Starting phenix.real_space_refine on Mon Apr 15 11:46:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djb_7935/04_2024/6djb_7935.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djb_7935/04_2024/6djb_7935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djb_7935/04_2024/6djb_7935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djb_7935/04_2024/6djb_7935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djb_7935/04_2024/6djb_7935.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djb_7935/04_2024/6djb_7935.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 150 5.16 5 C 22569 2.51 5 N 5889 2.21 5 O 6099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 34707 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5739 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 27, 'TRANS': 678} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 5830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5830 Classifications: {'peptide': 725} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 27, 'TRANS': 697} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 92 Chain: "E" Number of atoms: 5739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5739 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 27, 'TRANS': 678} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "F" Number of atoms: 5830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5830 Classifications: {'peptide': 725} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 27, 'TRANS': 697} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 5739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5739 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 27, 'TRANS': 678} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 5830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5830 Classifications: {'peptide': 725} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 27, 'TRANS': 697} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 92 Time building chain proxies: 16.50, per 1000 atoms: 0.48 Number of scatterers: 34707 At special positions: 0 Unit cell: (144.9, 146.05, 187.45, 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 150 16.00 O 6099 8.00 N 5889 7.00 C 22569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.02 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.02 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.01 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.02 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.02 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.01 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.02 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.02 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.01 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.14 Conformation dependent library (CDL) restraints added in 5.9 seconds 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8334 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 15 sheets defined 48.2% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 24 through 50 removed outlier: 3.979A pdb=" N ASP A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 141 removed outlier: 3.580A pdb=" N TYR A 124 " --> pdb=" O TRP A 120 " (cutoff:3.500A) Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.506A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.989A pdb=" N GLU A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 285 removed outlier: 3.679A pdb=" N ARG A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 314 through 345 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 370 through 383 Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.217A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.652A pdb=" N LEU A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 528 through 541 Processing helix chain 'A' and resid 559 through 566 removed outlier: 3.579A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 586 through 591 Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 703 through 707 Processing helix chain 'A' and resid 724 through 729 Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 770 through 775 removed outlier: 3.679A pdb=" N LEU A 773 " --> pdb=" O PRO A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 802 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 25 through 49 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.546A pdb=" N ASN B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 140 Processing helix chain 'B' and resid 146 through 164 removed outlier: 5.358A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 220 through 227 removed outlier: 3.630A pdb=" N VAL B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 255 Processing helix chain 'B' and resid 258 through 285 Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 313 through 346 removed outlier: 4.470A pdb=" N LEU B 317 " --> pdb=" O PRO B 313 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 346 " --> pdb=" O TRP B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 370 through 381 removed outlier: 3.788A pdb=" N GLN B 381 " --> pdb=" O HIS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 394 removed outlier: 4.094A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 Processing helix chain 'B' and resid 412 through 417 Processing helix chain 'B' and resid 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 528 through 540 Processing helix chain 'B' and resid 559 through 566 removed outlier: 4.008A pdb=" N THR B 563 " --> pdb=" O PRO B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 591 Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 657 through 661 Processing helix chain 'B' and resid 680 through 684 Processing helix chain 'B' and resid 701 through 706 removed outlier: 4.025A pdb=" N ILE B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 729 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.783A pdb=" N THR B 754 " --> pdb=" O GLY B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 776 Processing helix chain 'B' and resid 794 through 802 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 50 removed outlier: 3.979A pdb=" N ASP E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 141 removed outlier: 3.580A pdb=" N TYR E 124 " --> pdb=" O TRP E 120 " (cutoff:3.500A) Proline residue: E 126 - end of helix Processing helix chain 'E' and resid 149 through 165 Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.506A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.989A pdb=" N GLU E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 285 removed outlier: 3.679A pdb=" N ARG E 262 " --> pdb=" O ASP E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 314 through 345 Processing helix chain 'E' and resid 353 through 358 Processing helix chain 'E' and resid 370 through 383 Processing helix chain 'E' and resid 383 through 394 removed outlier: 4.218A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 411 Processing helix chain 'E' and resid 412 through 419 Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.652A pdb=" N LEU E 445 " --> pdb=" O VAL E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 468 Processing helix chain 'E' and resid 487 through 494 Processing helix chain 'E' and resid 528 through 541 Processing helix chain 'E' and resid 559 through 566 removed outlier: 3.579A pdb=" N THR E 563 " --> pdb=" O PRO E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 569 No H-bonds generated for 'chain 'E' and resid 567 through 569' Processing helix chain 'E' and resid 586 through 591 Processing helix chain 'E' and resid 634 through 638 Processing helix chain 'E' and resid 656 through 661 Processing helix chain 'E' and resid 703 through 707 Processing helix chain 'E' and resid 724 through 729 Processing helix chain 'E' and resid 747 through 753 Processing helix chain 'E' and resid 770 through 775 removed outlier: 3.679A pdb=" N LEU E 773 " --> pdb=" O PRO E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 794 through 802 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 25 through 49 Processing helix chain 'F' and resid 102 through 116 removed outlier: 3.547A pdb=" N ASN F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 124 through 140 Processing helix chain 'F' and resid 146 through 164 removed outlier: 5.358A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 Processing helix chain 'F' and resid 220 through 227 removed outlier: 3.629A pdb=" N VAL F 224 " --> pdb=" O GLU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 255 Processing helix chain 'F' and resid 258 through 285 Processing helix chain 'F' and resid 299 through 304 Processing helix chain 'F' and resid 313 through 346 removed outlier: 4.470A pdb=" N LEU F 317 " --> pdb=" O PRO F 313 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG F 346 " --> pdb=" O TRP F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 Processing helix chain 'F' and resid 370 through 381 removed outlier: 3.788A pdb=" N GLN F 381 " --> pdb=" O HIS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 394 removed outlier: 4.095A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 411 Processing helix chain 'F' and resid 412 through 417 Processing helix chain 'F' and resid 418 through 420 No H-bonds generated for 'chain 'F' and resid 418 through 420' Processing helix chain 'F' and resid 440 through 445 Processing helix chain 'F' and resid 487 through 492 Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 528 through 540 Processing helix chain 'F' and resid 559 through 566 removed outlier: 4.009A pdb=" N THR F 563 " --> pdb=" O PRO F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 591 Processing helix chain 'F' and resid 607 through 613 Processing helix chain 'F' and resid 634 through 638 Processing helix chain 'F' and resid 657 through 661 Processing helix chain 'F' and resid 680 through 684 Processing helix chain 'F' and resid 701 through 706 removed outlier: 4.025A pdb=" N ILE F 704 " --> pdb=" O PRO F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 729 Processing helix chain 'F' and resid 747 through 754 removed outlier: 3.783A pdb=" N THR F 754 " --> pdb=" O GLY F 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 772 through 776 Processing helix chain 'F' and resid 794 through 802 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 24 through 50 removed outlier: 3.979A pdb=" N ASP C 50 " --> pdb=" O GLN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 141 removed outlier: 3.581A pdb=" N TYR C 124 " --> pdb=" O TRP C 120 " (cutoff:3.500A) Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 149 through 165 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.507A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 256 removed outlier: 3.989A pdb=" N GLU C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 285 removed outlier: 3.679A pdb=" N ARG C 262 " --> pdb=" O ASP C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 314 through 345 Processing helix chain 'C' and resid 353 through 358 Processing helix chain 'C' and resid 370 through 383 Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.217A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 411 Processing helix chain 'C' and resid 412 through 419 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.652A pdb=" N LEU C 445 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 468 Processing helix chain 'C' and resid 487 through 494 Processing helix chain 'C' and resid 528 through 541 Processing helix chain 'C' and resid 559 through 566 removed outlier: 3.579A pdb=" N THR C 563 " --> pdb=" O PRO C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 569 No H-bonds generated for 'chain 'C' and resid 567 through 569' Processing helix chain 'C' and resid 586 through 591 Processing helix chain 'C' and resid 634 through 638 Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 703 through 707 Processing helix chain 'C' and resid 724 through 729 Processing helix chain 'C' and resid 747 through 753 Processing helix chain 'C' and resid 770 through 775 removed outlier: 3.679A pdb=" N LEU C 773 " --> pdb=" O PRO C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 802 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 25 through 49 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.545A pdb=" N ASN D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 124 through 140 Processing helix chain 'D' and resid 146 through 164 removed outlier: 5.358A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 220 through 227 removed outlier: 3.630A pdb=" N VAL D 224 " --> pdb=" O GLU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 255 Processing helix chain 'D' and resid 258 through 285 Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 313 through 346 removed outlier: 4.470A pdb=" N LEU D 317 " --> pdb=" O PRO D 313 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG D 346 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 370 through 381 removed outlier: 3.788A pdb=" N GLN D 381 " --> pdb=" O HIS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 394 removed outlier: 4.095A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 411 Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 418 through 420 No H-bonds generated for 'chain 'D' and resid 418 through 420' Processing helix chain 'D' and resid 440 through 445 Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 528 through 540 Processing helix chain 'D' and resid 559 through 566 removed outlier: 4.008A pdb=" N THR D 563 " --> pdb=" O PRO D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 591 Processing helix chain 'D' and resid 607 through 613 Processing helix chain 'D' and resid 634 through 638 Processing helix chain 'D' and resid 657 through 661 Processing helix chain 'D' and resid 680 through 684 Processing helix chain 'D' and resid 701 through 706 removed outlier: 4.026A pdb=" N ILE D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 729 Processing helix chain 'D' and resid 747 through 754 removed outlier: 3.784A pdb=" N THR D 754 " --> pdb=" O GLY D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 776 Processing helix chain 'D' and resid 794 through 802 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 421 removed outlier: 6.379A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 451 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N THR A 642 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU A 667 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU A 644 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 669 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR A 689 " --> pdb=" O GLU A 665 " (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 350 through 352 removed outlier: 3.686A pdb=" N TYR B 351 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL B 368 " --> pdb=" O TYR B 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 431 through 432 removed outlier: 3.556A pdb=" N ILE B 619 " --> pdb=" O CYS B 643 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR B 642 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU B 667 " --> pdb=" O THR B 642 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU B 644 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 669 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR B 689 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ARG B 762 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 738 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'E' and resid 420 through 421 removed outlier: 6.379A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 451 " --> pdb=" O GLU E 473 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N THR E 642 " --> pdb=" O GLU E 665 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU E 667 " --> pdb=" O THR E 642 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU E 644 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU E 669 " --> pdb=" O LEU E 644 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR E 689 " --> pdb=" O GLU E 665 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AA9, first strand: chain 'F' and resid 350 through 352 removed outlier: 3.686A pdb=" N TYR F 351 " --> pdb=" O VAL F 368 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL F 368 " --> pdb=" O TYR F 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 431 through 432 removed outlier: 3.555A pdb=" N ILE F 619 " --> pdb=" O CYS F 643 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR F 642 " --> pdb=" O GLU F 665 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU F 667 " --> pdb=" O THR F 642 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU F 644 " --> pdb=" O LEU F 667 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU F 669 " --> pdb=" O LEU F 644 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR F 689 " --> pdb=" O GLU F 665 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU F 736 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ARG F 762 " --> pdb=" O LEU F 736 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU F 738 " --> pdb=" O ARG F 762 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB3, first strand: chain 'C' and resid 420 through 421 removed outlier: 6.378A pdb=" N LEU C 430 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLU C 454 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU C 432 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 451 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N THR C 642 " --> pdb=" O GLU C 665 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU C 667 " --> pdb=" O THR C 642 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU C 644 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU C 669 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR C 689 " --> pdb=" O GLU C 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 352 removed outlier: 3.687A pdb=" N TYR D 351 " --> pdb=" O VAL D 368 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL D 368 " --> pdb=" O TYR D 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 431 through 432 removed outlier: 3.556A pdb=" N ILE D 619 " --> pdb=" O CYS D 643 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR D 642 " --> pdb=" O GLU D 665 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU D 667 " --> pdb=" O THR D 642 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU D 644 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU D 669 " --> pdb=" O LEU D 644 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR D 689 " --> pdb=" O GLU D 665 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU D 736 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ARG D 762 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU D 738 " --> pdb=" O ARG D 762 " (cutoff:3.500A) 1644 hydrogen bonds defined for protein. 4401 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: 12.57 Time building geometry restraints manager: 13.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8361 1.33 - 1.46: 9004 1.46 - 1.58: 17894 1.58 - 1.71: 3 1.71 - 1.84: 201 Bond restraints: 35463 Sorted by residual: bond pdb=" CB ILE F 629 " pdb=" CG2 ILE F 629 " ideal model delta sigma weight residual 1.521 1.395 0.126 3.30e-02 9.18e+02 1.46e+01 bond pdb=" CB ILE B 629 " pdb=" CG2 ILE B 629 " ideal model delta sigma weight residual 1.521 1.395 0.126 3.30e-02 9.18e+02 1.45e+01 bond pdb=" CB ILE D 629 " pdb=" CG2 ILE D 629 " ideal model delta sigma weight residual 1.521 1.395 0.126 3.30e-02 9.18e+02 1.45e+01 bond pdb=" CB CYS F 310 " pdb=" SG CYS F 310 " ideal model delta sigma weight residual 1.808 1.684 0.124 3.30e-02 9.18e+02 1.42e+01 bond pdb=" CB CYS B 310 " pdb=" SG CYS B 310 " ideal model delta sigma weight residual 1.808 1.684 0.124 3.30e-02 9.18e+02 1.42e+01 ... (remaining 35458 not shown) Histogram of bond angle deviations from ideal: 98.51 - 106.04: 950 106.04 - 113.57: 19502 113.57 - 121.10: 17800 121.10 - 128.63: 9559 128.63 - 136.16: 297 Bond angle restraints: 48108 Sorted by residual: angle pdb=" N SER E 464 " pdb=" CA SER E 464 " pdb=" C SER E 464 " ideal model delta sigma weight residual 112.54 102.53 10.01 1.51e+00 4.39e-01 4.39e+01 angle pdb=" N SER A 464 " pdb=" CA SER A 464 " pdb=" C SER A 464 " ideal model delta sigma weight residual 112.54 102.56 9.98 1.51e+00 4.39e-01 4.37e+01 angle pdb=" N SER C 464 " pdb=" CA SER C 464 " pdb=" C SER C 464 " ideal model delta sigma weight residual 112.54 102.58 9.96 1.51e+00 4.39e-01 4.35e+01 angle pdb=" C ILE B 654 " pdb=" N PRO B 655 " pdb=" CA PRO B 655 " ideal model delta sigma weight residual 119.84 127.51 -7.67 1.25e+00 6.40e-01 3.76e+01 angle pdb=" C ILE F 654 " pdb=" N PRO F 655 " pdb=" CA PRO F 655 " ideal model delta sigma weight residual 119.84 127.49 -7.65 1.25e+00 6.40e-01 3.75e+01 ... (remaining 48103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 20608 16.11 - 32.21: 710 32.21 - 48.32: 66 48.32 - 64.42: 72 64.42 - 80.53: 6 Dihedral angle restraints: 21462 sinusoidal: 8685 harmonic: 12777 Sorted by residual: dihedral pdb=" N LEU F 432 " pdb=" C LEU F 432 " pdb=" CA LEU F 432 " pdb=" CB LEU F 432 " ideal model delta harmonic sigma weight residual 122.80 111.49 11.31 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" N LEU B 432 " pdb=" C LEU B 432 " pdb=" CA LEU B 432 " pdb=" CB LEU B 432 " ideal model delta harmonic sigma weight residual 122.80 111.51 11.29 0 2.50e+00 1.60e-01 2.04e+01 dihedral pdb=" N LEU D 432 " pdb=" C LEU D 432 " pdb=" CA LEU D 432 " pdb=" CB LEU D 432 " ideal model delta harmonic sigma weight residual 122.80 111.52 11.28 0 2.50e+00 1.60e-01 2.04e+01 ... (remaining 21459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4338 0.081 - 0.163: 1064 0.163 - 0.244: 184 0.244 - 0.326: 18 0.326 - 0.407: 12 Chirality restraints: 5616 Sorted by residual: chirality pdb=" CB ILE F 629 " pdb=" CA ILE F 629 " pdb=" CG1 ILE F 629 " pdb=" CG2 ILE F 629 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CB ILE B 629 " pdb=" CA ILE B 629 " pdb=" CG1 ILE B 629 " pdb=" CG2 ILE B 629 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CB ILE D 629 " pdb=" CA ILE D 629 " pdb=" CG1 ILE D 629 " pdb=" CG2 ILE D 629 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 5613 not shown) Planarity restraints: 5961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 513 " 0.015 2.00e-02 2.50e+03 4.59e-02 4.20e+01 pdb=" CG TYR F 513 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TYR F 513 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR F 513 " -0.088 2.00e-02 2.50e+03 pdb=" CE1 TYR F 513 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR F 513 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR F 513 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 513 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 513 " 0.015 2.00e-02 2.50e+03 4.58e-02 4.19e+01 pdb=" CG TYR D 513 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR D 513 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR D 513 " -0.088 2.00e-02 2.50e+03 pdb=" CE1 TYR D 513 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR D 513 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR D 513 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 513 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 513 " -0.015 2.00e-02 2.50e+03 4.57e-02 4.19e+01 pdb=" CG TYR B 513 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR B 513 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR B 513 " 0.088 2.00e-02 2.50e+03 pdb=" CE1 TYR B 513 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR B 513 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR B 513 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 513 " -0.022 2.00e-02 2.50e+03 ... (remaining 5958 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 12797 2.88 - 3.39: 34341 3.39 - 3.89: 59480 3.89 - 4.40: 68776 4.40 - 4.90: 109204 Nonbonded interactions: 284598 Sorted by model distance: nonbonded pdb=" NZ LYS E 98 " pdb=" OD2 ASP D 100 " model vdw 2.377 2.520 nonbonded pdb=" NZ LYS A 98 " pdb=" OD2 ASP F 100 " model vdw 2.377 2.520 nonbonded pdb=" OD2 ASP B 100 " pdb=" NZ LYS C 98 " model vdw 2.377 2.520 nonbonded pdb=" NZ LYS B 580 " pdb=" OD2 ASP B 602 " model vdw 2.398 2.520 nonbonded pdb=" NZ LYS F 580 " pdb=" OD2 ASP F 602 " model vdw 2.398 2.520 ... (remaining 284593 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 15 through 174 or (resid 232 through 233 and (name N or na \ me CA or name C or name O or name CB )) or resid 234 through 802)) selection = (chain 'B' and (resid 15 through 174 or resid 232 through 802)) selection = (chain 'C' and (resid 15 through 174 or (resid 232 through 233 and (name N or na \ me CA or name C or name O or name CB )) or resid 234 through 802)) selection = (chain 'D' and (resid 15 through 174 or resid 232 through 802)) selection = (chain 'E' and (resid 15 through 174 or (resid 232 through 233 and (name N or na \ me CA or name C or name O or name CB )) or resid 234 through 802)) selection = (chain 'F' and (resid 15 through 174 or resid 232 through 802)) } 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: 1.550 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: 0.020 Extract box with map and model: 7.090 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 84.520 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.013 0.140 35463 Z= 0.850 Angle : 1.590 10.006 48108 Z= 0.996 Chirality : 0.074 0.407 5616 Planarity : 0.010 0.065 5961 Dihedral : 9.158 80.525 13074 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.40 % Favored : 92.39 % Rotamer: Outliers : 0.08 % Allowed : 1.03 % Favored : 98.89 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.13), residues: 4257 helix: -0.40 (0.12), residues: 1830 sheet: -1.78 (0.21), residues: 597 loop : -1.81 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.008 TRP C 647 HIS 0.021 0.004 HIS A 104 PHE 0.090 0.013 PHE B 443 TYR 0.096 0.015 TYR C 127 ARG 0.013 0.002 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1135 time to evaluate : 4.369 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: A 35 MET cc_start: 0.9346 (mtp) cc_final: 0.8873 (mtm) REVERT: A 99 TYR cc_start: 0.7503 (m-80) cc_final: 0.7226 (m-80) REVERT: A 151 SER cc_start: 0.8582 (p) cc_final: 0.8136 (m) REVERT: A 261 TYR cc_start: 0.8897 (t80) cc_final: 0.8507 (t80) REVERT: A 299 ILE cc_start: 0.9198 (pt) cc_final: 0.8945 (pt) REVERT: A 375 MET cc_start: 0.9331 (mtm) cc_final: 0.9125 (ptp) REVERT: A 434 MET cc_start: 0.7979 (mmm) cc_final: 0.7527 (mmm) REVERT: A 454 GLU cc_start: 0.8409 (pt0) cc_final: 0.6258 (pt0) REVERT: A 461 ILE cc_start: 0.8757 (mm) cc_final: 0.8453 (mm) REVERT: A 518 LEU cc_start: 0.7113 (mt) cc_final: 0.6895 (mt) REVERT: A 641 LEU cc_start: 0.9326 (tp) cc_final: 0.8881 (tt) REVERT: A 665 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7739 (mp0) REVERT: A 748 SER cc_start: 0.8563 (p) cc_final: 0.8085 (m) REVERT: B 35 MET cc_start: 0.8915 (mtt) cc_final: 0.8590 (ttm) REVERT: B 38 ILE cc_start: 0.9552 (tt) cc_final: 0.9279 (mm) REVERT: B 241 LYS cc_start: 0.9572 (tttt) cc_final: 0.9359 (tptp) REVERT: B 343 MET cc_start: 0.8415 (mtp) cc_final: 0.8102 (mtp) REVERT: B 402 LEU cc_start: 0.9429 (tp) cc_final: 0.9100 (tp) REVERT: B 440 ASP cc_start: 0.8489 (m-30) cc_final: 0.8186 (m-30) REVERT: B 476 LEU cc_start: 0.9146 (mt) cc_final: 0.8877 (tt) REVERT: B 491 LEU cc_start: 0.9441 (mt) cc_final: 0.9117 (tp) REVERT: B 519 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7690 (mm-30) REVERT: B 540 LEU cc_start: 0.8719 (mt) cc_final: 0.8354 (tt) REVERT: B 546 LEU cc_start: 0.9504 (tp) cc_final: 0.9164 (tp) REVERT: B 629 ILE cc_start: 0.8982 (tt) cc_final: 0.8777 (tt) REVERT: B 692 LEU cc_start: 0.9208 (mt) cc_final: 0.8893 (pp) REVERT: B 733 LEU cc_start: 0.8065 (tp) cc_final: 0.7660 (tp) REVERT: B 782 SER cc_start: 0.9292 (t) cc_final: 0.9073 (p) REVERT: E 35 MET cc_start: 0.9404 (mtp) cc_final: 0.8936 (mtm) REVERT: E 51 LYS cc_start: 0.9183 (mmtt) cc_final: 0.8846 (mtmt) REVERT: E 52 MET cc_start: 0.8298 (mmm) cc_final: 0.7724 (mmm) REVERT: E 99 TYR cc_start: 0.7435 (m-80) cc_final: 0.6891 (m-80) REVERT: E 110 ASP cc_start: 0.9204 (m-30) cc_final: 0.8894 (t0) REVERT: E 151 SER cc_start: 0.8502 (p) cc_final: 0.8130 (m) REVERT: E 261 TYR cc_start: 0.8954 (t80) cc_final: 0.8443 (t80) REVERT: E 299 ILE cc_start: 0.9216 (pt) cc_final: 0.8918 (pt) REVERT: E 326 ILE cc_start: 0.9574 (mt) cc_final: 0.9240 (tp) REVERT: E 380 ASP cc_start: 0.8185 (t70) cc_final: 0.7792 (t0) REVERT: E 434 MET cc_start: 0.7594 (mmm) cc_final: 0.6747 (mmm) REVERT: E 454 GLU cc_start: 0.8546 (pt0) cc_final: 0.6319 (pt0) REVERT: E 461 ILE cc_start: 0.8564 (mm) cc_final: 0.8274 (mm) REVERT: E 518 LEU cc_start: 0.7222 (mt) cc_final: 0.6824 (mt) REVERT: E 641 LEU cc_start: 0.9317 (tp) cc_final: 0.8923 (tt) REVERT: F 35 MET cc_start: 0.8911 (mtt) cc_final: 0.8406 (ttm) REVERT: F 51 LYS cc_start: 0.9201 (mmtt) cc_final: 0.8804 (mmmt) REVERT: F 52 MET cc_start: 0.8003 (tpp) cc_final: 0.7436 (tpp) REVERT: F 129 VAL cc_start: 0.9010 (t) cc_final: 0.8766 (p) REVERT: F 337 MET cc_start: 0.8786 (mmm) cc_final: 0.8529 (ppp) REVERT: F 343 MET cc_start: 0.8569 (mtp) cc_final: 0.8297 (mtp) REVERT: F 402 LEU cc_start: 0.9438 (tp) cc_final: 0.9112 (tp) REVERT: F 414 ASP cc_start: 0.8609 (m-30) cc_final: 0.8355 (m-30) REVERT: F 428 LEU cc_start: 0.7988 (mt) cc_final: 0.7588 (mm) REVERT: F 440 ASP cc_start: 0.8622 (m-30) cc_final: 0.8279 (m-30) REVERT: F 471 LEU cc_start: 0.9256 (tp) cc_final: 0.9015 (tt) REVERT: F 491 LEU cc_start: 0.9443 (mt) cc_final: 0.9116 (tp) REVERT: F 540 LEU cc_start: 0.8656 (mt) cc_final: 0.8289 (tt) REVERT: F 629 ILE cc_start: 0.8979 (tt) cc_final: 0.8759 (tt) REVERT: F 676 LYS cc_start: 0.8121 (pttt) cc_final: 0.7859 (tppt) REVERT: F 692 LEU cc_start: 0.9269 (mt) cc_final: 0.8842 (pp) REVERT: F 744 GLN cc_start: 0.8215 (mp10) cc_final: 0.7961 (pp30) REVERT: C 35 MET cc_start: 0.9333 (mtp) cc_final: 0.8822 (mtm) REVERT: C 52 MET cc_start: 0.8594 (mmm) cc_final: 0.7864 (mmm) REVERT: C 99 TYR cc_start: 0.7629 (m-80) cc_final: 0.7076 (m-80) REVERT: C 110 ASP cc_start: 0.9239 (m-30) cc_final: 0.8979 (t70) REVERT: C 129 VAL cc_start: 0.9187 (t) cc_final: 0.8802 (p) REVERT: C 151 SER cc_start: 0.8485 (p) cc_final: 0.7988 (m) REVERT: C 164 PHE cc_start: 0.8484 (t80) cc_final: 0.8167 (t80) REVERT: C 238 GLU cc_start: 0.8920 (tt0) cc_final: 0.8695 (mp0) REVERT: C 261 TYR cc_start: 0.8900 (t80) cc_final: 0.8348 (t80) REVERT: C 434 MET cc_start: 0.7774 (mmm) cc_final: 0.6646 (mmm) REVERT: C 454 GLU cc_start: 0.8574 (pt0) cc_final: 0.7063 (pt0) REVERT: C 461 ILE cc_start: 0.8560 (mm) cc_final: 0.8238 (mm) REVERT: C 518 LEU cc_start: 0.7125 (mt) cc_final: 0.6737 (mt) REVERT: C 641 LEU cc_start: 0.9344 (tp) cc_final: 0.9112 (tp) REVERT: D 28 THR cc_start: 0.9326 (m) cc_final: 0.9088 (p) REVERT: D 35 MET cc_start: 0.8964 (mtt) cc_final: 0.8394 (ttm) REVERT: D 38 ILE cc_start: 0.9512 (tt) cc_final: 0.9143 (mm) REVERT: D 129 VAL cc_start: 0.9156 (t) cc_final: 0.8706 (p) REVERT: D 239 GLN cc_start: 0.8916 (mt0) cc_final: 0.8442 (tt0) REVERT: D 308 TYR cc_start: 0.8744 (m-80) cc_final: 0.8517 (m-80) REVERT: D 325 TYR cc_start: 0.8967 (t80) cc_final: 0.8604 (t80) REVERT: D 337 MET cc_start: 0.8646 (mmm) cc_final: 0.8408 (ppp) REVERT: D 343 MET cc_start: 0.8722 (mtp) cc_final: 0.8427 (mtp) REVERT: D 402 LEU cc_start: 0.9443 (tp) cc_final: 0.9178 (tp) REVERT: D 432 LEU cc_start: 0.8919 (mt) cc_final: 0.8685 (mt) REVERT: D 438 ILE cc_start: 0.8618 (mm) cc_final: 0.8377 (pt) REVERT: D 440 ASP cc_start: 0.8511 (m-30) cc_final: 0.8250 (m-30) REVERT: D 491 LEU cc_start: 0.9415 (mt) cc_final: 0.9084 (tp) REVERT: D 540 LEU cc_start: 0.8559 (mt) cc_final: 0.8237 (tt) REVERT: D 629 ILE cc_start: 0.8935 (tt) cc_final: 0.8725 (tt) REVERT: D 676 LYS cc_start: 0.8119 (pttt) cc_final: 0.7853 (tppt) REVERT: D 692 LEU cc_start: 0.9231 (mt) cc_final: 0.8855 (pp) outliers start: 3 outliers final: 0 residues processed: 1138 average time/residue: 0.5205 time to fit residues: 920.2239 Evaluate side-chains 549 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 549 time to evaluate : 4.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 7.9990 chunk 322 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 333 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 386 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN A 478 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN ** A 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 HIS ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 ASN ** E 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 737 HIS ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 HIS C 418 GLN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35463 Z= 0.290 Angle : 0.804 9.861 48108 Z= 0.434 Chirality : 0.048 0.307 5616 Planarity : 0.005 0.056 5961 Dihedral : 5.132 26.793 4659 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.43 % Favored : 91.50 % Rotamer: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.13), residues: 4257 helix: -0.10 (0.12), residues: 1884 sheet: -1.44 (0.22), residues: 591 loop : -2.14 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 647 HIS 0.010 0.002 HIS D 312 PHE 0.031 0.003 PHE F 353 TYR 0.038 0.002 TYR C 477 ARG 0.015 0.001 ARG D 685 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 695 time to evaluate : 4.141 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 35 MET cc_start: 0.9351 (mtp) cc_final: 0.8870 (mtp) REVERT: A 99 TYR cc_start: 0.7388 (m-80) cc_final: 0.7172 (m-80) REVERT: A 261 TYR cc_start: 0.8555 (t80) cc_final: 0.8295 (t80) REVERT: A 265 MET cc_start: 0.9083 (mmt) cc_final: 0.7968 (mmm) REVERT: A 289 ILE cc_start: 0.9692 (mt) cc_final: 0.9222 (tt) REVERT: A 343 MET cc_start: 0.8776 (mmm) cc_final: 0.8238 (tmm) REVERT: A 434 MET cc_start: 0.7991 (mmm) cc_final: 0.7425 (mmt) REVERT: A 461 ILE cc_start: 0.8921 (mm) cc_final: 0.8709 (mm) REVERT: A 468 LEU cc_start: 0.8536 (mp) cc_final: 0.8289 (mt) REVERT: A 526 ASN cc_start: 0.9120 (m-40) cc_final: 0.8118 (p0) REVERT: A 623 ASP cc_start: 0.7888 (m-30) cc_final: 0.6898 (t0) REVERT: A 761 LEU cc_start: 0.8815 (mp) cc_final: 0.8483 (mp) REVERT: B 166 SER cc_start: 0.8064 (t) cc_final: 0.7698 (m) REVERT: B 308 TYR cc_start: 0.8744 (m-10) cc_final: 0.8486 (m-80) REVERT: B 337 MET cc_start: 0.7701 (ppp) cc_final: 0.7381 (tmm) REVERT: B 414 ASP cc_start: 0.8928 (m-30) cc_final: 0.8718 (m-30) REVERT: B 430 LEU cc_start: 0.8847 (tt) cc_final: 0.8558 (tp) REVERT: B 540 LEU cc_start: 0.8599 (mt) cc_final: 0.8164 (tt) REVERT: B 733 LEU cc_start: 0.8322 (tp) cc_final: 0.8008 (tp) REVERT: E 51 LYS cc_start: 0.9263 (mmtt) cc_final: 0.8737 (mtpp) REVERT: E 99 TYR cc_start: 0.7389 (m-80) cc_final: 0.7113 (m-80) REVERT: E 261 TYR cc_start: 0.8605 (t80) cc_final: 0.8203 (t80) REVERT: E 265 MET cc_start: 0.9218 (mmt) cc_final: 0.8038 (mmm) REVERT: E 343 MET cc_start: 0.8797 (mmm) cc_final: 0.8418 (tmm) REVERT: E 375 MET cc_start: 0.9556 (ptp) cc_final: 0.8925 (ptp) REVERT: E 434 MET cc_start: 0.7764 (mmm) cc_final: 0.7303 (mmt) REVERT: E 461 ILE cc_start: 0.8811 (mm) cc_final: 0.8603 (mm) REVERT: E 471 LEU cc_start: 0.9166 (tp) cc_final: 0.8954 (tt) REVERT: E 526 ASN cc_start: 0.9065 (m-40) cc_final: 0.8619 (p0) REVERT: E 623 ASP cc_start: 0.7627 (m-30) cc_final: 0.6799 (t0) REVERT: E 761 LEU cc_start: 0.8735 (mp) cc_final: 0.8439 (mt) REVERT: E 769 LEU cc_start: 0.8500 (tt) cc_final: 0.8163 (mp) REVERT: E 772 GLU cc_start: 0.9254 (mp0) cc_final: 0.8719 (mt-10) REVERT: F 51 LYS cc_start: 0.9248 (mmtt) cc_final: 0.8796 (mmmt) REVERT: F 52 MET cc_start: 0.7524 (tpp) cc_final: 0.7047 (tpp) REVERT: F 166 SER cc_start: 0.8300 (t) cc_final: 0.8008 (m) REVERT: F 308 TYR cc_start: 0.8750 (m-10) cc_final: 0.8091 (m-10) REVERT: F 414 ASP cc_start: 0.8804 (m-30) cc_final: 0.8467 (m-30) REVERT: F 430 LEU cc_start: 0.8728 (tt) cc_final: 0.8436 (tp) REVERT: F 496 ARG cc_start: 0.8441 (mmt-90) cc_final: 0.8099 (mmm160) REVERT: F 540 LEU cc_start: 0.8544 (mt) cc_final: 0.8250 (tt) REVERT: C 35 MET cc_start: 0.9343 (mtp) cc_final: 0.8814 (mtp) REVERT: C 99 TYR cc_start: 0.7430 (m-80) cc_final: 0.6252 (m-80) REVERT: C 261 TYR cc_start: 0.8593 (t80) cc_final: 0.8368 (t80) REVERT: C 265 MET cc_start: 0.9045 (mmt) cc_final: 0.7999 (mmm) REVERT: C 289 ILE cc_start: 0.9698 (mt) cc_final: 0.9275 (tt) REVERT: C 343 MET cc_start: 0.8850 (mmm) cc_final: 0.8466 (tmm) REVERT: C 434 MET cc_start: 0.7988 (mmm) cc_final: 0.7349 (mmt) REVERT: C 461 ILE cc_start: 0.8813 (mm) cc_final: 0.8602 (mm) REVERT: C 526 ASN cc_start: 0.9009 (m-40) cc_final: 0.8047 (p0) REVERT: C 623 ASP cc_start: 0.7926 (m-30) cc_final: 0.7267 (t0) REVERT: C 769 LEU cc_start: 0.8520 (tt) cc_final: 0.8248 (mp) REVERT: D 239 GLN cc_start: 0.8938 (mt0) cc_final: 0.8587 (pt0) REVERT: D 269 ILE cc_start: 0.8813 (mt) cc_final: 0.8563 (tp) REVERT: D 325 TYR cc_start: 0.9085 (t80) cc_final: 0.8631 (t80) REVERT: D 337 MET cc_start: 0.8717 (mmm) cc_final: 0.8438 (ppp) REVERT: D 410 GLU cc_start: 0.8632 (pp20) cc_final: 0.8404 (tm-30) REVERT: D 414 ASP cc_start: 0.8846 (m-30) cc_final: 0.8573 (m-30) REVERT: D 434 MET cc_start: 0.7458 (ptm) cc_final: 0.7233 (ptm) REVERT: D 436 SER cc_start: 0.8265 (p) cc_final: 0.8037 (p) REVERT: D 440 ASP cc_start: 0.8523 (m-30) cc_final: 0.8219 (m-30) REVERT: D 540 LEU cc_start: 0.8633 (mt) cc_final: 0.8270 (tt) REVERT: D 775 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8831 (mt-10) REVERT: D 782 SER cc_start: 0.9272 (t) cc_final: 0.9055 (p) outliers start: 2 outliers final: 0 residues processed: 697 average time/residue: 0.4666 time to fit residues: 528.2686 Evaluate side-chains 412 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 4.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 321 optimal weight: 9.9990 chunk 263 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 387 optimal weight: 4.9990 chunk 418 optimal weight: 0.0050 chunk 345 optimal weight: 9.9990 chunk 384 optimal weight: 8.9990 chunk 132 optimal weight: 0.0970 chunk 310 optimal weight: 20.0000 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN A 625 ASN ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 ASN B 105 GLN B 287 HIS ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 ASN ** E 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN ** C 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS D 614 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35463 Z= 0.218 Angle : 0.699 12.532 48108 Z= 0.373 Chirality : 0.046 0.367 5616 Planarity : 0.004 0.045 5961 Dihedral : 4.921 25.979 4659 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 4257 helix: 0.08 (0.12), residues: 1911 sheet: -1.25 (0.22), residues: 573 loop : -2.27 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 143 HIS 0.009 0.001 HIS A 312 PHE 0.043 0.002 PHE F 250 TYR 0.030 0.002 TYR A 477 ARG 0.008 0.001 ARG F 731 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 604 time to evaluate : 5.826 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 35 MET cc_start: 0.9250 (mtp) cc_final: 0.9027 (mtp) REVERT: A 52 MET cc_start: 0.8496 (mmp) cc_final: 0.7745 (mmp) REVERT: A 261 TYR cc_start: 0.8565 (t80) cc_final: 0.8306 (t80) REVERT: A 265 MET cc_start: 0.9197 (mmt) cc_final: 0.8100 (mmm) REVERT: A 328 LEU cc_start: 0.9698 (mm) cc_final: 0.9485 (mm) REVERT: A 343 MET cc_start: 0.8740 (mmm) cc_final: 0.8304 (tmm) REVERT: A 375 MET cc_start: 0.9524 (mtm) cc_final: 0.9109 (mtm) REVERT: A 380 ASP cc_start: 0.8628 (t0) cc_final: 0.7975 (m-30) REVERT: A 434 MET cc_start: 0.8033 (mmm) cc_final: 0.7359 (mmm) REVERT: A 471 LEU cc_start: 0.9152 (tp) cc_final: 0.8934 (tp) REVERT: A 526 ASN cc_start: 0.9065 (m-40) cc_final: 0.8106 (p0) REVERT: A 623 ASP cc_start: 0.7512 (m-30) cc_final: 0.6980 (t0) REVERT: A 738 LEU cc_start: 0.9655 (mt) cc_final: 0.9374 (mp) REVERT: B 166 SER cc_start: 0.7963 (t) cc_final: 0.7626 (m) REVERT: B 262 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.8074 (mtp180) REVERT: B 308 TYR cc_start: 0.8771 (m-10) cc_final: 0.8388 (m-80) REVERT: B 430 LEU cc_start: 0.8890 (tt) cc_final: 0.8673 (tp) REVERT: B 540 LEU cc_start: 0.8491 (mt) cc_final: 0.8203 (tt) REVERT: B 689 TYR cc_start: 0.7757 (m-80) cc_final: 0.7476 (m-10) REVERT: B 733 LEU cc_start: 0.8267 (tp) cc_final: 0.7948 (tp) REVERT: E 234 LYS cc_start: 0.6973 (mmmt) cc_final: 0.6694 (mmmt) REVERT: E 261 TYR cc_start: 0.8610 (t80) cc_final: 0.8347 (t80) REVERT: E 375 MET cc_start: 0.9542 (ptp) cc_final: 0.9017 (ptp) REVERT: E 434 MET cc_start: 0.7573 (mmm) cc_final: 0.6729 (mmm) REVERT: E 468 LEU cc_start: 0.8509 (mt) cc_final: 0.7692 (tt) REVERT: E 471 LEU cc_start: 0.9118 (tp) cc_final: 0.8589 (tt) REVERT: E 506 LYS cc_start: 0.9448 (tptp) cc_final: 0.9237 (tptp) REVERT: E 526 ASN cc_start: 0.8925 (m-40) cc_final: 0.8508 (p0) REVERT: E 623 ASP cc_start: 0.7418 (m-30) cc_final: 0.6952 (t0) REVERT: E 738 LEU cc_start: 0.9593 (mt) cc_final: 0.9251 (mp) REVERT: F 35 MET cc_start: 0.9189 (ttp) cc_final: 0.8973 (ttm) REVERT: F 51 LYS cc_start: 0.9245 (mmtt) cc_final: 0.8800 (mmmt) REVERT: F 52 MET cc_start: 0.7491 (tpp) cc_final: 0.6954 (tpp) REVERT: F 166 SER cc_start: 0.8153 (t) cc_final: 0.7840 (m) REVERT: F 308 TYR cc_start: 0.8839 (m-10) cc_final: 0.7884 (m-10) REVERT: F 434 MET cc_start: 0.7157 (ptm) cc_final: 0.6915 (ptm) REVERT: F 491 LEU cc_start: 0.9578 (mt) cc_final: 0.9157 (tp) REVERT: F 496 ARG cc_start: 0.8393 (mmt-90) cc_final: 0.7906 (mmm160) REVERT: F 540 LEU cc_start: 0.8543 (mt) cc_final: 0.8320 (tt) REVERT: F 736 LEU cc_start: 0.9238 (tp) cc_final: 0.8964 (tt) REVERT: C 35 MET cc_start: 0.9400 (mtp) cc_final: 0.8877 (mtp) REVERT: C 52 MET cc_start: 0.8525 (mmm) cc_final: 0.8184 (tpt) REVERT: C 99 TYR cc_start: 0.6797 (m-80) cc_final: 0.6043 (m-80) REVERT: C 289 ILE cc_start: 0.9661 (mt) cc_final: 0.9169 (tt) REVERT: C 434 MET cc_start: 0.8015 (mmm) cc_final: 0.7023 (mpp) REVERT: C 468 LEU cc_start: 0.8628 (mt) cc_final: 0.7885 (tt) REVERT: C 471 LEU cc_start: 0.9120 (tp) cc_final: 0.8605 (tt) REVERT: C 493 GLU cc_start: 0.8953 (pt0) cc_final: 0.8734 (tm-30) REVERT: C 526 ASN cc_start: 0.8892 (m-40) cc_final: 0.8034 (p0) REVERT: C 623 ASP cc_start: 0.7551 (m-30) cc_final: 0.7315 (t0) REVERT: C 651 ILE cc_start: 0.9348 (pt) cc_final: 0.9036 (tp) REVERT: D 133 THR cc_start: 0.9040 (p) cc_final: 0.8815 (p) REVERT: D 239 GLN cc_start: 0.8941 (mt0) cc_final: 0.8521 (pt0) REVERT: D 325 TYR cc_start: 0.9026 (t80) cc_final: 0.8693 (t80) REVERT: D 337 MET cc_start: 0.8704 (mmm) cc_final: 0.8139 (tmm) REVERT: D 434 MET cc_start: 0.7496 (ptm) cc_final: 0.7178 (ptm) REVERT: D 540 LEU cc_start: 0.8482 (mt) cc_final: 0.8252 (tt) outliers start: 2 outliers final: 0 residues processed: 605 average time/residue: 0.4585 time to fit residues: 461.0296 Evaluate side-chains 380 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 4.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 0.0170 chunk 291 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 260 optimal weight: 3.9990 chunk 388 optimal weight: 0.1980 chunk 411 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 368 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 overall best weight: 2.2422 ------------------------------------------------------------------------------- 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 ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 105 GLN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 HIS E 132 HIS E 499 HIS E 576 ASN E 625 ASN ** E 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN F 104 HIS C 104 HIS C 418 GLN C 478 HIS ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 HIS ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 657 GLN C 737 HIS D 49 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35463 Z= 0.219 Angle : 0.672 22.802 48108 Z= 0.354 Chirality : 0.045 0.289 5616 Planarity : 0.004 0.082 5961 Dihedral : 4.842 28.269 4659 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.13), residues: 4257 helix: 0.15 (0.12), residues: 1881 sheet: -1.23 (0.22), residues: 573 loop : -2.31 (0.15), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 143 HIS 0.008 0.001 HIS A 312 PHE 0.044 0.002 PHE B 390 TYR 0.037 0.002 TYR E 477 ARG 0.012 0.000 ARG B 550 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 519 time to evaluate : 3.993 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 35 MET cc_start: 0.9281 (mtp) cc_final: 0.9040 (mtp) REVERT: A 434 MET cc_start: 0.7902 (mmm) cc_final: 0.7412 (mmm) REVERT: A 468 LEU cc_start: 0.8596 (mt) cc_final: 0.7805 (tt) REVERT: A 471 LEU cc_start: 0.9185 (tp) cc_final: 0.8725 (tt) REVERT: A 526 ASN cc_start: 0.9004 (m-40) cc_final: 0.8045 (p0) REVERT: A 623 ASP cc_start: 0.7366 (m-30) cc_final: 0.6885 (t0) REVERT: A 651 ILE cc_start: 0.9155 (pt) cc_final: 0.8807 (tp) REVERT: B 52 MET cc_start: 0.7011 (tpt) cc_final: 0.5655 (tpt) REVERT: B 133 THR cc_start: 0.9426 (m) cc_final: 0.9079 (m) REVERT: B 166 SER cc_start: 0.7788 (t) cc_final: 0.7376 (m) REVERT: B 262 ARG cc_start: 0.8279 (mtt-85) cc_final: 0.8059 (mtp180) REVERT: B 308 TYR cc_start: 0.8865 (m-10) cc_final: 0.8466 (m-80) REVERT: B 337 MET cc_start: 0.7824 (ppp) cc_final: 0.7619 (tmm) REVERT: B 491 LEU cc_start: 0.9384 (mp) cc_final: 0.8874 (tp) REVERT: B 540 LEU cc_start: 0.8606 (mt) cc_final: 0.8255 (tt) REVERT: B 733 LEU cc_start: 0.8418 (tp) cc_final: 0.7881 (tp) REVERT: E 52 MET cc_start: 0.8579 (mmm) cc_final: 0.8358 (tpt) REVERT: E 261 TYR cc_start: 0.8586 (t80) cc_final: 0.8214 (t80) REVERT: E 265 MET cc_start: 0.9106 (mmt) cc_final: 0.8223 (mmm) REVERT: E 343 MET cc_start: 0.8824 (mmm) cc_final: 0.8503 (tmm) REVERT: E 348 LEU cc_start: 0.8686 (mm) cc_final: 0.8336 (mt) REVERT: E 468 LEU cc_start: 0.8562 (mt) cc_final: 0.7734 (tt) REVERT: E 471 LEU cc_start: 0.9174 (tp) cc_final: 0.8688 (tt) REVERT: E 478 HIS cc_start: 0.7936 (m90) cc_final: 0.7647 (m90) REVERT: E 526 ASN cc_start: 0.8818 (m-40) cc_final: 0.8437 (p0) REVERT: E 623 ASP cc_start: 0.7483 (m-30) cc_final: 0.7153 (t0) REVERT: E 710 LEU cc_start: 0.8604 (mt) cc_final: 0.8387 (mt) REVERT: F 35 MET cc_start: 0.9162 (ttp) cc_final: 0.8857 (ttm) REVERT: F 52 MET cc_start: 0.7497 (tpp) cc_final: 0.6896 (tpp) REVERT: F 133 THR cc_start: 0.9246 (m) cc_final: 0.8786 (m) REVERT: F 166 SER cc_start: 0.8132 (t) cc_final: 0.7788 (m) REVERT: F 291 PHE cc_start: 0.8011 (t80) cc_final: 0.7730 (t80) REVERT: F 308 TYR cc_start: 0.8961 (m-10) cc_final: 0.7563 (m-10) REVERT: F 434 MET cc_start: 0.7113 (ptm) cc_final: 0.6878 (ptm) REVERT: F 496 ARG cc_start: 0.8366 (mmt-90) cc_final: 0.7928 (mmm160) REVERT: F 540 LEU cc_start: 0.8659 (mt) cc_final: 0.8345 (tt) REVERT: C 35 MET cc_start: 0.9413 (mtp) cc_final: 0.8895 (mtp) REVERT: C 52 MET cc_start: 0.8634 (mmm) cc_final: 0.8301 (tpt) REVERT: C 99 TYR cc_start: 0.7143 (m-80) cc_final: 0.6730 (m-80) REVERT: C 261 TYR cc_start: 0.8630 (t80) cc_final: 0.8414 (t80) REVERT: C 471 LEU cc_start: 0.9177 (tp) cc_final: 0.8910 (tt) REVERT: C 493 GLU cc_start: 0.8953 (pt0) cc_final: 0.8635 (tm-30) REVERT: C 526 ASN cc_start: 0.8851 (m-40) cc_final: 0.7984 (p0) REVERT: C 623 ASP cc_start: 0.7769 (m-30) cc_final: 0.7450 (t0) REVERT: C 651 ILE cc_start: 0.9301 (pt) cc_final: 0.9052 (tp) REVERT: D 52 MET cc_start: 0.7062 (tpt) cc_final: 0.5946 (tpt) REVERT: D 239 GLN cc_start: 0.8952 (mt0) cc_final: 0.8637 (pt0) REVERT: D 337 MET cc_start: 0.8839 (mmm) cc_final: 0.8118 (tmm) REVERT: D 399 GLU cc_start: 0.8887 (tt0) cc_final: 0.8677 (tp30) REVERT: D 434 MET cc_start: 0.7636 (ptm) cc_final: 0.7335 (ptm) REVERT: D 593 LEU cc_start: 0.8177 (mp) cc_final: 0.7607 (tt) REVERT: D 733 LEU cc_start: 0.8406 (tp) cc_final: 0.8093 (tp) REVERT: D 775 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8396 (mt-10) outliers start: 1 outliers final: 0 residues processed: 520 average time/residue: 0.4443 time to fit residues: 384.1024 Evaluate side-chains 353 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 4.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 0.0870 chunk 233 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 chunk 169 optimal weight: 0.3980 chunk 351 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 369 optimal weight: 0.0270 chunk 103 optimal weight: 3.9990 overall best weight: 1.5020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN A 499 HIS A 614 HIS ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 576 ASN ** E 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35463 Z= 0.180 Angle : 0.643 16.133 48108 Z= 0.335 Chirality : 0.045 0.304 5616 Planarity : 0.004 0.071 5961 Dihedral : 4.735 26.673 4659 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 4257 helix: 0.23 (0.12), residues: 1887 sheet: -1.23 (0.22), residues: 576 loop : -2.39 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 647 HIS 0.008 0.001 HIS C 568 PHE 0.036 0.002 PHE C 433 TYR 0.035 0.002 TYR C 477 ARG 0.004 0.000 ARG B 640 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 514 time to evaluate : 4.323 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: A 308 TYR cc_start: 0.9141 (m-80) cc_final: 0.8923 (m-80) REVERT: A 328 LEU cc_start: 0.9692 (mm) cc_final: 0.9487 (mm) REVERT: A 380 ASP cc_start: 0.8657 (t0) cc_final: 0.8026 (m-30) REVERT: A 434 MET cc_start: 0.7956 (mmm) cc_final: 0.7686 (mmm) REVERT: A 468 LEU cc_start: 0.8627 (mt) cc_final: 0.7810 (tt) REVERT: A 471 LEU cc_start: 0.9095 (tp) cc_final: 0.8701 (tt) REVERT: A 526 ASN cc_start: 0.9063 (m-40) cc_final: 0.8104 (p0) REVERT: A 623 ASP cc_start: 0.7358 (m-30) cc_final: 0.6917 (t0) REVERT: A 651 ILE cc_start: 0.9111 (pt) cc_final: 0.8800 (tp) REVERT: A 769 LEU cc_start: 0.8604 (tt) cc_final: 0.8340 (mp) REVERT: B 52 MET cc_start: 0.7226 (tpt) cc_final: 0.6853 (tpp) REVERT: B 110 ASP cc_start: 0.8851 (m-30) cc_final: 0.8623 (m-30) REVERT: B 166 SER cc_start: 0.7827 (t) cc_final: 0.7372 (m) REVERT: B 308 TYR cc_start: 0.8913 (m-10) cc_final: 0.8395 (m-80) REVERT: B 320 ILE cc_start: 0.9695 (mt) cc_final: 0.9438 (tt) REVERT: B 491 LEU cc_start: 0.9364 (mp) cc_final: 0.8847 (tp) REVERT: B 540 LEU cc_start: 0.8627 (mt) cc_final: 0.8240 (tt) REVERT: B 593 LEU cc_start: 0.8262 (mp) cc_final: 0.7971 (tt) REVERT: B 620 ASP cc_start: 0.8048 (t0) cc_final: 0.7765 (t0) REVERT: B 733 LEU cc_start: 0.8443 (tp) cc_final: 0.7923 (tp) REVERT: E 36 LEU cc_start: 0.9522 (tt) cc_final: 0.9283 (tp) REVERT: E 52 MET cc_start: 0.8449 (mmm) cc_final: 0.8210 (tpt) REVERT: E 234 LYS cc_start: 0.7193 (mmtt) cc_final: 0.6000 (ptmm) REVERT: E 265 MET cc_start: 0.9116 (mmt) cc_final: 0.8534 (mmt) REVERT: E 348 LEU cc_start: 0.8597 (mm) cc_final: 0.8357 (mm) REVERT: E 375 MET cc_start: 0.9508 (ptp) cc_final: 0.8988 (ptp) REVERT: E 468 LEU cc_start: 0.8590 (mt) cc_final: 0.7885 (tt) REVERT: E 471 LEU cc_start: 0.9098 (tp) cc_final: 0.8804 (tt) REVERT: E 526 ASN cc_start: 0.8802 (m-40) cc_final: 0.8396 (p0) REVERT: E 623 ASP cc_start: 0.7450 (m-30) cc_final: 0.7037 (t0) REVERT: F 35 MET cc_start: 0.9193 (ttp) cc_final: 0.8792 (ttm) REVERT: F 52 MET cc_start: 0.7507 (tpp) cc_final: 0.6926 (tpp) REVERT: F 133 THR cc_start: 0.9219 (m) cc_final: 0.8809 (m) REVERT: F 166 SER cc_start: 0.8046 (t) cc_final: 0.7625 (m) REVERT: F 434 MET cc_start: 0.7084 (ptm) cc_final: 0.6880 (ptm) REVERT: F 496 ARG cc_start: 0.8392 (mmt-90) cc_final: 0.7960 (mmm160) REVERT: F 540 LEU cc_start: 0.8577 (mt) cc_final: 0.8358 (tt) REVERT: F 733 LEU cc_start: 0.8284 (tp) cc_final: 0.7979 (tp) REVERT: C 35 MET cc_start: 0.9394 (mtp) cc_final: 0.8875 (mtm) REVERT: C 52 MET cc_start: 0.8573 (mmm) cc_final: 0.8304 (tpt) REVERT: C 261 TYR cc_start: 0.8629 (t80) cc_final: 0.8276 (t80) REVERT: C 468 LEU cc_start: 0.8514 (mt) cc_final: 0.7796 (tt) REVERT: C 471 LEU cc_start: 0.9156 (tp) cc_final: 0.8686 (tt) REVERT: C 493 GLU cc_start: 0.8974 (pt0) cc_final: 0.8683 (tm-30) REVERT: C 526 ASN cc_start: 0.8762 (m-40) cc_final: 0.7898 (p0) REVERT: C 623 ASP cc_start: 0.7704 (m-30) cc_final: 0.7344 (t0) REVERT: C 651 ILE cc_start: 0.9270 (pt) cc_final: 0.9016 (tp) REVERT: D 52 MET cc_start: 0.7154 (tpt) cc_final: 0.6038 (tpt) REVERT: D 53 ILE cc_start: 0.9236 (mm) cc_final: 0.9000 (mm) REVERT: D 239 GLN cc_start: 0.8834 (mt0) cc_final: 0.8539 (pt0) REVERT: D 308 TYR cc_start: 0.8579 (m-80) cc_final: 0.8148 (m-80) REVERT: D 337 MET cc_start: 0.8840 (mmm) cc_final: 0.8114 (tmm) REVERT: D 399 GLU cc_start: 0.8806 (tt0) cc_final: 0.8598 (tp30) REVERT: D 434 MET cc_start: 0.7631 (ptm) cc_final: 0.7363 (ptm) REVERT: D 445 LEU cc_start: 0.9193 (mm) cc_final: 0.8958 (mm) REVERT: D 632 ILE cc_start: 0.8583 (tt) cc_final: 0.8265 (tt) REVERT: D 733 LEU cc_start: 0.8330 (tp) cc_final: 0.7999 (tp) REVERT: D 775 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8624 (mt-10) outliers start: 0 outliers final: 0 residues processed: 514 average time/residue: 0.4409 time to fit residues: 379.8932 Evaluate side-chains 350 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 9.9990 chunk 370 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 241 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 412 optimal weight: 20.0000 chunk 342 optimal weight: 7.9990 chunk 190 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 216 optimal weight: 0.7980 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 105 GLN ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS B 104 HIS ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 ASN C 49 GLN C 105 GLN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 35463 Z= 0.413 Angle : 0.823 16.771 48108 Z= 0.429 Chirality : 0.048 0.315 5616 Planarity : 0.005 0.052 5961 Dihedral : 5.214 31.500 4659 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.01 (0.13), residues: 4257 helix: -0.21 (0.12), residues: 1884 sheet: -1.44 (0.22), residues: 591 loop : -2.52 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 647 HIS 0.010 0.002 HIS A 119 PHE 0.039 0.003 PHE D 291 TYR 0.031 0.003 TYR A 477 ARG 0.008 0.001 ARG B 666 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 4.321 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 52 MET cc_start: 0.8391 (mmp) cc_final: 0.7647 (mmp) REVERT: A 140 SER cc_start: 0.9439 (t) cc_final: 0.8981 (p) REVERT: A 265 MET cc_start: 0.9165 (tpp) cc_final: 0.8866 (mmp) REVERT: A 471 LEU cc_start: 0.9146 (tp) cc_final: 0.8854 (tt) REVERT: A 526 ASN cc_start: 0.9187 (m-40) cc_final: 0.8242 (p0) REVERT: A 600 ARG cc_start: 0.8653 (tmt170) cc_final: 0.8330 (tpt90) REVERT: A 623 ASP cc_start: 0.7487 (m-30) cc_final: 0.7042 (t0) REVERT: A 651 ILE cc_start: 0.9256 (pt) cc_final: 0.8987 (tp) REVERT: B 35 MET cc_start: 0.9347 (mtm) cc_final: 0.9147 (mtm) REVERT: B 52 MET cc_start: 0.7715 (tpt) cc_final: 0.6287 (tpp) REVERT: B 239 GLN cc_start: 0.8702 (mt0) cc_final: 0.8355 (pt0) REVERT: B 337 MET cc_start: 0.7756 (ppp) cc_final: 0.6730 (ppp) REVERT: B 491 LEU cc_start: 0.9463 (mp) cc_final: 0.8991 (tp) REVERT: B 593 LEU cc_start: 0.8537 (mp) cc_final: 0.8186 (tt) REVERT: B 620 ASP cc_start: 0.8054 (t0) cc_final: 0.7815 (t0) REVERT: B 733 LEU cc_start: 0.8470 (tp) cc_final: 0.7992 (tp) REVERT: E 52 MET cc_start: 0.8447 (mmm) cc_final: 0.8151 (tpt) REVERT: E 265 MET cc_start: 0.9215 (mmt) cc_final: 0.8816 (mmm) REVERT: E 323 SER cc_start: 0.8947 (m) cc_final: 0.8276 (t) REVERT: E 434 MET cc_start: 0.7763 (mmp) cc_final: 0.6794 (mmm) REVERT: E 471 LEU cc_start: 0.9263 (tp) cc_final: 0.9034 (tt) REVERT: E 526 ASN cc_start: 0.8949 (m-40) cc_final: 0.8602 (p0) REVERT: E 623 ASP cc_start: 0.7380 (m-30) cc_final: 0.6976 (t0) REVERT: F 35 MET cc_start: 0.9268 (ttp) cc_final: 0.8938 (ttm) REVERT: F 52 MET cc_start: 0.7857 (tpp) cc_final: 0.7302 (tpp) REVERT: F 133 THR cc_start: 0.9367 (m) cc_final: 0.9156 (t) REVERT: F 239 GLN cc_start: 0.8790 (mt0) cc_final: 0.8559 (pt0) REVERT: F 265 MET cc_start: 0.8717 (mmm) cc_final: 0.8438 (tpp) REVERT: F 281 TYR cc_start: 0.7869 (t80) cc_final: 0.7642 (t80) REVERT: F 308 TYR cc_start: 0.8931 (m-10) cc_final: 0.8464 (m-80) REVERT: F 343 MET cc_start: 0.8369 (ttm) cc_final: 0.7905 (ttm) REVERT: F 411 TRP cc_start: 0.8467 (m100) cc_final: 0.7234 (m100) REVERT: F 434 MET cc_start: 0.7164 (ptm) cc_final: 0.6925 (ptm) REVERT: F 496 ARG cc_start: 0.8405 (mmt-90) cc_final: 0.7996 (mmm160) REVERT: F 540 LEU cc_start: 0.8604 (mt) cc_final: 0.8343 (tt) REVERT: F 593 LEU cc_start: 0.8503 (mt) cc_final: 0.8239 (tp) REVERT: F 733 LEU cc_start: 0.8596 (tp) cc_final: 0.8269 (tp) REVERT: F 775 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8908 (mt-10) REVERT: C 35 MET cc_start: 0.9464 (mtp) cc_final: 0.9036 (mtp) REVERT: C 52 MET cc_start: 0.8543 (mmm) cc_final: 0.8322 (tpt) REVERT: C 99 TYR cc_start: 0.7784 (m-80) cc_final: 0.7310 (m-80) REVERT: C 261 TYR cc_start: 0.8771 (t80) cc_final: 0.8492 (t80) REVERT: C 458 ASP cc_start: 0.7291 (m-30) cc_final: 0.7038 (p0) REVERT: C 468 LEU cc_start: 0.8687 (mt) cc_final: 0.7907 (tt) REVERT: C 471 LEU cc_start: 0.9165 (tp) cc_final: 0.8702 (tt) REVERT: C 493 GLU cc_start: 0.9046 (pt0) cc_final: 0.8652 (tm-30) REVERT: C 526 ASN cc_start: 0.8894 (m-40) cc_final: 0.7974 (p0) REVERT: C 623 ASP cc_start: 0.7795 (m-30) cc_final: 0.7456 (t0) REVERT: C 651 ILE cc_start: 0.9331 (pt) cc_final: 0.9130 (tp) REVERT: D 52 MET cc_start: 0.7579 (tpt) cc_final: 0.6341 (tpt) REVERT: D 239 GLN cc_start: 0.8942 (mt0) cc_final: 0.8696 (pt0) REVERT: D 308 TYR cc_start: 0.8823 (m-80) cc_final: 0.8433 (m-80) REVERT: D 337 MET cc_start: 0.8921 (mmm) cc_final: 0.8139 (tmm) REVERT: D 434 MET cc_start: 0.7461 (ptm) cc_final: 0.7193 (ptm) REVERT: D 733 LEU cc_start: 0.8547 (tp) cc_final: 0.8178 (tp) outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.4743 time to fit residues: 346.7113 Evaluate side-chains 296 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 4.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 234 optimal weight: 0.7980 chunk 300 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 346 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 chunk 410 optimal weight: 6.9990 chunk 256 optimal weight: 9.9990 chunk 250 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN E 239 GLN E 253 HIS ** E 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 ASN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35463 Z= 0.272 Angle : 0.710 17.883 48108 Z= 0.369 Chirality : 0.046 0.273 5616 Planarity : 0.004 0.084 5961 Dihedral : 5.060 29.103 4659 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.85 % Favored : 89.12 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.13), residues: 4257 helix: -0.02 (0.12), residues: 1881 sheet: -1.41 (0.22), residues: 594 loop : -2.51 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 647 HIS 0.010 0.001 HIS A 119 PHE 0.073 0.002 PHE B 390 TYR 0.036 0.002 TYR B 386 ARG 0.015 0.001 ARG D 550 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 4.033 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 110 ASP cc_start: 0.9134 (m-30) cc_final: 0.8788 (t70) REVERT: A 140 SER cc_start: 0.9384 (t) cc_final: 0.8952 (p) REVERT: A 265 MET cc_start: 0.9094 (tpp) cc_final: 0.8883 (mmp) REVERT: A 468 LEU cc_start: 0.8654 (mt) cc_final: 0.7983 (tt) REVERT: A 471 LEU cc_start: 0.9172 (tp) cc_final: 0.8890 (tt) REVERT: A 526 ASN cc_start: 0.9214 (m-40) cc_final: 0.8324 (p0) REVERT: A 623 ASP cc_start: 0.7397 (m-30) cc_final: 0.6951 (t0) REVERT: A 651 ILE cc_start: 0.9282 (pt) cc_final: 0.9051 (tp) REVERT: B 52 MET cc_start: 0.7413 (tpt) cc_final: 0.6034 (tpp) REVERT: B 133 THR cc_start: 0.9471 (m) cc_final: 0.9178 (m) REVERT: B 239 GLN cc_start: 0.8749 (mt0) cc_final: 0.8453 (pt0) REVERT: B 337 MET cc_start: 0.7812 (ppp) cc_final: 0.7605 (tmm) REVERT: B 491 LEU cc_start: 0.9404 (mp) cc_final: 0.8949 (tp) REVERT: B 520 GLU cc_start: 0.8779 (tt0) cc_final: 0.8555 (tt0) REVERT: B 546 LEU cc_start: 0.9561 (tp) cc_final: 0.9208 (pp) REVERT: B 733 LEU cc_start: 0.8447 (tp) cc_final: 0.7996 (tp) REVERT: E 36 LEU cc_start: 0.9562 (tt) cc_final: 0.9326 (tp) REVERT: E 52 MET cc_start: 0.8421 (mmm) cc_final: 0.8169 (tpt) REVERT: E 265 MET cc_start: 0.8939 (mmm) cc_final: 0.8524 (mmm) REVERT: E 308 TYR cc_start: 0.9265 (m-80) cc_final: 0.8964 (m-80) REVERT: E 323 SER cc_start: 0.8856 (m) cc_final: 0.8173 (t) REVERT: E 343 MET cc_start: 0.8875 (tpt) cc_final: 0.8343 (tpp) REVERT: E 348 LEU cc_start: 0.9004 (mm) cc_final: 0.8724 (tp) REVERT: E 434 MET cc_start: 0.7600 (mmp) cc_final: 0.7007 (mmm) REVERT: E 468 LEU cc_start: 0.8637 (mt) cc_final: 0.7943 (tt) REVERT: E 471 LEU cc_start: 0.9250 (tp) cc_final: 0.8929 (tt) REVERT: E 526 ASN cc_start: 0.8855 (m-40) cc_final: 0.8521 (p0) REVERT: E 623 ASP cc_start: 0.7288 (m-30) cc_final: 0.6886 (t0) REVERT: F 35 MET cc_start: 0.9240 (ttp) cc_final: 0.8935 (ttm) REVERT: F 52 MET cc_start: 0.7431 (tpp) cc_final: 0.6774 (tpp) REVERT: F 133 THR cc_start: 0.9345 (m) cc_final: 0.8941 (t) REVERT: F 160 LEU cc_start: 0.8392 (mp) cc_final: 0.8104 (mp) REVERT: F 239 GLN cc_start: 0.8796 (mt0) cc_final: 0.8588 (pt0) REVERT: F 281 TYR cc_start: 0.7798 (t80) cc_final: 0.7565 (t80) REVERT: F 308 TYR cc_start: 0.9013 (m-10) cc_final: 0.8393 (m-80) REVERT: F 343 MET cc_start: 0.8358 (ttm) cc_final: 0.7914 (ttm) REVERT: F 411 TRP cc_start: 0.8417 (m100) cc_final: 0.6810 (m100) REVERT: F 434 MET cc_start: 0.7166 (ptm) cc_final: 0.6935 (ptm) REVERT: F 496 ARG cc_start: 0.8469 (mmt-90) cc_final: 0.8072 (mmm160) REVERT: F 546 LEU cc_start: 0.9582 (tp) cc_final: 0.9214 (pp) REVERT: F 733 LEU cc_start: 0.8459 (tp) cc_final: 0.8091 (tp) REVERT: F 775 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8901 (mt-10) REVERT: C 35 MET cc_start: 0.9407 (mtp) cc_final: 0.8998 (mtp) REVERT: C 36 LEU cc_start: 0.9520 (tt) cc_final: 0.9179 (tp) REVERT: C 261 TYR cc_start: 0.8755 (t80) cc_final: 0.8545 (t80) REVERT: C 471 LEU cc_start: 0.9243 (tp) cc_final: 0.8972 (tt) REVERT: C 493 GLU cc_start: 0.9039 (pt0) cc_final: 0.8641 (tm-30) REVERT: C 623 ASP cc_start: 0.7642 (m-30) cc_final: 0.7102 (t0) REVERT: C 651 ILE cc_start: 0.9303 (pt) cc_final: 0.9045 (tp) REVERT: D 52 MET cc_start: 0.7439 (tpt) cc_final: 0.6297 (tpt) REVERT: D 239 GLN cc_start: 0.9017 (mt0) cc_final: 0.8635 (pt0) REVERT: D 265 MET cc_start: 0.8629 (mmm) cc_final: 0.7791 (tpp) REVERT: D 308 TYR cc_start: 0.8838 (m-80) cc_final: 0.8440 (m-80) REVERT: D 337 MET cc_start: 0.8907 (mmm) cc_final: 0.8090 (tmm) REVERT: D 434 MET cc_start: 0.7447 (ptm) cc_final: 0.7206 (ptm) REVERT: D 546 LEU cc_start: 0.9591 (tp) cc_final: 0.9188 (pp) REVERT: D 733 LEU cc_start: 0.8375 (tp) cc_final: 0.7956 (tp) REVERT: D 775 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8588 (pt0) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.4382 time to fit residues: 310.6801 Evaluate side-chains 312 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 4.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 245 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 261 optimal weight: 10.0000 chunk 279 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 322 optimal weight: 9.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 ASN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 GLN ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 ASN ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.6264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35463 Z= 0.277 Angle : 0.712 15.952 48108 Z= 0.370 Chirality : 0.046 0.271 5616 Planarity : 0.004 0.060 5961 Dihedral : 5.053 30.810 4659 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 0.05 % Allowed : 1.51 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 4257 helix: 0.08 (0.12), residues: 1854 sheet: -1.47 (0.21), residues: 609 loop : -2.42 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 647 HIS 0.010 0.001 HIS A 119 PHE 0.047 0.002 PHE B 390 TYR 0.031 0.002 TYR C 477 ARG 0.007 0.001 ARG B 666 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 404 time to evaluate : 4.299 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 110 ASP cc_start: 0.9118 (m-30) cc_final: 0.8913 (t70) REVERT: A 140 SER cc_start: 0.9382 (t) cc_final: 0.8939 (p) REVERT: A 375 MET cc_start: 0.9487 (mtm) cc_final: 0.9260 (ptp) REVERT: A 471 LEU cc_start: 0.9172 (tp) cc_final: 0.8873 (tt) REVERT: A 526 ASN cc_start: 0.9189 (m-40) cc_final: 0.8356 (p0) REVERT: A 623 ASP cc_start: 0.7470 (m-30) cc_final: 0.6952 (t0) REVERT: A 651 ILE cc_start: 0.9291 (pt) cc_final: 0.9070 (tp) REVERT: B 35 MET cc_start: 0.9209 (mtp) cc_final: 0.8959 (ttm) REVERT: B 52 MET cc_start: 0.7438 (tpt) cc_final: 0.6019 (tpp) REVERT: B 239 GLN cc_start: 0.8734 (mt0) cc_final: 0.8425 (pt0) REVERT: B 491 LEU cc_start: 0.9438 (mp) cc_final: 0.9049 (tp) REVERT: B 520 GLU cc_start: 0.8804 (tt0) cc_final: 0.8563 (tt0) REVERT: B 733 LEU cc_start: 0.8418 (tp) cc_final: 0.7983 (tp) REVERT: E 52 MET cc_start: 0.8358 (mmm) cc_final: 0.8155 (tpt) REVERT: E 265 MET cc_start: 0.9023 (mmm) cc_final: 0.8516 (mmm) REVERT: E 308 TYR cc_start: 0.9251 (m-80) cc_final: 0.8919 (m-80) REVERT: E 323 SER cc_start: 0.8843 (m) cc_final: 0.8181 (t) REVERT: E 343 MET cc_start: 0.8895 (tpt) cc_final: 0.8453 (tpp) REVERT: E 348 LEU cc_start: 0.9046 (mm) cc_final: 0.8698 (tp) REVERT: E 434 MET cc_start: 0.7653 (mmp) cc_final: 0.7088 (mmm) REVERT: E 468 LEU cc_start: 0.8739 (mt) cc_final: 0.8378 (tp) REVERT: E 471 LEU cc_start: 0.9276 (tp) cc_final: 0.8939 (tt) REVERT: E 526 ASN cc_start: 0.8846 (m-40) cc_final: 0.8515 (p0) REVERT: E 623 ASP cc_start: 0.7395 (m-30) cc_final: 0.6907 (t0) REVERT: F 52 MET cc_start: 0.7478 (tpp) cc_final: 0.6828 (tpp) REVERT: F 239 GLN cc_start: 0.8799 (mt0) cc_final: 0.8586 (pt0) REVERT: F 281 TYR cc_start: 0.7754 (t80) cc_final: 0.7442 (t80) REVERT: F 324 PHE cc_start: 0.8635 (t80) cc_final: 0.8412 (t80) REVERT: F 411 TRP cc_start: 0.8403 (m100) cc_final: 0.6656 (m100) REVERT: F 434 MET cc_start: 0.7147 (ptm) cc_final: 0.6935 (ptm) REVERT: F 496 ARG cc_start: 0.8444 (mmt-90) cc_final: 0.8036 (mmm160) REVERT: F 546 LEU cc_start: 0.9617 (tp) cc_final: 0.9227 (pp) REVERT: F 733 LEU cc_start: 0.8506 (tp) cc_final: 0.8133 (tp) REVERT: F 775 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8907 (mt-10) REVERT: C 35 MET cc_start: 0.9403 (mtp) cc_final: 0.8984 (mtm) REVERT: C 36 LEU cc_start: 0.9538 (tt) cc_final: 0.9188 (tp) REVERT: C 52 MET cc_start: 0.8718 (mmm) cc_final: 0.8160 (mmm) REVERT: C 99 TYR cc_start: 0.7737 (m-80) cc_final: 0.7537 (m-80) REVERT: C 233 ASP cc_start: 0.8366 (m-30) cc_final: 0.8104 (t0) REVERT: C 380 ASP cc_start: 0.8815 (t0) cc_final: 0.8185 (m-30) REVERT: C 471 LEU cc_start: 0.9270 (tp) cc_final: 0.8963 (tt) REVERT: C 623 ASP cc_start: 0.7666 (m-30) cc_final: 0.7050 (t0) REVERT: C 651 ILE cc_start: 0.9304 (pt) cc_final: 0.9051 (tp) REVERT: D 52 MET cc_start: 0.7469 (tpt) cc_final: 0.6299 (tpt) REVERT: D 239 GLN cc_start: 0.8972 (mt0) cc_final: 0.8646 (pt0) REVERT: D 308 TYR cc_start: 0.8857 (m-80) cc_final: 0.8498 (m-80) REVERT: D 324 PHE cc_start: 0.8521 (t80) cc_final: 0.8269 (t80) REVERT: D 337 MET cc_start: 0.8913 (mmm) cc_final: 0.8085 (tmm) REVERT: D 445 LEU cc_start: 0.9272 (mm) cc_final: 0.9061 (mm) REVERT: D 546 LEU cc_start: 0.9651 (tp) cc_final: 0.9211 (pp) REVERT: D 733 LEU cc_start: 0.8461 (tp) cc_final: 0.8046 (tp) REVERT: D 775 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8628 (pt0) outliers start: 2 outliers final: 0 residues processed: 406 average time/residue: 0.4358 time to fit residues: 300.3442 Evaluate side-chains 307 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 4.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 0.7980 chunk 393 optimal weight: 0.8980 chunk 358 optimal weight: 6.9990 chunk 382 optimal weight: 0.0010 chunk 230 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 300 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 345 optimal weight: 6.9990 chunk 361 optimal weight: 3.9990 chunk 381 optimal weight: 4.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 ASN ** E 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN C 532 ASN ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 ASN ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.6399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35463 Z= 0.190 Angle : 0.670 15.841 48108 Z= 0.345 Chirality : 0.045 0.359 5616 Planarity : 0.004 0.060 5961 Dihedral : 4.913 28.371 4659 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.22 % Favored : 89.76 % Rotamer: Outliers : 0.08 % Allowed : 0.82 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.13), residues: 4257 helix: 0.22 (0.12), residues: 1854 sheet: -1.39 (0.22), residues: 606 loop : -2.42 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 647 HIS 0.008 0.001 HIS A 312 PHE 0.046 0.002 PHE C 502 TYR 0.036 0.002 TYR C 477 ARG 0.006 0.000 ARG C 266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 416 time to evaluate : 4.383 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: A 110 ASP cc_start: 0.9110 (m-30) cc_final: 0.8882 (t70) REVERT: A 140 SER cc_start: 0.9340 (t) cc_final: 0.8895 (p) REVERT: A 261 TYR cc_start: 0.8742 (t80) cc_final: 0.8478 (t80) REVERT: A 325 TYR cc_start: 0.9047 (t80) cc_final: 0.8804 (t80) REVERT: A 471 LEU cc_start: 0.9134 (tp) cc_final: 0.8785 (tt) REVERT: A 526 ASN cc_start: 0.9206 (m-40) cc_final: 0.8426 (p0) REVERT: A 623 ASP cc_start: 0.7459 (m-30) cc_final: 0.6935 (t0) REVERT: A 651 ILE cc_start: 0.9257 (pt) cc_final: 0.9003 (tp) REVERT: B 35 MET cc_start: 0.9191 (mtp) cc_final: 0.8930 (ttm) REVERT: B 52 MET cc_start: 0.7376 (tpt) cc_final: 0.6051 (tpp) REVERT: B 239 GLN cc_start: 0.8676 (mt0) cc_final: 0.8436 (pt0) REVERT: B 445 LEU cc_start: 0.9374 (mm) cc_final: 0.9172 (mm) REVERT: B 491 LEU cc_start: 0.9402 (mp) cc_final: 0.9030 (tp) REVERT: B 520 GLU cc_start: 0.8772 (tt0) cc_final: 0.8531 (tt0) REVERT: B 733 LEU cc_start: 0.8279 (tp) cc_final: 0.7855 (tp) REVERT: E 52 MET cc_start: 0.8276 (mmm) cc_final: 0.8016 (tpt) REVERT: E 265 MET cc_start: 0.9131 (mmm) cc_final: 0.8627 (mmm) REVERT: E 308 TYR cc_start: 0.9122 (m-80) cc_final: 0.8752 (m-80) REVERT: E 323 SER cc_start: 0.8798 (m) cc_final: 0.8120 (t) REVERT: E 468 LEU cc_start: 0.8679 (mt) cc_final: 0.8065 (tt) REVERT: E 471 LEU cc_start: 0.9255 (tp) cc_final: 0.8958 (tt) REVERT: E 526 ASN cc_start: 0.8843 (m-40) cc_final: 0.8513 (p0) REVERT: E 623 ASP cc_start: 0.7378 (m-30) cc_final: 0.6857 (t0) REVERT: F 52 MET cc_start: 0.7467 (tpp) cc_final: 0.6864 (tpp) REVERT: F 308 TYR cc_start: 0.8936 (m-10) cc_final: 0.8191 (m-80) REVERT: F 411 TRP cc_start: 0.8351 (m100) cc_final: 0.6581 (m100) REVERT: F 445 LEU cc_start: 0.9323 (mm) cc_final: 0.9113 (mm) REVERT: F 496 ARG cc_start: 0.8387 (mmt-90) cc_final: 0.7789 (mmm160) REVERT: F 546 LEU cc_start: 0.9599 (tp) cc_final: 0.9208 (pp) REVERT: F 733 LEU cc_start: 0.8331 (tp) cc_final: 0.7894 (tp) REVERT: F 775 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8893 (mt-10) REVERT: C 35 MET cc_start: 0.9385 (mtp) cc_final: 0.8989 (mtp) REVERT: C 36 LEU cc_start: 0.9513 (tt) cc_final: 0.9171 (tp) REVERT: C 233 ASP cc_start: 0.8293 (m-30) cc_final: 0.7988 (t0) REVERT: C 380 ASP cc_start: 0.8733 (t0) cc_final: 0.8105 (m-30) REVERT: C 471 LEU cc_start: 0.9242 (tp) cc_final: 0.8893 (tt) REVERT: C 623 ASP cc_start: 0.7627 (m-30) cc_final: 0.7009 (t0) REVERT: C 651 ILE cc_start: 0.9272 (pt) cc_final: 0.9022 (tp) REVERT: D 52 MET cc_start: 0.7340 (tpt) cc_final: 0.6195 (tpt) REVERT: D 239 GLN cc_start: 0.8948 (mt0) cc_final: 0.8605 (pt0) REVERT: D 337 MET cc_start: 0.8876 (mmm) cc_final: 0.8031 (tmm) REVERT: D 445 LEU cc_start: 0.9242 (mm) cc_final: 0.8970 (mm) REVERT: D 546 LEU cc_start: 0.9641 (tp) cc_final: 0.9193 (pp) REVERT: D 733 LEU cc_start: 0.8350 (tp) cc_final: 0.7898 (tp) REVERT: D 775 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8605 (pt0) outliers start: 3 outliers final: 0 residues processed: 419 average time/residue: 0.4426 time to fit residues: 312.1100 Evaluate side-chains 315 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 4.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 251 optimal weight: 3.9990 chunk 404 optimal weight: 0.4980 chunk 246 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 281 optimal weight: 20.0000 chunk 424 optimal weight: 0.3980 chunk 390 optimal weight: 3.9990 chunk 337 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 261 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 576 ASN E 663 ASN ** E 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 HIS ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 ASN ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.6558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35463 Z= 0.197 Angle : 0.668 13.161 48108 Z= 0.346 Chirality : 0.046 0.318 5616 Planarity : 0.004 0.055 5961 Dihedral : 4.863 29.412 4659 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.97 % Favored : 89.01 % Rotamer: Outliers : 0.08 % Allowed : 0.45 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 4257 helix: 0.28 (0.12), residues: 1851 sheet: -1.44 (0.22), residues: 606 loop : -2.43 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 511 HIS 0.008 0.001 HIS A 312 PHE 0.034 0.002 PHE B 390 TYR 0.035 0.002 TYR C 477 ARG 0.007 0.000 ARG C 266 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 405 time to evaluate : 4.216 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 35 MET cc_start: 0.9097 (mtp) cc_final: 0.8570 (mtm) REVERT: A 110 ASP cc_start: 0.9147 (m-30) cc_final: 0.8730 (t0) REVERT: A 140 SER cc_start: 0.9372 (t) cc_final: 0.8877 (p) REVERT: A 325 TYR cc_start: 0.9058 (t80) cc_final: 0.8822 (t80) REVERT: A 471 LEU cc_start: 0.9174 (tp) cc_final: 0.8828 (tt) REVERT: A 526 ASN cc_start: 0.9222 (m-40) cc_final: 0.8420 (p0) REVERT: A 623 ASP cc_start: 0.7581 (m-30) cc_final: 0.6986 (t0) REVERT: B 52 MET cc_start: 0.7415 (tpt) cc_final: 0.6061 (tpp) REVERT: B 239 GLN cc_start: 0.8676 (mt0) cc_final: 0.8442 (pt0) REVERT: B 445 LEU cc_start: 0.9347 (mm) cc_final: 0.9131 (mm) REVERT: B 491 LEU cc_start: 0.9419 (mp) cc_final: 0.9038 (tp) REVERT: B 520 GLU cc_start: 0.8794 (tt0) cc_final: 0.8514 (tt0) REVERT: B 733 LEU cc_start: 0.8367 (tp) cc_final: 0.7978 (tp) REVERT: E 52 MET cc_start: 0.8218 (mmm) cc_final: 0.7968 (tpt) REVERT: E 265 MET cc_start: 0.8948 (mmm) cc_final: 0.8678 (mmm) REVERT: E 308 TYR cc_start: 0.9106 (m-80) cc_final: 0.8798 (m-80) REVERT: E 323 SER cc_start: 0.8787 (m) cc_final: 0.8083 (t) REVERT: E 434 MET cc_start: 0.7745 (mmp) cc_final: 0.7526 (mmm) REVERT: E 468 LEU cc_start: 0.8614 (mt) cc_final: 0.8376 (tp) REVERT: E 471 LEU cc_start: 0.9248 (tp) cc_final: 0.8943 (tt) REVERT: E 526 ASN cc_start: 0.8802 (m-40) cc_final: 0.8457 (p0) REVERT: E 623 ASP cc_start: 0.7461 (m-30) cc_final: 0.6934 (t0) REVERT: F 35 MET cc_start: 0.8961 (ttm) cc_final: 0.8550 (ttm) REVERT: F 52 MET cc_start: 0.7529 (tpp) cc_final: 0.6918 (tpp) REVERT: F 308 TYR cc_start: 0.8934 (m-10) cc_final: 0.8218 (m-80) REVERT: F 411 TRP cc_start: 0.8388 (m100) cc_final: 0.7137 (m100) REVERT: F 445 LEU cc_start: 0.9332 (mm) cc_final: 0.9110 (mm) REVERT: F 496 ARG cc_start: 0.8352 (mmt-90) cc_final: 0.7954 (mmm160) REVERT: F 546 LEU cc_start: 0.9606 (tp) cc_final: 0.9224 (pp) REVERT: F 733 LEU cc_start: 0.8350 (tp) cc_final: 0.7904 (tp) REVERT: C 36 LEU cc_start: 0.9515 (tt) cc_final: 0.9181 (tp) REVERT: C 156 PHE cc_start: 0.9140 (t80) cc_final: 0.8699 (t80) REVERT: C 233 ASP cc_start: 0.8198 (m-30) cc_final: 0.7949 (t0) REVERT: C 471 LEU cc_start: 0.9237 (tp) cc_final: 0.8873 (tt) REVERT: C 600 ARG cc_start: 0.8334 (tmt170) cc_final: 0.7678 (ttp80) REVERT: C 623 ASP cc_start: 0.7664 (m-30) cc_final: 0.7022 (t0) REVERT: C 651 ILE cc_start: 0.9314 (pt) cc_final: 0.9094 (tp) REVERT: D 52 MET cc_start: 0.7349 (tpt) cc_final: 0.6010 (tpt) REVERT: D 239 GLN cc_start: 0.8904 (mt0) cc_final: 0.8596 (pt0) REVERT: D 337 MET cc_start: 0.8887 (mmm) cc_final: 0.8030 (tmm) REVERT: D 445 LEU cc_start: 0.9283 (mm) cc_final: 0.9016 (mm) REVERT: D 546 LEU cc_start: 0.9654 (tp) cc_final: 0.9209 (pp) REVERT: D 590 MET cc_start: 0.7123 (mmp) cc_final: 0.6917 (mmp) REVERT: D 733 LEU cc_start: 0.8367 (tp) cc_final: 0.7925 (tp) REVERT: D 775 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8645 (pt0) outliers start: 3 outliers final: 0 residues processed: 408 average time/residue: 0.4324 time to fit residues: 297.7590 Evaluate side-chains 305 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 268 optimal weight: 8.9990 chunk 360 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 311 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 338 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 347 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 ASN ** E 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 GLN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 ASN D 531 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.079077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.061865 restraints weight = 164048.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.063814 restraints weight = 88492.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.065107 restraints weight = 56005.669| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35463 Z= 0.164 Angle : 0.657 14.240 48108 Z= 0.335 Chirality : 0.046 0.257 5616 Planarity : 0.004 0.054 5961 Dihedral : 4.741 27.559 4659 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.77 % Favored : 90.20 % Rotamer: Outliers : 0.08 % Allowed : 0.50 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.13), residues: 4257 helix: 0.32 (0.12), residues: 1854 sheet: -1.42 (0.22), residues: 606 loop : -2.38 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 143 HIS 0.008 0.001 HIS A 312 PHE 0.053 0.002 PHE A 502 TYR 0.039 0.001 TYR C 477 ARG 0.009 0.000 ARG E 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7776.55 seconds wall clock time: 142 minutes 51.56 seconds (8571.56 seconds total)