 seconds total)