Starting phenix.real_space_refine on Fri Feb 23 02:22:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6aui_7006/02_2024/6aui_7006_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6aui_7006/02_2024/6aui_7006.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6aui_7006/02_2024/6aui_7006_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6aui_7006/02_2024/6aui_7006_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6aui_7006/02_2024/6aui_7006_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6aui_7006/02_2024/6aui_7006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6aui_7006/02_2024/6aui_7006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6aui_7006/02_2024/6aui_7006_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6aui_7006/02_2024/6aui_7006_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 12 5.21 5 S 204 5.16 5 C 22938 2.51 5 N 6150 2.21 5 O 6954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 6": "NH1" <-> "NH2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ARG 516": "NH1" <-> "NH2" Residue "A TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 627": "NH1" <-> "NH2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "B ARG 6": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B ARG 413": "NH1" <-> "NH2" Residue "B ARG 516": "NH1" <-> "NH2" Residue "B TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 627": "NH1" <-> "NH2" Residue "B ARG 698": "NH1" <-> "NH2" Residue "C ARG 6": "NH1" <-> "NH2" Residue "C ARG 9": "NH1" <-> "NH2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C ARG 516": "NH1" <-> "NH2" Residue "C TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 627": "NH1" <-> "NH2" Residue "C ARG 698": "NH1" <-> "NH2" Residue "D ARG 6": "NH1" <-> "NH2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D ARG 413": "NH1" <-> "NH2" Residue "D ARG 516": "NH1" <-> "NH2" Residue "D TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 627": "NH1" <-> "NH2" Residue "D ARG 698": "NH1" <-> "NH2" Residue "E ARG 6": "NH1" <-> "NH2" Residue "E ARG 9": "NH1" <-> "NH2" Residue "E ARG 196": "NH1" <-> "NH2" Residue "E ARG 413": "NH1" <-> "NH2" Residue "E ARG 516": "NH1" <-> "NH2" Residue "E TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 627": "NH1" <-> "NH2" Residue "E ARG 698": "NH1" <-> "NH2" Residue "F ARG 6": "NH1" <-> "NH2" Residue "F ARG 9": "NH1" <-> "NH2" Residue "F ARG 196": "NH1" <-> "NH2" Residue "F ARG 413": "NH1" <-> "NH2" Residue "F ARG 516": "NH1" <-> "NH2" Residue "F TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 627": "NH1" <-> "NH2" Residue "F ARG 698": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36306 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5958 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 715} Chain: "B" Number of atoms: 5958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5958 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 715} Chain: "C" Number of atoms: 5958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5958 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 715} Chain: "D" Number of atoms: 5958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5958 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 715} Chain: "E" Number of atoms: 5958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5958 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 715} Chain: "F" Number of atoms: 5958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5958 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 715} Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 19.59, per 1000 atoms: 0.54 Number of scatterers: 36306 At special positions: 0 Unit cell: (178.16, 195.19, 116.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 204 16.00 P 48 15.00 Mg 12 11.99 O 6954 8.00 N 6150 7.00 C 22938 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.34 Conformation dependent library (CDL) restraints added in 6.7 seconds 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 210 helices and 36 sheets defined 46.3% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.43 Creating SS restraints... Processing helix chain 'A' and resid 15 through 22 removed outlier: 3.951A pdb=" N THR A 19 " --> pdb=" O ASP A 16 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 22 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 36 through 46 removed outlier: 3.709A pdb=" N GLY A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 69 removed outlier: 5.046A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 89 removed outlier: 3.538A pdb=" N ALA A 75 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 77 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 79 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 82 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 83 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 84 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 88 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 128 through 134 removed outlier: 3.603A pdb=" N SER A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 removed outlier: 3.726A pdb=" N ASP A 140 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE A 141 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 154 removed outlier: 3.940A pdb=" N SER A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 178 Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 228 through 243 Processing helix chain 'A' and resid 273 through 285 Processing helix chain 'A' and resid 306 through 312 removed outlier: 4.517A pdb=" N PHE A 309 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 464 through 480 removed outlier: 3.767A pdb=" N GLU A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 497 removed outlier: 4.175A pdb=" N LEU A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 514 Processing helix chain 'A' and resid 522 through 550 removed outlier: 3.722A pdb=" N LYS A 529 " --> pdb=" O GLN A 525 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 549 " --> pdb=" O ASP A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 570 No H-bonds generated for 'chain 'A' and resid 567 through 570' Processing helix chain 'A' and resid 581 through 591 Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 639 through 648 removed outlier: 3.674A pdb=" N GLU A 647 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 662 removed outlier: 4.060A pdb=" N ALA A 661 " --> pdb=" O ASN A 657 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N CYS A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 676 through 679 No H-bonds generated for 'chain 'A' and resid 676 through 679' Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 688 through 701 Processing helix chain 'A' and resid 717 through 730 Processing helix chain 'B' and resid 15 through 22 removed outlier: 3.951A pdb=" N THR B 19 " --> pdb=" O ASP B 16 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 22 " --> pdb=" O THR B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 26 No H-bonds generated for 'chain 'B' and resid 24 through 26' Processing helix chain 'B' and resid 36 through 46 removed outlier: 3.710A pdb=" N GLY B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 69 removed outlier: 5.046A pdb=" N THR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 89 removed outlier: 3.538A pdb=" N ALA B 75 " --> pdb=" O PRO B 72 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 77 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 79 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 82 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 83 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 84 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 88 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 128 through 134 removed outlier: 3.603A pdb=" N SER B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 removed outlier: 3.727A pdb=" N ASP B 140 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE B 141 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.940A pdb=" N SER B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 306 through 312 removed outlier: 4.518A pdb=" N PHE B 309 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 365 through 376 Processing helix chain 'B' and resid 386 through 399 Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 464 through 480 removed outlier: 3.768A pdb=" N GLU B 468 " --> pdb=" O LYS B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 497 removed outlier: 4.175A pdb=" N LEU B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 514 Processing helix chain 'B' and resid 522 through 550 removed outlier: 3.722A pdb=" N LYS B 529 " --> pdb=" O GLN B 525 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 570 No H-bonds generated for 'chain 'B' and resid 567 through 570' Processing helix chain 'B' and resid 581 through 591 Processing helix chain 'B' and resid 605 through 611 Processing helix chain 'B' and resid 639 through 648 removed outlier: 3.674A pdb=" N GLU B 647 " --> pdb=" O LYS B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 662 removed outlier: 4.060A pdb=" N ALA B 661 " --> pdb=" O ASN B 657 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N CYS B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 676 through 679 No H-bonds generated for 'chain 'B' and resid 676 through 679' Processing helix chain 'B' and resid 683 through 685 No H-bonds generated for 'chain 'B' and resid 683 through 685' Processing helix chain 'B' and resid 688 through 701 Processing helix chain 'B' and resid 717 through 730 Processing helix chain 'C' and resid 15 through 22 removed outlier: 3.952A pdb=" N THR C 19 " --> pdb=" O ASP C 16 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 22 " --> pdb=" O THR C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 36 through 46 removed outlier: 3.710A pdb=" N GLY C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 69 removed outlier: 5.046A pdb=" N THR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 89 removed outlier: 3.538A pdb=" N ALA C 75 " --> pdb=" O PRO C 72 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 77 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 79 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 82 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL C 83 " --> pdb=" O ARG C 80 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 84 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C 88 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 128 through 134 removed outlier: 3.603A pdb=" N SER C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 removed outlier: 3.725A pdb=" N ASP C 140 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE C 141 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 154 removed outlier: 3.940A pdb=" N SER C 154 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 178 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 228 through 243 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 306 through 312 removed outlier: 4.518A pdb=" N PHE C 309 " --> pdb=" O LEU C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 323 No H-bonds generated for 'chain 'C' and resid 321 through 323' Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 365 through 376 Processing helix chain 'C' and resid 386 through 399 Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 464 through 480 removed outlier: 3.768A pdb=" N GLU C 468 " --> pdb=" O LYS C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 497 removed outlier: 4.174A pdb=" N LEU C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 514 Processing helix chain 'C' and resid 522 through 550 removed outlier: 3.721A pdb=" N LYS C 529 " --> pdb=" O GLN C 525 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU C 549 " --> pdb=" O ASP C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 570 No H-bonds generated for 'chain 'C' and resid 567 through 570' Processing helix chain 'C' and resid 581 through 591 Processing helix chain 'C' and resid 605 through 611 Processing helix chain 'C' and resid 639 through 648 removed outlier: 3.674A pdb=" N GLU C 647 " --> pdb=" O LYS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 662 removed outlier: 4.060A pdb=" N ALA C 661 " --> pdb=" O ASN C 657 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N CYS C 662 " --> pdb=" O GLN C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 676 through 679 No H-bonds generated for 'chain 'C' and resid 676 through 679' Processing helix chain 'C' and resid 683 through 685 No H-bonds generated for 'chain 'C' and resid 683 through 685' Processing helix chain 'C' and resid 688 through 701 Processing helix chain 'C' and resid 717 through 730 Processing helix chain 'D' and resid 15 through 22 removed outlier: 3.950A pdb=" N THR D 19 " --> pdb=" O ASP D 16 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 22 " --> pdb=" O THR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' Processing helix chain 'D' and resid 36 through 46 removed outlier: 3.709A pdb=" N GLY D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 69 removed outlier: 5.046A pdb=" N THR D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 89 removed outlier: 3.538A pdb=" N ALA D 75 " --> pdb=" O PRO D 72 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 77 " --> pdb=" O TYR D 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 79 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 82 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL D 83 " --> pdb=" O ARG D 80 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER D 84 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS D 88 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 118 through 126 Processing helix chain 'D' and resid 128 through 134 removed outlier: 3.603A pdb=" N SER D 133 " --> pdb=" O ASP D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 142 removed outlier: 3.725A pdb=" N ASP D 140 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE D 141 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.940A pdb=" N SER D 154 " --> pdb=" O THR D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 178 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 228 through 243 Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 306 through 312 removed outlier: 4.518A pdb=" N PHE D 309 " --> pdb=" O LEU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 323 No H-bonds generated for 'chain 'D' and resid 321 through 323' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 365 through 376 Processing helix chain 'D' and resid 386 through 399 Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 464 through 480 removed outlier: 3.768A pdb=" N GLU D 468 " --> pdb=" O LYS D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 497 removed outlier: 4.176A pdb=" N LEU D 493 " --> pdb=" O PRO D 489 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 514 Processing helix chain 'D' and resid 522 through 550 removed outlier: 3.723A pdb=" N LYS D 529 " --> pdb=" O GLN D 525 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU D 549 " --> pdb=" O ASP D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 570 No H-bonds generated for 'chain 'D' and resid 567 through 570' Processing helix chain 'D' and resid 581 through 591 Processing helix chain 'D' and resid 605 through 611 Processing helix chain 'D' and resid 639 through 648 removed outlier: 3.674A pdb=" N GLU D 647 " --> pdb=" O LYS D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 662 removed outlier: 4.060A pdb=" N ALA D 661 " --> pdb=" O ASN D 657 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N CYS D 662 " --> pdb=" O GLN D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 668 No H-bonds generated for 'chain 'D' and resid 666 through 668' Processing helix chain 'D' and resid 676 through 679 No H-bonds generated for 'chain 'D' and resid 676 through 679' Processing helix chain 'D' and resid 683 through 685 No H-bonds generated for 'chain 'D' and resid 683 through 685' Processing helix chain 'D' and resid 688 through 701 Processing helix chain 'D' and resid 717 through 730 Processing helix chain 'E' and resid 15 through 22 removed outlier: 3.952A pdb=" N THR E 19 " --> pdb=" O ASP E 16 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE E 22 " --> pdb=" O THR E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 26 No H-bonds generated for 'chain 'E' and resid 24 through 26' Processing helix chain 'E' and resid 36 through 46 removed outlier: 3.711A pdb=" N GLY E 46 " --> pdb=" O LYS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 69 removed outlier: 5.046A pdb=" N THR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 89 removed outlier: 3.539A pdb=" N ALA E 75 " --> pdb=" O PRO E 72 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 77 " --> pdb=" O TYR E 74 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA E 79 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA E 82 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL E 83 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER E 84 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS E 88 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 102 Processing helix chain 'E' and resid 118 through 126 Processing helix chain 'E' and resid 128 through 134 removed outlier: 3.604A pdb=" N SER E 133 " --> pdb=" O ASP E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 removed outlier: 3.725A pdb=" N ASP E 140 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE E 141 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 154 removed outlier: 3.941A pdb=" N SER E 154 " --> pdb=" O THR E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 178 Processing helix chain 'E' and resid 184 through 194 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 228 through 243 Processing helix chain 'E' and resid 273 through 285 Processing helix chain 'E' and resid 306 through 312 removed outlier: 4.518A pdb=" N PHE E 309 " --> pdb=" O LEU E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 323 No H-bonds generated for 'chain 'E' and resid 321 through 323' Processing helix chain 'E' and resid 336 through 343 Processing helix chain 'E' and resid 365 through 376 Processing helix chain 'E' and resid 386 through 399 Processing helix chain 'E' and resid 408 through 413 Processing helix chain 'E' and resid 464 through 480 removed outlier: 3.769A pdb=" N GLU E 468 " --> pdb=" O LYS E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 497 removed outlier: 4.175A pdb=" N LEU E 493 " --> pdb=" O PRO E 489 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 514 Processing helix chain 'E' and resid 522 through 550 removed outlier: 3.722A pdb=" N LYS E 529 " --> pdb=" O GLN E 525 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 570 No H-bonds generated for 'chain 'E' and resid 567 through 570' Processing helix chain 'E' and resid 581 through 591 Processing helix chain 'E' and resid 605 through 611 Processing helix chain 'E' and resid 639 through 648 removed outlier: 3.673A pdb=" N GLU E 647 " --> pdb=" O LYS E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 662 removed outlier: 4.060A pdb=" N ALA E 661 " --> pdb=" O ASN E 657 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N CYS E 662 " --> pdb=" O GLN E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 666 through 668 No H-bonds generated for 'chain 'E' and resid 666 through 668' Processing helix chain 'E' and resid 676 through 679 No H-bonds generated for 'chain 'E' and resid 676 through 679' Processing helix chain 'E' and resid 683 through 685 No H-bonds generated for 'chain 'E' and resid 683 through 685' Processing helix chain 'E' and resid 688 through 701 Processing helix chain 'E' and resid 717 through 730 Processing helix chain 'F' and resid 15 through 22 removed outlier: 3.951A pdb=" N THR F 19 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE F 22 " --> pdb=" O THR F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 26 No H-bonds generated for 'chain 'F' and resid 24 through 26' Processing helix chain 'F' and resid 36 through 46 removed outlier: 3.709A pdb=" N GLY F 46 " --> pdb=" O LYS F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 69 removed outlier: 5.046A pdb=" N THR F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 89 removed outlier: 3.538A pdb=" N ALA F 75 " --> pdb=" O PRO F 72 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F 77 " --> pdb=" O TYR F 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA F 79 " --> pdb=" O ILE F 76 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 82 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL F 83 " --> pdb=" O ARG F 80 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER F 84 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS F 88 " --> pdb=" O ASN F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 102 Processing helix chain 'F' and resid 118 through 126 Processing helix chain 'F' and resid 128 through 134 removed outlier: 3.603A pdb=" N SER F 133 " --> pdb=" O ASP F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 removed outlier: 3.726A pdb=" N ASP F 140 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE F 141 " --> pdb=" O ASP F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 removed outlier: 3.940A pdb=" N SER F 154 " --> pdb=" O THR F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 178 Processing helix chain 'F' and resid 184 through 194 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 228 through 243 Processing helix chain 'F' and resid 273 through 285 Processing helix chain 'F' and resid 306 through 312 removed outlier: 4.518A pdb=" N PHE F 309 " --> pdb=" O LEU F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 323 No H-bonds generated for 'chain 'F' and resid 321 through 323' Processing helix chain 'F' and resid 336 through 343 Processing helix chain 'F' and resid 365 through 376 Processing helix chain 'F' and resid 386 through 399 Processing helix chain 'F' and resid 408 through 413 Processing helix chain 'F' and resid 464 through 480 removed outlier: 3.768A pdb=" N GLU F 468 " --> pdb=" O LYS F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 497 removed outlier: 4.174A pdb=" N LEU F 493 " --> pdb=" O PRO F 489 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER F 494 " --> pdb=" O GLU F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 514 Processing helix chain 'F' and resid 522 through 550 removed outlier: 3.721A pdb=" N LYS F 529 " --> pdb=" O GLN F 525 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU F 549 " --> pdb=" O ASP F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 567 through 570 No H-bonds generated for 'chain 'F' and resid 567 through 570' Processing helix chain 'F' and resid 581 through 591 Processing helix chain 'F' and resid 605 through 611 Processing helix chain 'F' and resid 639 through 648 removed outlier: 3.674A pdb=" N GLU F 647 " --> pdb=" O LYS F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 662 removed outlier: 4.060A pdb=" N ALA F 661 " --> pdb=" O ASN F 657 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N CYS F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 666 through 668 No H-bonds generated for 'chain 'F' and resid 666 through 668' Processing helix chain 'F' and resid 676 through 679 No H-bonds generated for 'chain 'F' and resid 676 through 679' Processing helix chain 'F' and resid 683 through 685 No H-bonds generated for 'chain 'F' and resid 683 through 685' Processing helix chain 'F' and resid 688 through 701 Processing helix chain 'F' and resid 717 through 730 Processing sheet with id= A, first strand: chain 'A' and resid 2 through 5 Processing sheet with id= B, first strand: chain 'A' and resid 198 through 200 Processing sheet with id= C, first strand: chain 'A' and resid 442 through 444 removed outlier: 6.651A pdb=" N PHE A 329 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU A 301 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA A 331 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR A 404 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE A 334 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU A 406 " --> pdb=" O ILE A 334 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 347 through 350 Processing sheet with id= E, first strand: chain 'A' and resid 624 through 629 Processing sheet with id= F, first strand: chain 'A' and resid 709 through 711 removed outlier: 5.576A pdb=" N TYR A 738 " --> pdb=" O ILE A 710 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= H, first strand: chain 'B' and resid 198 through 200 Processing sheet with id= I, first strand: chain 'B' and resid 442 through 444 removed outlier: 6.651A pdb=" N PHE B 329 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU B 301 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA B 331 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR B 404 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE B 334 " --> pdb=" O TYR B 404 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU B 406 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 347 through 350 Processing sheet with id= K, first strand: chain 'B' and resid 624 through 629 Processing sheet with id= L, first strand: chain 'B' and resid 709 through 711 removed outlier: 5.577A pdb=" N TYR B 738 " --> pdb=" O ILE B 710 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 2 through 5 Processing sheet with id= N, first strand: chain 'C' and resid 198 through 200 Processing sheet with id= O, first strand: chain 'C' and resid 442 through 444 removed outlier: 6.652A pdb=" N PHE C 329 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU C 301 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA C 331 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR C 404 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE C 334 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU C 406 " --> pdb=" O ILE C 334 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 347 through 350 Processing sheet with id= Q, first strand: chain 'C' and resid 624 through 629 Processing sheet with id= R, first strand: chain 'C' and resid 709 through 711 removed outlier: 5.576A pdb=" N TYR C 738 " --> pdb=" O ILE C 710 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 2 through 5 Processing sheet with id= T, first strand: chain 'D' and resid 198 through 200 Processing sheet with id= U, first strand: chain 'D' and resid 442 through 444 removed outlier: 6.651A pdb=" N PHE D 329 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU D 301 " --> pdb=" O PHE D 329 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA D 331 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR D 404 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE D 334 " --> pdb=" O TYR D 404 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU D 406 " --> pdb=" O ILE D 334 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 347 through 350 Processing sheet with id= W, first strand: chain 'D' and resid 624 through 629 Processing sheet with id= X, first strand: chain 'D' and resid 709 through 711 removed outlier: 5.576A pdb=" N TYR D 738 " --> pdb=" O ILE D 710 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 2 through 5 Processing sheet with id= Z, first strand: chain 'E' and resid 198 through 200 Processing sheet with id= AA, first strand: chain 'E' and resid 442 through 444 removed outlier: 6.652A pdb=" N PHE E 329 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU E 301 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA E 331 " --> pdb=" O LEU E 301 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR E 404 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE E 334 " --> pdb=" O TYR E 404 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU E 406 " --> pdb=" O ILE E 334 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 347 through 350 Processing sheet with id= AC, first strand: chain 'E' and resid 624 through 629 Processing sheet with id= AD, first strand: chain 'E' and resid 709 through 711 removed outlier: 5.577A pdb=" N TYR E 738 " --> pdb=" O ILE E 710 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'F' and resid 2 through 5 Processing sheet with id= AF, first strand: chain 'F' and resid 198 through 200 Processing sheet with id= AG, first strand: chain 'F' and resid 442 through 444 removed outlier: 6.650A pdb=" N PHE F 329 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU F 301 " --> pdb=" O PHE F 329 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA F 331 " --> pdb=" O LEU F 301 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR F 404 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE F 334 " --> pdb=" O TYR F 404 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU F 406 " --> pdb=" O ILE F 334 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 347 through 350 Processing sheet with id= AI, first strand: chain 'F' and resid 624 through 629 Processing sheet with id= AJ, first strand: chain 'F' and resid 709 through 711 removed outlier: 5.576A pdb=" N TYR F 738 " --> pdb=" O ILE F 710 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ 1308 hydrogen bonds defined for protein. 3564 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.02 Time building geometry restraints manager: 15.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7868 1.33 - 1.45: 8201 1.45 - 1.57: 20591 1.57 - 1.69: 78 1.69 - 1.81: 330 Bond restraints: 37068 Sorted by residual: bond pdb=" C3' CDP B 805 " pdb=" C4' CDP B 805 " ideal model delta sigma weight residual 1.305 1.510 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C3' CDP D 805 " pdb=" C4' CDP D 805 " ideal model delta sigma weight residual 1.305 1.509 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C3' CDP F 805 " pdb=" C4' CDP F 805 " ideal model delta sigma weight residual 1.305 1.508 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C3' CDP E 805 " pdb=" C4' CDP E 805 " ideal model delta sigma weight residual 1.305 1.508 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C3' CDP A 805 " pdb=" C4' CDP A 805 " ideal model delta sigma weight residual 1.305 1.507 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 37063 not shown) Histogram of bond angle deviations from ideal: 97.59 - 104.92: 710 104.92 - 112.25: 18320 112.25 - 119.57: 13500 119.57 - 126.90: 17314 126.90 - 134.23: 466 Bond angle restraints: 50310 Sorted by residual: angle pdb=" PA DTP F 801 " pdb=" O3A DTP F 801 " pdb=" PB DTP F 801 " ideal model delta sigma weight residual 136.83 113.18 23.65 1.00e+00 1.00e+00 5.59e+02 angle pdb=" PA DTP D 801 " pdb=" O3A DTP D 801 " pdb=" PB DTP D 801 " ideal model delta sigma weight residual 136.83 113.39 23.44 1.00e+00 1.00e+00 5.49e+02 angle pdb=" PB DTP B 803 " pdb=" O3B DTP B 803 " pdb=" PG DTP B 803 " ideal model delta sigma weight residual 139.87 116.90 22.97 1.00e+00 1.00e+00 5.28e+02 angle pdb=" PA DTP B 801 " pdb=" O3A DTP B 801 " pdb=" PB DTP B 801 " ideal model delta sigma weight residual 136.83 114.09 22.74 1.00e+00 1.00e+00 5.17e+02 angle pdb=" PB DTP E 803 " pdb=" O3B DTP E 803 " pdb=" PG DTP E 803 " ideal model delta sigma weight residual 139.87 117.14 22.73 1.00e+00 1.00e+00 5.17e+02 ... (remaining 50305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.59: 22110 28.59 - 57.18: 277 57.18 - 85.78: 52 85.78 - 114.37: 7 114.37 - 142.96: 6 Dihedral angle restraints: 22452 sinusoidal: 9330 harmonic: 13122 Sorted by residual: dihedral pdb=" CA GLU A 615 " pdb=" C GLU A 615 " pdb=" N SER A 616 " pdb=" CA SER A 616 " ideal model delta harmonic sigma weight residual -180.00 -142.28 -37.72 0 5.00e+00 4.00e-02 5.69e+01 dihedral pdb=" CA GLU D 615 " pdb=" C GLU D 615 " pdb=" N SER D 616 " pdb=" CA SER D 616 " ideal model delta harmonic sigma weight residual -180.00 -142.29 -37.71 0 5.00e+00 4.00e-02 5.69e+01 dihedral pdb=" CA GLU E 615 " pdb=" C GLU E 615 " pdb=" N SER E 616 " pdb=" CA SER E 616 " ideal model delta harmonic sigma weight residual -180.00 -142.29 -37.71 0 5.00e+00 4.00e-02 5.69e+01 ... (remaining 22449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3589 0.049 - 0.097: 1463 0.097 - 0.146: 415 0.146 - 0.194: 43 0.194 - 0.243: 16 Chirality restraints: 5526 Sorted by residual: chirality pdb=" CB ILE D 659 " pdb=" CA ILE D 659 " pdb=" CG1 ILE D 659 " pdb=" CG2 ILE D 659 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE A 659 " pdb=" CA ILE A 659 " pdb=" CG1 ILE A 659 " pdb=" CG2 ILE A 659 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE C 659 " pdb=" CA ILE C 659 " pdb=" CG1 ILE C 659 " pdb=" CG2 ILE C 659 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 5523 not shown) Planarity restraints: 6336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 669 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.06e+01 pdb=" N PRO B 670 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 670 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 670 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 669 " -0.053 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO F 670 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO F 670 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 670 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 669 " -0.053 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO A 670 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " -0.045 5.00e-02 4.00e+02 ... (remaining 6333 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 460 2.60 - 3.17: 30621 3.17 - 3.75: 55145 3.75 - 4.32: 81016 4.32 - 4.90: 129568 Nonbonded interactions: 296810 Sorted by model distance: nonbonded pdb=" O2B DTP F 803 " pdb="MG MG F 804 " model vdw 2.024 2.170 nonbonded pdb=" O2B DTP D 803 " pdb="MG MG D 804 " model vdw 2.025 2.170 nonbonded pdb=" O1B DTP A 803 " pdb="MG MG A 804 " model vdw 2.028 2.170 nonbonded pdb=" O1B DTP E 803 " pdb="MG MG E 804 " model vdw 2.029 2.170 nonbonded pdb=" O1B DTP C 803 " pdb="MG MG C 804 " model vdw 2.034 2.170 ... (remaining 296805 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.990 Check model and map are aligned: 0.630 Set scattering table: 0.380 Process input model: 97.370 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.009 0.205 37068 Z= 0.601 Angle : 1.086 23.651 50310 Z= 0.735 Chirality : 0.055 0.243 5526 Planarity : 0.007 0.082 6336 Dihedral : 11.217 142.960 14028 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.10), residues: 4458 helix: -3.11 (0.07), residues: 2160 sheet: -1.70 (0.26), residues: 336 loop : -2.04 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 390 HIS 0.008 0.002 HIS B 724 PHE 0.021 0.003 PHE D 198 TYR 0.041 0.003 TYR F 300 ARG 0.007 0.001 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1097 time to evaluate : 4.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7415 (mtt) cc_final: 0.6769 (mtt) REVERT: A 26 CYS cc_start: 0.6897 (m) cc_final: 0.6642 (m) REVERT: A 62 GLU cc_start: 0.8220 (tt0) cc_final: 0.7913 (tm-30) REVERT: A 149 LYS cc_start: 0.8057 (tttt) cc_final: 0.7775 (tppt) REVERT: A 151 LEU cc_start: 0.8821 (tp) cc_final: 0.8548 (tt) REVERT: A 170 MET cc_start: 0.8071 (ttp) cc_final: 0.7818 (ttm) REVERT: A 175 SER cc_start: 0.8797 (m) cc_final: 0.8531 (t) REVERT: A 233 ASP cc_start: 0.7894 (m-30) cc_final: 0.7214 (m-30) REVERT: A 286 VAL cc_start: 0.8891 (t) cc_final: 0.8667 (m) REVERT: A 423 ILE cc_start: 0.9574 (mt) cc_final: 0.9311 (mm) REVERT: A 425 CYS cc_start: 0.8749 (p) cc_final: 0.8497 (p) REVERT: A 429 CYS cc_start: 0.7767 (m) cc_final: 0.7482 (m) REVERT: A 432 ILE cc_start: 0.8370 (mm) cc_final: 0.7872 (tp) REVERT: A 443 VAL cc_start: 0.9094 (t) cc_final: 0.8816 (t) REVERT: A 625 TYR cc_start: 0.7436 (p90) cc_final: 0.7209 (p90) REVERT: A 655 MET cc_start: 0.8206 (tpt) cc_final: 0.7722 (tpp) REVERT: A 677 LYS cc_start: 0.7748 (mttt) cc_final: 0.6948 (tptt) REVERT: A 708 LEU cc_start: 0.7971 (tp) cc_final: 0.7719 (mp) REVERT: A 739 LEU cc_start: 0.8703 (tp) cc_final: 0.8361 (tp) REVERT: B 149 LYS cc_start: 0.8184 (tttt) cc_final: 0.7686 (tppt) REVERT: B 172 MET cc_start: 0.7869 (tpp) cc_final: 0.7653 (tpp) REVERT: B 175 SER cc_start: 0.8865 (m) cc_final: 0.8579 (t) REVERT: B 189 THR cc_start: 0.7987 (m) cc_final: 0.7509 (m) REVERT: B 253 SER cc_start: 0.9027 (m) cc_final: 0.8826 (t) REVERT: B 433 VAL cc_start: 0.8845 (t) cc_final: 0.8585 (m) REVERT: B 643 LYS cc_start: 0.9113 (tttt) cc_final: 0.8911 (ttmm) REVERT: B 694 MET cc_start: 0.8004 (mtp) cc_final: 0.7748 (mtt) REVERT: B 708 LEU cc_start: 0.8228 (tp) cc_final: 0.7977 (mp) REVERT: C 16 ASP cc_start: 0.7069 (m-30) cc_final: 0.6605 (t0) REVERT: C 26 CYS cc_start: 0.7413 (m) cc_final: 0.7152 (m) REVERT: C 38 GLN cc_start: 0.8896 (mt0) cc_final: 0.8507 (mt0) REVERT: C 52 THR cc_start: 0.8699 (m) cc_final: 0.8339 (p) REVERT: C 223 MET cc_start: 0.8531 (mmt) cc_final: 0.8327 (mmm) REVERT: C 328 LEU cc_start: 0.8796 (mt) cc_final: 0.8523 (tp) REVERT: C 361 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7763 (tm-30) REVERT: C 432 ILE cc_start: 0.8527 (mm) cc_final: 0.7695 (tp) REVERT: C 433 VAL cc_start: 0.8855 (t) cc_final: 0.8644 (m) REVERT: C 438 LYS cc_start: 0.8886 (mttt) cc_final: 0.8297 (mptt) REVERT: C 443 VAL cc_start: 0.9114 (t) cc_final: 0.8838 (t) REVERT: C 444 CYS cc_start: 0.7424 (t) cc_final: 0.7134 (t) REVERT: C 493 LEU cc_start: 0.7553 (tp) cc_final: 0.7351 (mt) REVERT: C 497 ARG cc_start: 0.7958 (mtp180) cc_final: 0.7700 (mtp85) REVERT: C 515 MET cc_start: 0.7855 (mmm) cc_final: 0.7569 (tpp) REVERT: C 655 MET cc_start: 0.8485 (tpt) cc_final: 0.7920 (tpp) REVERT: C 677 LYS cc_start: 0.7263 (mttt) cc_final: 0.6630 (tptt) REVERT: C 694 MET cc_start: 0.7993 (mtp) cc_final: 0.7755 (mtt) REVERT: C 708 LEU cc_start: 0.7980 (tp) cc_final: 0.7495 (mt) REVERT: C 726 TYR cc_start: 0.8771 (t80) cc_final: 0.7687 (t80) REVERT: C 739 LEU cc_start: 0.8657 (tp) cc_final: 0.8369 (tp) REVERT: D 38 GLN cc_start: 0.8774 (mt0) cc_final: 0.8492 (mt0) REVERT: D 149 LYS cc_start: 0.8250 (tttt) cc_final: 0.7996 (tppt) REVERT: D 157 LEU cc_start: 0.9067 (mt) cc_final: 0.8797 (mp) REVERT: D 165 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7443 (mt-10) REVERT: D 175 SER cc_start: 0.8426 (m) cc_final: 0.8181 (t) REVERT: D 223 MET cc_start: 0.8397 (mmt) cc_final: 0.8128 (mmt) REVERT: D 429 CYS cc_start: 0.8098 (m) cc_final: 0.7834 (m) REVERT: D 432 ILE cc_start: 0.8563 (mm) cc_final: 0.7799 (tp) REVERT: D 433 VAL cc_start: 0.8880 (t) cc_final: 0.8623 (m) REVERT: D 438 LYS cc_start: 0.8922 (mttt) cc_final: 0.8365 (mptt) REVERT: D 443 VAL cc_start: 0.9139 (t) cc_final: 0.8735 (t) REVERT: D 444 CYS cc_start: 0.7475 (t) cc_final: 0.7171 (t) REVERT: D 497 ARG cc_start: 0.8112 (mtp180) cc_final: 0.7732 (mtp85) REVERT: D 515 MET cc_start: 0.7907 (mmm) cc_final: 0.7473 (tpp) REVERT: D 655 MET cc_start: 0.8511 (tpt) cc_final: 0.7991 (tpp) REVERT: D 694 MET cc_start: 0.8152 (mtp) cc_final: 0.7888 (mtt) REVERT: D 708 LEU cc_start: 0.7991 (tp) cc_final: 0.7363 (mp) REVERT: D 739 LEU cc_start: 0.8685 (tp) cc_final: 0.8394 (tp) REVERT: E 149 LYS cc_start: 0.8198 (tttt) cc_final: 0.7920 (tppt) REVERT: E 175 SER cc_start: 0.8864 (m) cc_final: 0.8587 (t) REVERT: E 189 THR cc_start: 0.7873 (m) cc_final: 0.7401 (m) REVERT: E 433 VAL cc_start: 0.8944 (t) cc_final: 0.8647 (m) REVERT: E 677 LYS cc_start: 0.7409 (mttt) cc_final: 0.7130 (tptt) REVERT: E 694 MET cc_start: 0.7932 (mtp) cc_final: 0.7687 (mtt) REVERT: E 739 LEU cc_start: 0.8560 (tp) cc_final: 0.8329 (tp) REVERT: F 1 MET cc_start: 0.7338 (mtt) cc_final: 0.6670 (mtt) REVERT: F 26 CYS cc_start: 0.7101 (m) cc_final: 0.6766 (m) REVERT: F 39 ILE cc_start: 0.9217 (mt) cc_final: 0.8957 (pt) REVERT: F 411 CYS cc_start: 0.8321 (m) cc_final: 0.8091 (m) REVERT: F 423 ILE cc_start: 0.9584 (mt) cc_final: 0.9321 (mm) REVERT: F 432 ILE cc_start: 0.8429 (mm) cc_final: 0.8018 (tp) REVERT: F 534 THR cc_start: 0.8748 (m) cc_final: 0.8438 (p) REVERT: F 625 TYR cc_start: 0.7481 (p90) cc_final: 0.7280 (p90) REVERT: F 655 MET cc_start: 0.8253 (tpt) cc_final: 0.7757 (tpp) REVERT: F 694 MET cc_start: 0.7870 (mtp) cc_final: 0.7615 (mtt) REVERT: F 708 LEU cc_start: 0.8101 (tp) cc_final: 0.7793 (mp) REVERT: F 726 TYR cc_start: 0.8842 (t80) cc_final: 0.7787 (t80) REVERT: F 739 LEU cc_start: 0.8574 (tp) cc_final: 0.8294 (tp) outliers start: 0 outliers final: 0 residues processed: 1097 average time/residue: 0.5313 time to fit residues: 920.1532 Evaluate side-chains 637 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 637 time to evaluate : 4.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 0.9990 chunk 336 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 348 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 211 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 403 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 688 GLN B 144 ASN ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 418 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN B 688 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 567 GLN C 635 GLN C 657 ASN C 688 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 ASN D 567 GLN D 688 GLN E 354 ASN E 418 GLN ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 GLN E 688 GLN E 706 GLN ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 ASN F 354 ASN F 635 GLN F 688 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37068 Z= 0.176 Angle : 0.572 8.979 50310 Z= 0.300 Chirality : 0.043 0.164 5526 Planarity : 0.005 0.055 6336 Dihedral : 10.705 142.488 5304 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.82 % Allowed : 8.73 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.98 (0.11), residues: 4458 helix: -1.03 (0.10), residues: 2208 sheet: -0.89 (0.27), residues: 306 loop : -1.61 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 571 HIS 0.003 0.001 HIS C 724 PHE 0.021 0.001 PHE D 519 TYR 0.024 0.002 TYR A 536 ARG 0.007 0.000 ARG E 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 696 time to evaluate : 4.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7094 (ttt180) cc_final: 0.6224 (mmt180) REVERT: A 62 GLU cc_start: 0.8046 (tt0) cc_final: 0.7836 (tm-30) REVERT: A 170 MET cc_start: 0.8047 (ttp) cc_final: 0.7755 (ttm) REVERT: A 307 ASP cc_start: 0.7814 (t0) cc_final: 0.7599 (t0) REVERT: A 368 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7667 (tp30) REVERT: A 405 MET cc_start: 0.7865 (mtp) cc_final: 0.7569 (mtp) REVERT: A 416 ASN cc_start: 0.7499 (t0) cc_final: 0.7237 (t0) REVERT: A 423 ILE cc_start: 0.9532 (mt) cc_final: 0.9288 (mm) REVERT: A 432 ILE cc_start: 0.8153 (mm) cc_final: 0.7828 (tp) REVERT: A 655 MET cc_start: 0.8314 (tpt) cc_final: 0.7971 (tpp) REVERT: A 677 LYS cc_start: 0.7668 (mttt) cc_final: 0.7024 (tptt) REVERT: A 681 LYS cc_start: 0.8289 (mtpt) cc_final: 0.7981 (mtpp) REVERT: B 21 ARG cc_start: 0.6824 (ttt180) cc_final: 0.6015 (mmt-90) REVERT: B 23 GLN cc_start: 0.7305 (pt0) cc_final: 0.7041 (pt0) REVERT: B 57 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7812 (m-30) REVERT: B 98 MET cc_start: 0.8800 (mmp) cc_final: 0.8503 (mmm) REVERT: B 189 THR cc_start: 0.8528 (m) cc_final: 0.8212 (m) REVERT: B 360 ASP cc_start: 0.7856 (p0) cc_final: 0.7440 (p0) REVERT: B 405 MET cc_start: 0.7781 (mtp) cc_final: 0.7508 (mtp) REVERT: B 677 LYS cc_start: 0.7627 (mttt) cc_final: 0.7189 (tptt) REVERT: B 681 LYS cc_start: 0.8244 (mtpt) cc_final: 0.7420 (ptmt) REVERT: B 694 MET cc_start: 0.7928 (mtp) cc_final: 0.7653 (mtt) REVERT: B 708 LEU cc_start: 0.8079 (tp) cc_final: 0.7864 (mp) REVERT: C 14 MET cc_start: 0.7588 (mpp) cc_final: 0.7225 (mpp) REVERT: C 21 ARG cc_start: 0.7064 (ttt180) cc_final: 0.6369 (mmt180) REVERT: C 89 GLU cc_start: 0.8349 (tp30) cc_final: 0.8108 (tm-30) REVERT: C 152 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7912 (tm-30) REVERT: C 307 ASP cc_start: 0.7981 (t0) cc_final: 0.7688 (t0) REVERT: C 320 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8576 (mtmt) REVERT: C 432 ILE cc_start: 0.8472 (mm) cc_final: 0.7448 (tp) REVERT: C 490 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8191 (mt-10) REVERT: C 493 LEU cc_start: 0.7536 (tp) cc_final: 0.7299 (mt) REVERT: C 515 MET cc_start: 0.7682 (mmm) cc_final: 0.7465 (mmt) REVERT: C 545 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: C 634 PHE cc_start: 0.6594 (p90) cc_final: 0.6361 (p90) REVERT: C 655 MET cc_start: 0.8284 (tpt) cc_final: 0.7888 (tpp) REVERT: C 677 LYS cc_start: 0.7120 (mttt) cc_final: 0.6774 (tptt) REVERT: C 681 LYS cc_start: 0.8330 (mtpt) cc_final: 0.7347 (ptmt) REVERT: C 694 MET cc_start: 0.8017 (mtp) cc_final: 0.7724 (mtt) REVERT: C 708 LEU cc_start: 0.7960 (tp) cc_final: 0.7610 (mp) REVERT: D 1 MET cc_start: 0.7725 (mtm) cc_final: 0.7461 (mtm) REVERT: D 21 ARG cc_start: 0.6636 (ttt180) cc_final: 0.5899 (mmt180) REVERT: D 57 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: D 149 LYS cc_start: 0.8095 (tttt) cc_final: 0.7869 (tppt) REVERT: D 152 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8217 (tm-30) REVERT: D 225 ASP cc_start: 0.8117 (t0) cc_final: 0.7876 (t70) REVERT: D 368 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7590 (tp30) REVERT: D 405 MET cc_start: 0.8084 (mtp) cc_final: 0.7867 (mtp) REVERT: D 429 CYS cc_start: 0.8407 (m) cc_final: 0.8193 (m) REVERT: D 515 MET cc_start: 0.7840 (mmm) cc_final: 0.7414 (mmt) REVERT: D 655 MET cc_start: 0.8329 (tpt) cc_final: 0.7945 (tpp) REVERT: D 677 LYS cc_start: 0.7291 (mttt) cc_final: 0.6804 (tptt) REVERT: D 681 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7339 (ptmt) REVERT: D 693 LYS cc_start: 0.9077 (tptm) cc_final: 0.8875 (tptm) REVERT: D 694 MET cc_start: 0.8158 (mtp) cc_final: 0.7876 (mtt) REVERT: D 708 LEU cc_start: 0.7959 (tp) cc_final: 0.7509 (mp) REVERT: D 726 TYR cc_start: 0.8784 (t80) cc_final: 0.8483 (t80) REVERT: E 21 ARG cc_start: 0.6885 (ttt180) cc_final: 0.5969 (mmt-90) REVERT: E 57 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: E 98 MET cc_start: 0.8825 (mmp) cc_final: 0.8455 (mmm) REVERT: E 149 LYS cc_start: 0.8028 (tttt) cc_final: 0.7751 (tppt) REVERT: E 152 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8119 (tm-30) REVERT: E 189 THR cc_start: 0.8367 (m) cc_final: 0.8052 (m) REVERT: E 405 MET cc_start: 0.7706 (mtp) cc_final: 0.7467 (mtp) REVERT: E 418 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6836 (mm110) REVERT: E 423 ILE cc_start: 0.9464 (mt) cc_final: 0.9260 (mm) REVERT: E 677 LYS cc_start: 0.7492 (mttt) cc_final: 0.7240 (tptt) REVERT: E 681 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7590 (ptmt) REVERT: E 694 MET cc_start: 0.7928 (mtp) cc_final: 0.7705 (mtt) REVERT: E 702 ILE cc_start: 0.8421 (mt) cc_final: 0.8153 (mt) REVERT: E 738 TYR cc_start: 0.8051 (m-80) cc_final: 0.7438 (m-80) REVERT: F 21 ARG cc_start: 0.6888 (ttt180) cc_final: 0.6249 (mmt180) REVERT: F 368 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7702 (tp30) REVERT: F 416 ASN cc_start: 0.7454 (t0) cc_final: 0.7242 (t0) REVERT: F 423 ILE cc_start: 0.9536 (mt) cc_final: 0.9286 (mm) REVERT: F 534 THR cc_start: 0.8758 (m) cc_final: 0.8456 (p) REVERT: F 655 MET cc_start: 0.8159 (tpt) cc_final: 0.7764 (tpp) REVERT: F 677 LYS cc_start: 0.7690 (mttt) cc_final: 0.7067 (tptt) REVERT: F 680 TYR cc_start: 0.8311 (m-80) cc_final: 0.7927 (m-80) REVERT: F 681 LYS cc_start: 0.8127 (mtpt) cc_final: 0.7839 (mtpp) REVERT: F 694 MET cc_start: 0.7790 (mtp) cc_final: 0.7560 (mtt) REVERT: F 708 LEU cc_start: 0.7949 (tp) cc_final: 0.7693 (mp) outliers start: 71 outliers final: 32 residues processed: 745 average time/residue: 0.4912 time to fit residues: 590.1744 Evaluate side-chains 585 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 548 time to evaluate : 4.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 418 GLN Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 624 ILE Chi-restraints excluded: chain F residue 627 ARG Chi-restraints excluded: chain F residue 646 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 335 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 403 optimal weight: 3.9990 chunk 436 optimal weight: 3.9990 chunk 359 optimal weight: 5.9990 chunk 400 optimal weight: 1.9990 chunk 137 optimal weight: 0.0170 chunk 324 optimal weight: 0.6980 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 418 GLN ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 GLN F 38 GLN ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37068 Z= 0.175 Angle : 0.549 8.967 50310 Z= 0.285 Chirality : 0.043 0.166 5526 Planarity : 0.004 0.045 6336 Dihedral : 8.932 115.049 5304 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.46 % Allowed : 10.16 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.16 (0.12), residues: 4458 helix: -0.25 (0.11), residues: 2250 sheet: -0.15 (0.33), residues: 246 loop : -1.39 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 571 HIS 0.005 0.001 HIS F 724 PHE 0.021 0.001 PHE A 519 TYR 0.023 0.001 TYR D 536 ARG 0.006 0.000 ARG F 698 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 612 time to evaluate : 4.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7167 (ttt180) cc_final: 0.6217 (mmt180) REVERT: A 89 GLU cc_start: 0.8209 (tp30) cc_final: 0.7824 (tm-30) REVERT: A 170 MET cc_start: 0.8078 (ttp) cc_final: 0.7822 (ttm) REVERT: A 196 ARG cc_start: 0.8035 (mtp-110) cc_final: 0.7762 (mtp-110) REVERT: A 250 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8653 (p) REVERT: A 307 ASP cc_start: 0.8046 (t0) cc_final: 0.7706 (t0) REVERT: A 405 MET cc_start: 0.7812 (mtp) cc_final: 0.7478 (mtp) REVERT: A 416 ASN cc_start: 0.7770 (t0) cc_final: 0.7499 (t0) REVERT: A 423 ILE cc_start: 0.9516 (mt) cc_final: 0.9264 (mm) REVERT: A 432 ILE cc_start: 0.8183 (mm) cc_final: 0.7894 (tp) REVERT: A 541 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7453 (tm-30) REVERT: A 677 LYS cc_start: 0.7653 (mttt) cc_final: 0.6993 (tptt) REVERT: A 681 LYS cc_start: 0.8351 (mtpt) cc_final: 0.7888 (mtpp) REVERT: A 708 LEU cc_start: 0.7709 (mp) cc_final: 0.7469 (mp) REVERT: A 726 TYR cc_start: 0.8736 (t80) cc_final: 0.8148 (t80) REVERT: B 21 ARG cc_start: 0.6919 (ttt180) cc_final: 0.6092 (mmt-90) REVERT: B 57 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: B 98 MET cc_start: 0.8785 (mmp) cc_final: 0.8541 (mmm) REVERT: B 189 THR cc_start: 0.8510 (m) cc_final: 0.8190 (m) REVERT: B 339 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7040 (mpp) REVERT: B 405 MET cc_start: 0.7754 (mtp) cc_final: 0.7443 (mtp) REVERT: B 602 MET cc_start: 0.8448 (pmm) cc_final: 0.8018 (pmm) REVERT: B 677 LYS cc_start: 0.7669 (mttt) cc_final: 0.7202 (tptt) REVERT: B 681 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7452 (ptpt) REVERT: B 694 MET cc_start: 0.7938 (mtp) cc_final: 0.7662 (mtt) REVERT: C 14 MET cc_start: 0.7501 (mpp) cc_final: 0.7113 (mpp) REVERT: C 21 ARG cc_start: 0.6907 (ttt180) cc_final: 0.6324 (mmt180) REVERT: C 41 MET cc_start: 0.7850 (ttm) cc_final: 0.7575 (mtp) REVERT: C 89 GLU cc_start: 0.8311 (tp30) cc_final: 0.8067 (tm-30) REVERT: C 149 LYS cc_start: 0.8000 (tttt) cc_final: 0.7748 (tppt) REVERT: C 152 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7891 (tm-30) REVERT: C 307 ASP cc_start: 0.7933 (t0) cc_final: 0.7617 (t0) REVERT: C 320 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8588 (mtmt) REVERT: C 322 GLU cc_start: 0.8513 (pt0) cc_final: 0.8270 (pt0) REVERT: C 493 LEU cc_start: 0.7555 (tp) cc_final: 0.7304 (mt) REVERT: C 515 MET cc_start: 0.7685 (mmm) cc_final: 0.7449 (mmt) REVERT: C 545 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: C 609 GLN cc_start: 0.8726 (tp-100) cc_final: 0.8432 (tp40) REVERT: C 655 MET cc_start: 0.8515 (tpt) cc_final: 0.8182 (tpp) REVERT: C 677 LYS cc_start: 0.7313 (mttt) cc_final: 0.6790 (tptt) REVERT: C 681 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7807 (mtpt) REVERT: C 694 MET cc_start: 0.8092 (mtp) cc_final: 0.7852 (mtt) REVERT: C 708 LEU cc_start: 0.7975 (tp) cc_final: 0.7644 (mp) REVERT: C 726 TYR cc_start: 0.8497 (t80) cc_final: 0.8145 (t80) REVERT: D 1 MET cc_start: 0.7681 (mtm) cc_final: 0.7408 (mtm) REVERT: D 21 ARG cc_start: 0.6891 (ttt180) cc_final: 0.6062 (mmt180) REVERT: D 57 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.7934 (m-30) REVERT: D 89 GLU cc_start: 0.8247 (tp30) cc_final: 0.7902 (tm-30) REVERT: D 165 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7823 (mt-10) REVERT: D 405 MET cc_start: 0.8073 (mtp) cc_final: 0.7837 (mtp) REVERT: D 416 ASN cc_start: 0.7512 (t0) cc_final: 0.7287 (t0) REVERT: D 515 MET cc_start: 0.7864 (mmm) cc_final: 0.7419 (mmt) REVERT: D 634 PHE cc_start: 0.7011 (p90) cc_final: 0.6653 (p90) REVERT: D 655 MET cc_start: 0.8353 (tpt) cc_final: 0.7902 (tpp) REVERT: D 677 LYS cc_start: 0.7268 (mttt) cc_final: 0.6668 (tptt) REVERT: D 680 TYR cc_start: 0.8123 (m-80) cc_final: 0.7912 (m-80) REVERT: D 681 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7768 (mtpt) REVERT: D 694 MET cc_start: 0.8221 (mtp) cc_final: 0.7967 (mtt) REVERT: D 708 LEU cc_start: 0.8033 (tp) cc_final: 0.7589 (mp) REVERT: D 726 TYR cc_start: 0.8753 (t80) cc_final: 0.7761 (t80) REVERT: E 21 ARG cc_start: 0.6962 (ttt180) cc_final: 0.6235 (mmt-90) REVERT: E 149 LYS cc_start: 0.7984 (tttt) cc_final: 0.7736 (tppt) REVERT: E 152 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8046 (tm-30) REVERT: E 189 THR cc_start: 0.8483 (m) cc_final: 0.8173 (m) REVERT: E 339 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.6816 (mpp) REVERT: E 405 MET cc_start: 0.7654 (mtp) cc_final: 0.7397 (mtp) REVERT: E 602 MET cc_start: 0.8499 (pmm) cc_final: 0.8065 (pmm) REVERT: E 677 LYS cc_start: 0.7441 (mttt) cc_final: 0.7198 (tptt) REVERT: E 681 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7464 (ptpt) REVERT: E 694 MET cc_start: 0.7918 (mtp) cc_final: 0.7688 (mtt) REVERT: F 14 MET cc_start: 0.7464 (mpp) cc_final: 0.7148 (mpp) REVERT: F 21 ARG cc_start: 0.7091 (ttt180) cc_final: 0.6262 (mmt180) REVERT: F 81 ILE cc_start: 0.8634 (tt) cc_final: 0.8427 (tp) REVERT: F 89 GLU cc_start: 0.8113 (tp30) cc_final: 0.7846 (tm-30) REVERT: F 250 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8702 (p) REVERT: F 416 ASN cc_start: 0.7703 (t0) cc_final: 0.7385 (t0) REVERT: F 423 ILE cc_start: 0.9500 (mt) cc_final: 0.9248 (mm) REVERT: F 515 MET cc_start: 0.7707 (tpp) cc_final: 0.7155 (mmt) REVERT: F 534 THR cc_start: 0.8702 (m) cc_final: 0.8372 (p) REVERT: F 655 MET cc_start: 0.8232 (tpt) cc_final: 0.7745 (tpp) REVERT: F 677 LYS cc_start: 0.7810 (mttt) cc_final: 0.7133 (tptt) REVERT: F 680 TYR cc_start: 0.8281 (m-80) cc_final: 0.8043 (m-80) REVERT: F 681 LYS cc_start: 0.8021 (mtpt) cc_final: 0.7704 (mtpp) REVERT: F 694 MET cc_start: 0.7752 (mtp) cc_final: 0.7511 (mtt) REVERT: F 708 LEU cc_start: 0.7944 (tp) cc_final: 0.7701 (mp) REVERT: F 726 TYR cc_start: 0.8562 (t80) cc_final: 0.8158 (t80) outliers start: 96 outliers final: 60 residues processed: 682 average time/residue: 0.4782 time to fit residues: 530.0365 Evaluate side-chains 600 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 533 time to evaluate : 4.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 698 ARG Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 698 ARG Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 533 GLU Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 672 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 0.0050 chunk 303 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 271 optimal weight: 5.9990 chunk 405 optimal weight: 6.9990 chunk 429 optimal weight: 0.0970 chunk 211 optimal weight: 10.0000 chunk 384 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37068 Z= 0.190 Angle : 0.532 9.356 50310 Z= 0.275 Chirality : 0.043 0.172 5526 Planarity : 0.004 0.041 6336 Dihedral : 8.520 117.004 5304 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.84 % Allowed : 11.55 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 4458 helix: 0.24 (0.11), residues: 2214 sheet: 0.02 (0.34), residues: 246 loop : -1.04 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 728 HIS 0.003 0.001 HIS C 724 PHE 0.015 0.001 PHE A 519 TYR 0.021 0.001 TYR F 517 ARG 0.005 0.000 ARG E 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 563 time to evaluate : 3.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7439 (ttt180) cc_final: 0.6435 (mmt180) REVERT: A 23 GLN cc_start: 0.8226 (tt0) cc_final: 0.7867 (pt0) REVERT: A 81 ILE cc_start: 0.8723 (tt) cc_final: 0.8488 (tp) REVERT: A 89 GLU cc_start: 0.8348 (tp30) cc_final: 0.8028 (tm-30) REVERT: A 307 ASP cc_start: 0.8148 (t0) cc_final: 0.7713 (t0) REVERT: A 405 MET cc_start: 0.7878 (mtp) cc_final: 0.7517 (mtp) REVERT: A 416 ASN cc_start: 0.7873 (t0) cc_final: 0.7553 (t0) REVERT: A 423 ILE cc_start: 0.9513 (mt) cc_final: 0.9261 (mm) REVERT: A 677 LYS cc_start: 0.7743 (mttt) cc_final: 0.7038 (tptt) REVERT: A 681 LYS cc_start: 0.8297 (mtpt) cc_final: 0.7798 (mtpp) REVERT: A 708 LEU cc_start: 0.8109 (mp) cc_final: 0.7817 (mp) REVERT: B 21 ARG cc_start: 0.7053 (ttt180) cc_final: 0.6323 (mmt-90) REVERT: B 57 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7594 (m-30) REVERT: B 189 THR cc_start: 0.8545 (m) cc_final: 0.8211 (m) REVERT: B 339 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7079 (mpp) REVERT: B 366 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: B 389 LEU cc_start: 0.8264 (tp) cc_final: 0.7970 (tp) REVERT: B 405 MET cc_start: 0.7793 (mtp) cc_final: 0.7561 (mtp) REVERT: B 434 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6586 (tm-30) REVERT: B 515 MET cc_start: 0.7422 (tpp) cc_final: 0.6360 (tpp) REVERT: B 517 TYR cc_start: 0.7745 (m-80) cc_final: 0.7180 (m-80) REVERT: B 602 MET cc_start: 0.8500 (pmm) cc_final: 0.8130 (pmm) REVERT: B 677 LYS cc_start: 0.7627 (mttt) cc_final: 0.7134 (tptt) REVERT: B 681 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7206 (mtmt) REVERT: B 694 MET cc_start: 0.7978 (mtp) cc_final: 0.7714 (mtt) REVERT: C 14 MET cc_start: 0.7610 (mpp) cc_final: 0.7203 (mpp) REVERT: C 21 ARG cc_start: 0.7046 (ttt180) cc_final: 0.6367 (mmt180) REVERT: C 23 GLN cc_start: 0.8314 (tt0) cc_final: 0.7749 (pt0) REVERT: C 41 MET cc_start: 0.7827 (ttm) cc_final: 0.7543 (mtp) REVERT: C 52 THR cc_start: 0.8664 (m) cc_final: 0.8229 (p) REVERT: C 89 GLU cc_start: 0.8376 (tp30) cc_final: 0.8083 (tm-30) REVERT: C 189 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8645 (m) REVERT: C 307 ASP cc_start: 0.7964 (t0) cc_final: 0.7652 (t0) REVERT: C 320 LYS cc_start: 0.8809 (mmmm) cc_final: 0.8552 (mtmt) REVERT: C 322 GLU cc_start: 0.8466 (pt0) cc_final: 0.8192 (pt0) REVERT: C 388 GLN cc_start: 0.8530 (tp-100) cc_final: 0.8169 (tp-100) REVERT: C 416 ASN cc_start: 0.7490 (t0) cc_final: 0.7233 (t0) REVERT: C 493 LEU cc_start: 0.7427 (tp) cc_final: 0.7205 (mt) REVERT: C 515 MET cc_start: 0.7803 (mmm) cc_final: 0.7393 (mmt) REVERT: C 655 MET cc_start: 0.8625 (tpt) cc_final: 0.8127 (tpp) REVERT: C 677 LYS cc_start: 0.7202 (mttt) cc_final: 0.6810 (tptt) REVERT: C 681 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7791 (mtpt) REVERT: C 694 MET cc_start: 0.7937 (mtp) cc_final: 0.7699 (mtt) REVERT: C 708 LEU cc_start: 0.8011 (tp) cc_final: 0.7690 (mp) REVERT: C 726 TYR cc_start: 0.8551 (t80) cc_final: 0.7930 (t80) REVERT: D 21 ARG cc_start: 0.7091 (ttt180) cc_final: 0.6188 (mmt180) REVERT: D 57 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: D 89 GLU cc_start: 0.8321 (tp30) cc_final: 0.7913 (tm-30) REVERT: D 405 MET cc_start: 0.8084 (mtp) cc_final: 0.7845 (mtp) REVERT: D 416 ASN cc_start: 0.7787 (t0) cc_final: 0.7436 (t0) REVERT: D 433 VAL cc_start: 0.8824 (t) cc_final: 0.8590 (m) REVERT: D 434 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7498 (mt-10) REVERT: D 515 MET cc_start: 0.7865 (mmm) cc_final: 0.7429 (mmt) REVERT: D 634 PHE cc_start: 0.6719 (p90) cc_final: 0.6388 (p90) REVERT: D 655 MET cc_start: 0.8479 (tpt) cc_final: 0.7988 (tpp) REVERT: D 657 ASN cc_start: 0.8891 (t0) cc_final: 0.8619 (m-40) REVERT: D 677 LYS cc_start: 0.7376 (mttt) cc_final: 0.6834 (tptt) REVERT: D 681 LYS cc_start: 0.8196 (mtpt) cc_final: 0.7662 (mtpt) REVERT: D 694 MET cc_start: 0.8255 (mtp) cc_final: 0.8009 (mtt) REVERT: D 708 LEU cc_start: 0.8018 (tp) cc_final: 0.7391 (mp) REVERT: D 726 TYR cc_start: 0.8679 (t80) cc_final: 0.7980 (t80) REVERT: E 21 ARG cc_start: 0.7252 (ttt180) cc_final: 0.6437 (mmt-90) REVERT: E 149 LYS cc_start: 0.8010 (tttt) cc_final: 0.7756 (tppt) REVERT: E 152 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8102 (tm-30) REVERT: E 189 THR cc_start: 0.8572 (m) cc_final: 0.8242 (m) REVERT: E 339 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.6964 (mpp) REVERT: E 405 MET cc_start: 0.7713 (mtp) cc_final: 0.7452 (mtp) REVERT: E 602 MET cc_start: 0.8530 (pmm) cc_final: 0.8169 (pmm) REVERT: E 677 LYS cc_start: 0.7426 (mttt) cc_final: 0.7074 (tptt) REVERT: E 694 MET cc_start: 0.7972 (mtp) cc_final: 0.7711 (mtt) REVERT: E 702 ILE cc_start: 0.8275 (mt) cc_final: 0.8066 (mt) REVERT: F 21 ARG cc_start: 0.7126 (ttt180) cc_final: 0.6344 (mmt180) REVERT: F 81 ILE cc_start: 0.8775 (tt) cc_final: 0.8549 (tp) REVERT: F 89 GLU cc_start: 0.8157 (tp30) cc_final: 0.7831 (tm-30) REVERT: F 416 ASN cc_start: 0.7729 (t0) cc_final: 0.7487 (t0) REVERT: F 423 ILE cc_start: 0.9493 (mt) cc_final: 0.9262 (mm) REVERT: F 655 MET cc_start: 0.8261 (tpt) cc_final: 0.7690 (tpp) REVERT: F 677 LYS cc_start: 0.7801 (mttt) cc_final: 0.7214 (tptt) REVERT: F 681 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7747 (mtpp) REVERT: F 694 MET cc_start: 0.7753 (mtp) cc_final: 0.7506 (mtt) REVERT: F 708 LEU cc_start: 0.7968 (tp) cc_final: 0.7748 (mp) outliers start: 111 outliers final: 73 residues processed: 643 average time/residue: 0.4722 time to fit residues: 496.7675 Evaluate side-chains 588 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 509 time to evaluate : 4.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 534 THR Chi-restraints excluded: chain E residue 624 ILE Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 627 ARG Chi-restraints excluded: chain F residue 672 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 319 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 366 optimal weight: 4.9990 chunk 296 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 219 optimal weight: 8.9990 chunk 385 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 37068 Z= 0.238 Angle : 0.550 10.107 50310 Z= 0.284 Chirality : 0.044 0.173 5526 Planarity : 0.004 0.040 6336 Dihedral : 8.525 114.685 5304 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.84 % Allowed : 12.78 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 4458 helix: 0.48 (0.11), residues: 2190 sheet: -0.09 (0.33), residues: 306 loop : -0.89 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 197 HIS 0.004 0.001 HIS F 724 PHE 0.015 0.002 PHE A 701 TYR 0.019 0.001 TYR E 517 ARG 0.006 0.000 ARG E 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 533 time to evaluate : 4.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7457 (ttt180) cc_final: 0.6312 (mmt180) REVERT: A 23 GLN cc_start: 0.8213 (tt0) cc_final: 0.7877 (pt0) REVERT: A 81 ILE cc_start: 0.8797 (tt) cc_final: 0.8560 (tp) REVERT: A 307 ASP cc_start: 0.8309 (t0) cc_final: 0.7810 (t0) REVERT: A 405 MET cc_start: 0.7892 (mtp) cc_final: 0.7529 (mtp) REVERT: A 416 ASN cc_start: 0.7833 (t0) cc_final: 0.7545 (t0) REVERT: A 423 ILE cc_start: 0.9540 (mt) cc_final: 0.9276 (mm) REVERT: A 543 SER cc_start: 0.9403 (OUTLIER) cc_final: 0.8717 (p) REVERT: A 677 LYS cc_start: 0.7786 (mttt) cc_final: 0.7114 (tptt) REVERT: A 681 LYS cc_start: 0.8342 (mtpt) cc_final: 0.7897 (mtpp) REVERT: A 708 LEU cc_start: 0.8160 (mp) cc_final: 0.7889 (mp) REVERT: B 21 ARG cc_start: 0.7160 (ttt180) cc_final: 0.6468 (mmt-90) REVERT: B 57 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7600 (m-30) REVERT: B 189 THR cc_start: 0.8631 (m) cc_final: 0.8297 (m) REVERT: B 339 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7062 (mpp) REVERT: B 389 LEU cc_start: 0.8352 (tp) cc_final: 0.8105 (tp) REVERT: B 405 MET cc_start: 0.7812 (mtp) cc_final: 0.7562 (mtp) REVERT: B 602 MET cc_start: 0.8545 (pmm) cc_final: 0.8230 (pmm) REVERT: B 677 LYS cc_start: 0.7471 (mttt) cc_final: 0.7106 (tptt) REVERT: B 694 MET cc_start: 0.8065 (mtp) cc_final: 0.7751 (mtt) REVERT: C 14 MET cc_start: 0.7879 (mpp) cc_final: 0.7468 (mpp) REVERT: C 21 ARG cc_start: 0.7087 (ttt180) cc_final: 0.6306 (mmt180) REVERT: C 23 GLN cc_start: 0.8305 (tt0) cc_final: 0.7775 (pt0) REVERT: C 41 MET cc_start: 0.7874 (ttm) cc_final: 0.7496 (mtp) REVERT: C 52 THR cc_start: 0.8670 (m) cc_final: 0.8259 (p) REVERT: C 89 GLU cc_start: 0.8360 (tp30) cc_final: 0.7986 (tm-30) REVERT: C 233 ASP cc_start: 0.8066 (m-30) cc_final: 0.7363 (m-30) REVERT: C 307 ASP cc_start: 0.8048 (t0) cc_final: 0.7705 (t0) REVERT: C 388 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8197 (tp-100) REVERT: C 416 ASN cc_start: 0.7682 (t0) cc_final: 0.7422 (t0) REVERT: C 444 CYS cc_start: 0.7302 (t) cc_final: 0.7100 (t) REVERT: C 515 MET cc_start: 0.7856 (mmm) cc_final: 0.7617 (mmt) REVERT: C 577 ASP cc_start: 0.8353 (t0) cc_final: 0.8147 (t0) REVERT: C 627 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.5715 (mmp80) REVERT: C 655 MET cc_start: 0.8594 (tpt) cc_final: 0.8305 (tpp) REVERT: C 677 LYS cc_start: 0.7219 (mttt) cc_final: 0.6846 (tptt) REVERT: C 681 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7818 (mtpt) REVERT: C 694 MET cc_start: 0.8038 (mtp) cc_final: 0.7755 (mtt) REVERT: C 708 LEU cc_start: 0.8018 (tp) cc_final: 0.7524 (mp) REVERT: C 726 TYR cc_start: 0.8582 (t80) cc_final: 0.7977 (t80) REVERT: D 21 ARG cc_start: 0.7138 (ttt180) cc_final: 0.6308 (mmt180) REVERT: D 39 ILE cc_start: 0.9050 (mt) cc_final: 0.8844 (tt) REVERT: D 57 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8047 (m-30) REVERT: D 89 GLU cc_start: 0.8307 (tp30) cc_final: 0.7976 (tm-30) REVERT: D 223 MET cc_start: 0.8770 (mmm) cc_final: 0.8371 (mmm) REVERT: D 405 MET cc_start: 0.8100 (mtp) cc_final: 0.7842 (mtp) REVERT: D 416 ASN cc_start: 0.8036 (t0) cc_final: 0.7712 (t0) REVERT: D 431 GLU cc_start: 0.7376 (pm20) cc_final: 0.6966 (pm20) REVERT: D 433 VAL cc_start: 0.8823 (t) cc_final: 0.8489 (m) REVERT: D 434 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7370 (mt-10) REVERT: D 515 MET cc_start: 0.7987 (mmm) cc_final: 0.7686 (mmt) REVERT: D 634 PHE cc_start: 0.6750 (p90) cc_final: 0.6449 (p90) REVERT: D 655 MET cc_start: 0.8518 (tpt) cc_final: 0.8005 (tpp) REVERT: D 657 ASN cc_start: 0.8945 (t0) cc_final: 0.8657 (m-40) REVERT: D 677 LYS cc_start: 0.7402 (mttt) cc_final: 0.6845 (tptt) REVERT: D 681 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7691 (mtpt) REVERT: D 694 MET cc_start: 0.8112 (mtp) cc_final: 0.7827 (mtt) REVERT: D 708 LEU cc_start: 0.8084 (tp) cc_final: 0.7427 (mp) REVERT: D 726 TYR cc_start: 0.8734 (t80) cc_final: 0.8113 (t80) REVERT: D 736 MET cc_start: 0.7721 (tmm) cc_final: 0.7512 (tmm) REVERT: E 21 ARG cc_start: 0.7413 (ttt180) cc_final: 0.6532 (mmt-90) REVERT: E 149 LYS cc_start: 0.8074 (tttt) cc_final: 0.7804 (tppt) REVERT: E 152 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8130 (tm-30) REVERT: E 189 THR cc_start: 0.8666 (m) cc_final: 0.8328 (m) REVERT: E 339 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.6969 (mpp) REVERT: E 405 MET cc_start: 0.7692 (mtp) cc_final: 0.7482 (mtp) REVERT: E 515 MET cc_start: 0.7330 (tpp) cc_final: 0.6663 (tpp) REVERT: E 602 MET cc_start: 0.8572 (pmm) cc_final: 0.8274 (pmm) REVERT: E 627 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6378 (mmp80) REVERT: E 655 MET cc_start: 0.6984 (tpp) cc_final: 0.6037 (tpp) REVERT: F 21 ARG cc_start: 0.7330 (ttt180) cc_final: 0.6511 (mmt180) REVERT: F 81 ILE cc_start: 0.8799 (tt) cc_final: 0.8568 (tp) REVERT: F 89 GLU cc_start: 0.8234 (tp30) cc_final: 0.7872 (tm-30) REVERT: F 416 ASN cc_start: 0.7859 (t0) cc_final: 0.7623 (t0) REVERT: F 423 ILE cc_start: 0.9521 (mt) cc_final: 0.9292 (mm) REVERT: F 655 MET cc_start: 0.8272 (tpt) cc_final: 0.8012 (tpp) REVERT: F 677 LYS cc_start: 0.7831 (mttt) cc_final: 0.7221 (tptt) REVERT: F 681 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7783 (mtpp) REVERT: F 694 MET cc_start: 0.7875 (mtp) cc_final: 0.7604 (mtt) REVERT: F 708 LEU cc_start: 0.8053 (tp) cc_final: 0.7677 (mp) outliers start: 111 outliers final: 81 residues processed: 615 average time/residue: 0.4927 time to fit residues: 495.7373 Evaluate side-chains 584 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 496 time to evaluate : 4.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 698 ARG Chi-restraints excluded: chain B residue 716 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 698 ARG Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 534 THR Chi-restraints excluded: chain E residue 624 ILE Chi-restraints excluded: chain E residue 627 ARG Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain E residue 716 ASN Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 534 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 627 ARG Chi-restraints excluded: chain F residue 672 ILE Chi-restraints excluded: chain F residue 692 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 4.9990 chunk 386 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 251 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 429 optimal weight: 6.9990 chunk 356 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 225 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 GLN B 38 GLN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 567 GLN E 23 GLN ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 706 GLN ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 37068 Z= 0.255 Angle : 0.562 10.325 50310 Z= 0.289 Chirality : 0.044 0.178 5526 Planarity : 0.004 0.040 6336 Dihedral : 8.508 111.926 5304 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.05 % Allowed : 12.98 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.13), residues: 4458 helix: 0.53 (0.11), residues: 2208 sheet: -0.07 (0.33), residues: 306 loop : -0.81 (0.15), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 197 HIS 0.004 0.001 HIS C 724 PHE 0.015 0.002 PHE C 701 TYR 0.018 0.002 TYR B 517 ARG 0.005 0.000 ARG E 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 542 time to evaluate : 4.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7605 (ttt180) cc_final: 0.6388 (mmt180) REVERT: A 23 GLN cc_start: 0.8204 (tt0) cc_final: 0.7898 (pt0) REVERT: A 81 ILE cc_start: 0.8862 (tt) cc_final: 0.8637 (tp) REVERT: A 307 ASP cc_start: 0.8275 (t0) cc_final: 0.7833 (t0) REVERT: A 405 MET cc_start: 0.7916 (mtp) cc_final: 0.7588 (mtp) REVERT: A 416 ASN cc_start: 0.7805 (t0) cc_final: 0.7449 (t0) REVERT: A 423 ILE cc_start: 0.9556 (mt) cc_final: 0.9283 (mm) REVERT: A 515 MET cc_start: 0.7803 (tpp) cc_final: 0.7221 (mmm) REVERT: A 543 SER cc_start: 0.9416 (m) cc_final: 0.8757 (p) REVERT: A 677 LYS cc_start: 0.7772 (mttt) cc_final: 0.7128 (tptt) REVERT: A 681 LYS cc_start: 0.8477 (mtpt) cc_final: 0.7996 (mtpp) REVERT: A 708 LEU cc_start: 0.8186 (mp) cc_final: 0.7895 (mp) REVERT: B 14 MET cc_start: 0.7864 (mpp) cc_final: 0.7240 (mpp) REVERT: B 21 ARG cc_start: 0.7339 (ttt180) cc_final: 0.6675 (mmt-90) REVERT: B 57 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8103 (m-30) REVERT: B 81 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8542 (tp) REVERT: B 189 THR cc_start: 0.8740 (m) cc_final: 0.8415 (m) REVERT: B 339 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7051 (mpp) REVERT: B 351 MET cc_start: 0.7579 (ptp) cc_final: 0.7237 (mtm) REVERT: B 389 LEU cc_start: 0.8344 (tp) cc_final: 0.8028 (tp) REVERT: B 405 MET cc_start: 0.7790 (mtp) cc_final: 0.7527 (mtp) REVERT: B 416 ASN cc_start: 0.7604 (t0) cc_final: 0.7300 (t0) REVERT: B 515 MET cc_start: 0.7619 (tpp) cc_final: 0.6861 (tpp) REVERT: B 602 MET cc_start: 0.8633 (pmm) cc_final: 0.8280 (pmm) REVERT: B 677 LYS cc_start: 0.7656 (mttt) cc_final: 0.7095 (tptt) REVERT: B 694 MET cc_start: 0.7971 (mtp) cc_final: 0.7686 (mtt) REVERT: C 14 MET cc_start: 0.7923 (mpp) cc_final: 0.7538 (mpp) REVERT: C 21 ARG cc_start: 0.7258 (ttt180) cc_final: 0.6391 (mmt180) REVERT: C 23 GLN cc_start: 0.8351 (tt0) cc_final: 0.7814 (pt0) REVERT: C 89 GLU cc_start: 0.8335 (tp30) cc_final: 0.7965 (tm-30) REVERT: C 189 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8808 (p) REVERT: C 233 ASP cc_start: 0.8058 (m-30) cc_final: 0.7372 (m-30) REVERT: C 388 GLN cc_start: 0.8584 (tp-100) cc_final: 0.8268 (tp-100) REVERT: C 416 ASN cc_start: 0.7837 (t0) cc_final: 0.7633 (t0) REVERT: C 444 CYS cc_start: 0.7460 (t) cc_final: 0.7248 (t) REVERT: C 515 MET cc_start: 0.7890 (mmm) cc_final: 0.7648 (mmt) REVERT: C 577 ASP cc_start: 0.8335 (t0) cc_final: 0.8129 (t0) REVERT: C 627 ARG cc_start: 0.6517 (OUTLIER) cc_final: 0.5883 (mmp80) REVERT: C 655 MET cc_start: 0.8572 (tpt) cc_final: 0.8314 (tpp) REVERT: C 677 LYS cc_start: 0.7291 (mttt) cc_final: 0.6860 (tptt) REVERT: C 681 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7854 (mtpt) REVERT: C 694 MET cc_start: 0.8001 (mtp) cc_final: 0.7637 (mtt) REVERT: C 708 LEU cc_start: 0.8057 (tp) cc_final: 0.7519 (mp) REVERT: C 726 TYR cc_start: 0.8578 (t80) cc_final: 0.7981 (t80) REVERT: D 21 ARG cc_start: 0.7249 (ttt180) cc_final: 0.6372 (mmt180) REVERT: D 57 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8264 (m-30) REVERT: D 89 GLU cc_start: 0.8275 (tp30) cc_final: 0.7782 (tm-30) REVERT: D 233 ASP cc_start: 0.8190 (m-30) cc_final: 0.7708 (m-30) REVERT: D 339 MET cc_start: 0.8087 (ttp) cc_final: 0.7768 (ttp) REVERT: D 388 GLN cc_start: 0.8629 (tp-100) cc_final: 0.8336 (tp-100) REVERT: D 416 ASN cc_start: 0.8052 (t0) cc_final: 0.7728 (t0) REVERT: D 515 MET cc_start: 0.7957 (mmm) cc_final: 0.7669 (mmt) REVERT: D 570 MET cc_start: 0.7153 (mtt) cc_final: 0.6868 (mtm) REVERT: D 627 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6355 (mmp80) REVERT: D 655 MET cc_start: 0.8503 (tpt) cc_final: 0.7970 (tpp) REVERT: D 657 ASN cc_start: 0.9014 (t0) cc_final: 0.8719 (m-40) REVERT: D 677 LYS cc_start: 0.7384 (mttt) cc_final: 0.6875 (tptt) REVERT: D 681 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7746 (mtpt) REVERT: D 694 MET cc_start: 0.8129 (mtp) cc_final: 0.7708 (mtt) REVERT: D 708 LEU cc_start: 0.7957 (tp) cc_final: 0.7392 (mp) REVERT: D 726 TYR cc_start: 0.8703 (t80) cc_final: 0.8176 (t80) REVERT: E 149 LYS cc_start: 0.8133 (tttt) cc_final: 0.7811 (tppt) REVERT: E 152 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8165 (tm-30) REVERT: E 189 THR cc_start: 0.8743 (m) cc_final: 0.8402 (m) REVERT: E 339 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.6933 (mpp) REVERT: E 405 MET cc_start: 0.7677 (mtp) cc_final: 0.7457 (mtp) REVERT: E 416 ASN cc_start: 0.7881 (t0) cc_final: 0.7675 (t0) REVERT: E 602 MET cc_start: 0.8571 (pmm) cc_final: 0.8231 (pmm) REVERT: E 609 GLN cc_start: 0.8572 (tp-100) cc_final: 0.8293 (tp40) REVERT: E 625 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7083 (p90) REVERT: E 627 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6268 (mmp80) REVERT: F 21 ARG cc_start: 0.7303 (ttt180) cc_final: 0.6574 (mmt180) REVERT: F 81 ILE cc_start: 0.8861 (tt) cc_final: 0.8636 (tp) REVERT: F 233 ASP cc_start: 0.8047 (m-30) cc_final: 0.7418 (m-30) REVERT: F 416 ASN cc_start: 0.7882 (t0) cc_final: 0.7599 (t0) REVERT: F 423 ILE cc_start: 0.9539 (mt) cc_final: 0.9308 (mm) REVERT: F 515 MET cc_start: 0.7561 (tpp) cc_final: 0.6872 (tpp) REVERT: F 543 SER cc_start: 0.9178 (m) cc_final: 0.8620 (p) REVERT: F 655 MET cc_start: 0.8268 (tpt) cc_final: 0.7987 (tpp) REVERT: F 677 LYS cc_start: 0.7923 (mttt) cc_final: 0.7284 (tptt) REVERT: F 681 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8062 (mtpp) REVERT: F 694 MET cc_start: 0.7920 (mtp) cc_final: 0.7702 (mtt) REVERT: F 708 LEU cc_start: 0.8068 (tp) cc_final: 0.7736 (mp) outliers start: 119 outliers final: 88 residues processed: 629 average time/residue: 0.4776 time to fit residues: 492.9768 Evaluate side-chains 611 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 513 time to evaluate : 4.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 698 ARG Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 698 ARG Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 698 ARG Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 533 GLU Chi-restraints excluded: chain E residue 534 THR Chi-restraints excluded: chain E residue 624 ILE Chi-restraints excluded: chain E residue 625 TYR Chi-restraints excluded: chain E residue 627 ARG Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 513 ILE Chi-restraints excluded: chain F residue 534 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 624 ILE Chi-restraints excluded: chain F residue 627 ARG Chi-restraints excluded: chain F residue 672 ILE Chi-restraints excluded: chain F residue 692 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 313 optimal weight: 5.9990 chunk 243 optimal weight: 0.8980 chunk 361 optimal weight: 8.9990 chunk 239 optimal weight: 4.9990 chunk 427 optimal weight: 6.9990 chunk 267 optimal weight: 9.9990 chunk 260 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN A 288 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 ASN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.139 37068 Z= 0.456 Angle : 0.695 11.030 50310 Z= 0.360 Chirality : 0.049 0.189 5526 Planarity : 0.004 0.045 6336 Dihedral : 9.245 108.403 5304 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.33 % Allowed : 13.67 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.13), residues: 4458 helix: 0.26 (0.11), residues: 2178 sheet: -0.28 (0.32), residues: 306 loop : -0.98 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 197 HIS 0.004 0.001 HIS F 724 PHE 0.020 0.002 PHE C 148 TYR 0.018 0.002 TYR B 517 ARG 0.010 0.001 ARG E 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 495 time to evaluate : 4.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 CYS cc_start: 0.7525 (m) cc_final: 0.7120 (m) REVERT: A 81 ILE cc_start: 0.8776 (tt) cc_final: 0.8522 (tp) REVERT: A 233 ASP cc_start: 0.8089 (m-30) cc_final: 0.7547 (m-30) REVERT: A 307 ASP cc_start: 0.8296 (t0) cc_final: 0.7904 (t0) REVERT: A 405 MET cc_start: 0.7983 (mtp) cc_final: 0.7648 (mtp) REVERT: A 416 ASN cc_start: 0.7877 (t0) cc_final: 0.7505 (t0) REVERT: A 423 ILE cc_start: 0.9599 (mt) cc_final: 0.9329 (mm) REVERT: A 453 MET cc_start: 0.7079 (mmp) cc_final: 0.6868 (mpp) REVERT: A 515 MET cc_start: 0.7938 (tpp) cc_final: 0.7271 (tpp) REVERT: A 543 SER cc_start: 0.9503 (m) cc_final: 0.8842 (p) REVERT: A 674 ASP cc_start: 0.7390 (t0) cc_final: 0.7139 (t0) REVERT: A 677 LYS cc_start: 0.7787 (mttt) cc_final: 0.7141 (tptt) REVERT: A 681 LYS cc_start: 0.8363 (mtpt) cc_final: 0.8103 (mtpp) REVERT: A 708 LEU cc_start: 0.8196 (mp) cc_final: 0.7866 (mp) REVERT: B 14 MET cc_start: 0.7907 (mpp) cc_final: 0.7306 (mpp) REVERT: B 21 ARG cc_start: 0.7602 (ttt180) cc_final: 0.6792 (mmt-90) REVERT: B 57 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8204 (m-30) REVERT: B 81 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8612 (tp) REVERT: B 189 THR cc_start: 0.8902 (m) cc_final: 0.8576 (m) REVERT: B 339 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7205 (mpp) REVERT: B 405 MET cc_start: 0.7823 (mtp) cc_final: 0.7525 (mtp) REVERT: B 416 ASN cc_start: 0.7957 (t0) cc_final: 0.7637 (t0) REVERT: B 602 MET cc_start: 0.8633 (pmm) cc_final: 0.8184 (pmm) REVERT: B 677 LYS cc_start: 0.7452 (mttt) cc_final: 0.7052 (tptt) REVERT: B 694 MET cc_start: 0.8048 (mtp) cc_final: 0.7777 (mtt) REVERT: C 14 MET cc_start: 0.7950 (mpp) cc_final: 0.7609 (mpp) REVERT: C 21 ARG cc_start: 0.7519 (ttt180) cc_final: 0.6492 (mmt180) REVERT: C 23 GLN cc_start: 0.8436 (tt0) cc_final: 0.7940 (pt0) REVERT: C 89 GLU cc_start: 0.8346 (tp30) cc_final: 0.7858 (tm-30) REVERT: C 233 ASP cc_start: 0.8177 (m-30) cc_final: 0.7310 (m-30) REVERT: C 416 ASN cc_start: 0.8155 (t0) cc_final: 0.7825 (t0) REVERT: C 444 CYS cc_start: 0.7616 (t) cc_final: 0.7325 (t) REVERT: C 577 ASP cc_start: 0.8467 (t0) cc_final: 0.8227 (t0) REVERT: C 627 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.5888 (mmp80) REVERT: C 655 MET cc_start: 0.8450 (tpt) cc_final: 0.8207 (tpp) REVERT: C 674 ASP cc_start: 0.7173 (t0) cc_final: 0.6866 (t0) REVERT: C 677 LYS cc_start: 0.7384 (mttt) cc_final: 0.6807 (tptt) REVERT: C 681 LYS cc_start: 0.8353 (mtpt) cc_final: 0.7440 (ptmt) REVERT: C 694 MET cc_start: 0.8037 (mtp) cc_final: 0.7347 (mtt) REVERT: C 698 ARG cc_start: 0.6247 (OUTLIER) cc_final: 0.5819 (ptt90) REVERT: C 708 LEU cc_start: 0.7941 (tp) cc_final: 0.7461 (mp) REVERT: C 726 TYR cc_start: 0.8661 (t80) cc_final: 0.8438 (t80) REVERT: D 21 ARG cc_start: 0.7356 (ttt180) cc_final: 0.6300 (mmt180) REVERT: D 23 GLN cc_start: 0.8214 (tt0) cc_final: 0.7785 (pt0) REVERT: D 57 ASP cc_start: 0.9110 (OUTLIER) cc_final: 0.8545 (m-30) REVERT: D 59 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7863 (tt) REVERT: D 89 GLU cc_start: 0.8389 (tp30) cc_final: 0.7950 (tm-30) REVERT: D 233 ASP cc_start: 0.8199 (m-30) cc_final: 0.7356 (m-30) REVERT: D 323 GLN cc_start: 0.8319 (mt0) cc_final: 0.8091 (pt0) REVERT: D 416 ASN cc_start: 0.8145 (t0) cc_final: 0.7807 (t0) REVERT: D 515 MET cc_start: 0.8053 (mmm) cc_final: 0.7661 (mmm) REVERT: D 627 ARG cc_start: 0.6359 (OUTLIER) cc_final: 0.5648 (mmp80) REVERT: D 655 MET cc_start: 0.8235 (tpt) cc_final: 0.7817 (tpp) REVERT: D 657 ASN cc_start: 0.9032 (t0) cc_final: 0.7765 (t0) REVERT: D 674 ASP cc_start: 0.7307 (t0) cc_final: 0.6889 (t0) REVERT: D 677 LYS cc_start: 0.7427 (mttt) cc_final: 0.6805 (tptt) REVERT: D 681 LYS cc_start: 0.8341 (mtpt) cc_final: 0.7379 (ptmt) REVERT: D 694 MET cc_start: 0.8162 (mtp) cc_final: 0.7802 (mtt) REVERT: D 708 LEU cc_start: 0.8067 (tp) cc_final: 0.7427 (mp) REVERT: D 726 TYR cc_start: 0.8773 (t80) cc_final: 0.8359 (t80) REVERT: E 81 ILE cc_start: 0.8903 (tt) cc_final: 0.8599 (tp) REVERT: E 149 LYS cc_start: 0.8318 (tttt) cc_final: 0.7936 (tppt) REVERT: E 152 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8135 (tm-30) REVERT: E 189 THR cc_start: 0.8878 (m) cc_final: 0.8553 (m) REVERT: E 339 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7109 (mpp) REVERT: E 388 GLN cc_start: 0.8457 (tp40) cc_final: 0.8182 (tp40) REVERT: E 405 MET cc_start: 0.7697 (mtp) cc_final: 0.7443 (mtp) REVERT: E 416 ASN cc_start: 0.7931 (t0) cc_final: 0.7700 (t0) REVERT: E 515 MET cc_start: 0.7447 (tpp) cc_final: 0.6808 (tpp) REVERT: E 602 MET cc_start: 0.8553 (pmm) cc_final: 0.8051 (pmm) REVERT: E 625 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7153 (p90) REVERT: E 627 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.5905 (mmp80) REVERT: E 694 MET cc_start: 0.7911 (mtt) cc_final: 0.7662 (mtm) REVERT: F 14 MET cc_start: 0.7801 (mpp) cc_final: 0.7455 (mpp) REVERT: F 21 ARG cc_start: 0.7313 (ttt180) cc_final: 0.6530 (mmt180) REVERT: F 233 ASP cc_start: 0.8089 (m-30) cc_final: 0.7544 (m-30) REVERT: F 307 ASP cc_start: 0.7934 (t0) cc_final: 0.7609 (t0) REVERT: F 416 ASN cc_start: 0.7962 (t0) cc_final: 0.7573 (t0) REVERT: F 423 ILE cc_start: 0.9565 (mt) cc_final: 0.9320 (mm) REVERT: F 431 GLU cc_start: 0.7208 (pm20) cc_final: 0.7005 (pm20) REVERT: F 543 SER cc_start: 0.9284 (m) cc_final: 0.8699 (p) REVERT: F 655 MET cc_start: 0.8313 (tpt) cc_final: 0.8008 (tpp) REVERT: F 674 ASP cc_start: 0.6974 (t0) cc_final: 0.6549 (t0) REVERT: F 677 LYS cc_start: 0.7675 (mttt) cc_final: 0.7001 (tptt) REVERT: F 681 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8198 (mtpp) REVERT: F 694 MET cc_start: 0.7978 (mtp) cc_final: 0.7718 (mtt) REVERT: F 698 ARG cc_start: 0.6320 (OUTLIER) cc_final: 0.6076 (ptt90) REVERT: F 708 LEU cc_start: 0.8101 (tp) cc_final: 0.7874 (mp) outliers start: 130 outliers final: 93 residues processed: 591 average time/residue: 0.4948 time to fit residues: 482.1106 Evaluate side-chains 582 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 477 time to evaluate : 4.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 698 ARG Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 534 THR Chi-restraints excluded: chain E residue 624 ILE Chi-restraints excluded: chain E residue 625 TYR Chi-restraints excluded: chain E residue 627 ARG Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 534 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 624 ILE Chi-restraints excluded: chain F residue 627 ARG Chi-restraints excluded: chain F residue 672 ILE Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 698 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 255 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 272 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 336 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN B 418 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN D 427 ASN E 38 GLN ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 688 GLN ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 ASN F 288 GLN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37068 Z= 0.166 Angle : 0.557 10.530 50310 Z= 0.281 Chirality : 0.043 0.176 5526 Planarity : 0.003 0.038 6336 Dihedral : 8.299 107.038 5304 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.64 % Allowed : 14.87 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.13), residues: 4458 helix: 0.60 (0.11), residues: 2208 sheet: -0.22 (0.33), residues: 306 loop : -0.72 (0.15), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 728 HIS 0.005 0.001 HIS C 459 PHE 0.012 0.001 PHE A 519 TYR 0.019 0.001 TYR C 536 ARG 0.008 0.000 ARG D 742 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 555 time to evaluate : 4.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7425 (ttt180) cc_final: 0.6432 (mmt90) REVERT: A 26 CYS cc_start: 0.7578 (m) cc_final: 0.7288 (m) REVERT: A 81 ILE cc_start: 0.8813 (tt) cc_final: 0.8573 (tp) REVERT: A 131 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6505 (tt) REVERT: A 307 ASP cc_start: 0.8170 (t0) cc_final: 0.7693 (t0) REVERT: A 405 MET cc_start: 0.7840 (mtp) cc_final: 0.7638 (mtp) REVERT: A 515 MET cc_start: 0.7886 (tpp) cc_final: 0.7152 (tpp) REVERT: A 543 SER cc_start: 0.9422 (m) cc_final: 0.8755 (p) REVERT: A 674 ASP cc_start: 0.7211 (t0) cc_final: 0.6897 (t0) REVERT: A 677 LYS cc_start: 0.8105 (mttt) cc_final: 0.7607 (tptt) REVERT: A 681 LYS cc_start: 0.8363 (mtpt) cc_final: 0.7938 (mtpp) REVERT: A 708 LEU cc_start: 0.8134 (mp) cc_final: 0.7852 (mp) REVERT: B 12 ARG cc_start: 0.6939 (mmt180) cc_final: 0.6095 (mmt180) REVERT: B 14 MET cc_start: 0.7804 (mpp) cc_final: 0.7272 (mpp) REVERT: B 21 ARG cc_start: 0.7521 (ttt180) cc_final: 0.6851 (mmt-90) REVERT: B 81 ILE cc_start: 0.8830 (tt) cc_final: 0.8512 (tp) REVERT: B 339 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.6941 (mpp) REVERT: B 351 MET cc_start: 0.7555 (ptp) cc_final: 0.7344 (mtm) REVERT: B 416 ASN cc_start: 0.7769 (t0) cc_final: 0.7507 (t0) REVERT: B 515 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7159 (tpp) REVERT: B 602 MET cc_start: 0.8556 (pmm) cc_final: 0.8190 (pmm) REVERT: B 609 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8298 (tp40) REVERT: B 694 MET cc_start: 0.7875 (mtp) cc_final: 0.7588 (mtt) REVERT: C 14 MET cc_start: 0.7825 (mpp) cc_final: 0.7457 (mpp) REVERT: C 21 ARG cc_start: 0.7491 (ttt180) cc_final: 0.6529 (mmt180) REVERT: C 23 GLN cc_start: 0.8418 (tt0) cc_final: 0.7937 (pt0) REVERT: C 416 ASN cc_start: 0.7858 (t0) cc_final: 0.7627 (t0) REVERT: C 515 MET cc_start: 0.7882 (mmm) cc_final: 0.7654 (tpp) REVERT: C 570 MET cc_start: 0.7011 (mtt) cc_final: 0.6775 (mtm) REVERT: C 577 ASP cc_start: 0.8350 (t0) cc_final: 0.8129 (t0) REVERT: C 655 MET cc_start: 0.8578 (tpt) cc_final: 0.8254 (tpp) REVERT: C 674 ASP cc_start: 0.7129 (t0) cc_final: 0.6806 (t0) REVERT: C 677 LYS cc_start: 0.7287 (mttt) cc_final: 0.6893 (tptt) REVERT: C 681 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7821 (mtpt) REVERT: C 694 MET cc_start: 0.7927 (mtp) cc_final: 0.7247 (mtt) REVERT: C 698 ARG cc_start: 0.6192 (OUTLIER) cc_final: 0.5914 (ptt90) REVERT: C 708 LEU cc_start: 0.7941 (tp) cc_final: 0.7483 (mp) REVERT: C 726 TYR cc_start: 0.8659 (t80) cc_final: 0.8085 (t80) REVERT: D 21 ARG cc_start: 0.7236 (ttt180) cc_final: 0.6323 (mmt180) REVERT: D 59 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7826 (tt) REVERT: D 199 THR cc_start: 0.8065 (p) cc_final: 0.7817 (p) REVERT: D 416 ASN cc_start: 0.8024 (t0) cc_final: 0.7792 (t0) REVERT: D 515 MET cc_start: 0.7964 (mmm) cc_final: 0.7685 (mmt) REVERT: D 570 MET cc_start: 0.7072 (mtt) cc_final: 0.6826 (mtm) REVERT: D 627 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.5764 (mmp80) REVERT: D 655 MET cc_start: 0.8334 (tpt) cc_final: 0.8127 (tpp) REVERT: D 674 ASP cc_start: 0.7169 (t0) cc_final: 0.6788 (t0) REVERT: D 677 LYS cc_start: 0.7337 (mttt) cc_final: 0.7105 (tptt) REVERT: D 681 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7220 (ptmt) REVERT: D 694 MET cc_start: 0.8021 (mtp) cc_final: 0.7608 (mtt) REVERT: D 708 LEU cc_start: 0.8061 (tp) cc_final: 0.7395 (mp) REVERT: D 736 MET cc_start: 0.7853 (tmm) cc_final: 0.7629 (tmm) REVERT: E 21 ARG cc_start: 0.7734 (ttt180) cc_final: 0.6690 (mmt-90) REVERT: E 81 ILE cc_start: 0.8869 (tt) cc_final: 0.8564 (tp) REVERT: E 152 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8555 (tm-30) REVERT: E 339 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6816 (mpp) REVERT: E 351 MET cc_start: 0.7553 (ptp) cc_final: 0.7352 (mtm) REVERT: E 388 GLN cc_start: 0.8248 (tp40) cc_final: 0.7976 (tp40) REVERT: E 515 MET cc_start: 0.7244 (tpp) cc_final: 0.6658 (tpp) REVERT: E 602 MET cc_start: 0.8526 (pmm) cc_final: 0.8244 (pmm) REVERT: E 609 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8388 (tp40) REVERT: E 627 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.6480 (mmp80) REVERT: E 653 GLU cc_start: 0.6894 (mp0) cc_final: 0.6687 (mp0) REVERT: E 655 MET cc_start: 0.7317 (tpp) cc_final: 0.6930 (tpp) REVERT: F 21 ARG cc_start: 0.7083 (ttt180) cc_final: 0.6522 (mmt90) REVERT: F 81 ILE cc_start: 0.8782 (tt) cc_final: 0.8525 (tp) REVERT: F 307 ASP cc_start: 0.7847 (t0) cc_final: 0.7502 (t0) REVERT: F 416 ASN cc_start: 0.7892 (t0) cc_final: 0.7661 (t0) REVERT: F 423 ILE cc_start: 0.9478 (mt) cc_final: 0.9231 (mm) REVERT: F 515 MET cc_start: 0.7641 (tpp) cc_final: 0.6940 (tpp) REVERT: F 543 SER cc_start: 0.9221 (m) cc_final: 0.8601 (p) REVERT: F 655 MET cc_start: 0.8296 (tpt) cc_final: 0.7970 (tpp) REVERT: F 674 ASP cc_start: 0.6968 (t0) cc_final: 0.6679 (t0) REVERT: F 677 LYS cc_start: 0.8012 (mttt) cc_final: 0.7564 (tptt) REVERT: F 681 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7981 (mtpp) REVERT: F 694 MET cc_start: 0.8058 (mtp) cc_final: 0.7827 (mtt) REVERT: F 726 TYR cc_start: 0.8243 (t80) cc_final: 0.7836 (t80) outliers start: 103 outliers final: 67 residues processed: 628 average time/residue: 0.4732 time to fit residues: 483.7934 Evaluate side-chains 567 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 492 time to evaluate : 4.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 698 ARG Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 698 ARG Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 698 ARG Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 533 GLU Chi-restraints excluded: chain E residue 627 ARG Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 624 ILE Chi-restraints excluded: chain F residue 627 ARG Chi-restraints excluded: chain F residue 672 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 4.9990 chunk 409 optimal weight: 3.9990 chunk 374 optimal weight: 3.9990 chunk 398 optimal weight: 0.9990 chunk 240 optimal weight: 0.0670 chunk 173 optimal weight: 3.9990 chunk 313 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 360 optimal weight: 0.5980 chunk 377 optimal weight: 4.9990 chunk 397 optimal weight: 5.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN A 288 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 ASN F 288 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 37068 Z= 0.245 Angle : 0.596 10.766 50310 Z= 0.303 Chirality : 0.045 0.203 5526 Planarity : 0.004 0.038 6336 Dihedral : 8.372 109.310 5304 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.43 % Allowed : 15.62 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 4458 helix: 0.61 (0.11), residues: 2226 sheet: -0.17 (0.32), residues: 306 loop : -0.83 (0.15), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 651 HIS 0.005 0.001 HIS E 724 PHE 0.016 0.002 PHE E 701 TYR 0.018 0.001 TYR C 536 ARG 0.004 0.000 ARG E 698 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 504 time to evaluate : 4.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7497 (ttt180) cc_final: 0.6531 (mpt180) REVERT: A 26 CYS cc_start: 0.7568 (m) cc_final: 0.7280 (m) REVERT: A 81 ILE cc_start: 0.8826 (tt) cc_final: 0.8584 (tp) REVERT: A 131 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6565 (tp) REVERT: A 233 ASP cc_start: 0.8049 (m-30) cc_final: 0.7455 (m-30) REVERT: A 307 ASP cc_start: 0.8161 (t0) cc_final: 0.7698 (t0) REVERT: A 405 MET cc_start: 0.7802 (mtp) cc_final: 0.7514 (mtp) REVERT: A 515 MET cc_start: 0.7904 (tpp) cc_final: 0.7139 (tpp) REVERT: A 543 SER cc_start: 0.9425 (m) cc_final: 0.8753 (p) REVERT: A 654 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7930 (tp30) REVERT: A 674 ASP cc_start: 0.7315 (t0) cc_final: 0.7074 (t0) REVERT: A 677 LYS cc_start: 0.8138 (mttt) cc_final: 0.7614 (tptt) REVERT: A 681 LYS cc_start: 0.8398 (mtpt) cc_final: 0.7975 (mtpp) REVERT: A 708 LEU cc_start: 0.8180 (mp) cc_final: 0.7840 (mp) REVERT: B 12 ARG cc_start: 0.6870 (mmt180) cc_final: 0.5834 (mmt180) REVERT: B 14 MET cc_start: 0.7784 (mpp) cc_final: 0.7147 (mpp) REVERT: B 21 ARG cc_start: 0.7572 (ttt180) cc_final: 0.6832 (mmt-90) REVERT: B 81 ILE cc_start: 0.8880 (tt) cc_final: 0.8556 (tp) REVERT: B 416 ASN cc_start: 0.7756 (t0) cc_final: 0.7519 (t0) REVERT: B 515 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7150 (tpp) REVERT: B 602 MET cc_start: 0.8574 (pmm) cc_final: 0.8198 (pmm) REVERT: B 655 MET cc_start: 0.7284 (tpp) cc_final: 0.6847 (tpp) REVERT: B 694 MET cc_start: 0.7899 (mtp) cc_final: 0.7607 (mtt) REVERT: C 14 MET cc_start: 0.7867 (mpp) cc_final: 0.7497 (mpp) REVERT: C 21 ARG cc_start: 0.7497 (ttt180) cc_final: 0.6527 (mmt180) REVERT: C 23 GLN cc_start: 0.8431 (tt0) cc_final: 0.7920 (pt0) REVERT: C 81 ILE cc_start: 0.8870 (tt) cc_final: 0.8628 (tp) REVERT: C 233 ASP cc_start: 0.8063 (m-30) cc_final: 0.7391 (m-30) REVERT: C 416 ASN cc_start: 0.8015 (t0) cc_final: 0.7756 (t0) REVERT: C 515 MET cc_start: 0.7885 (mmm) cc_final: 0.7464 (tpp) REVERT: C 577 ASP cc_start: 0.8363 (t0) cc_final: 0.8137 (t0) REVERT: C 627 ARG cc_start: 0.6476 (OUTLIER) cc_final: 0.5745 (mmp80) REVERT: C 655 MET cc_start: 0.8570 (tpt) cc_final: 0.8259 (tpp) REVERT: C 674 ASP cc_start: 0.7166 (t0) cc_final: 0.6888 (t0) REVERT: C 677 LYS cc_start: 0.7344 (mttt) cc_final: 0.6922 (tptt) REVERT: C 681 LYS cc_start: 0.8294 (mtpt) cc_final: 0.7810 (mtpt) REVERT: C 694 MET cc_start: 0.7967 (mtp) cc_final: 0.7302 (mtt) REVERT: C 708 LEU cc_start: 0.7942 (tp) cc_final: 0.7484 (mp) REVERT: C 726 TYR cc_start: 0.8669 (t80) cc_final: 0.8100 (t80) REVERT: D 21 ARG cc_start: 0.7341 (ttt180) cc_final: 0.6339 (mmt180) REVERT: D 59 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7916 (tt) REVERT: D 199 THR cc_start: 0.8065 (p) cc_final: 0.7810 (p) REVERT: D 233 ASP cc_start: 0.8132 (m-30) cc_final: 0.7433 (m-30) REVERT: D 515 MET cc_start: 0.7974 (mmm) cc_final: 0.7678 (mmt) REVERT: D 627 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.5920 (mmp80) REVERT: D 655 MET cc_start: 0.8324 (tpt) cc_final: 0.8064 (tpp) REVERT: D 674 ASP cc_start: 0.7263 (t0) cc_final: 0.6924 (t0) REVERT: D 677 LYS cc_start: 0.7349 (mttt) cc_final: 0.7054 (tptt) REVERT: D 681 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7259 (ptmt) REVERT: D 694 MET cc_start: 0.8067 (mtp) cc_final: 0.7485 (mtt) REVERT: D 708 LEU cc_start: 0.8036 (tp) cc_final: 0.7391 (mp) REVERT: E 81 ILE cc_start: 0.8938 (tt) cc_final: 0.8638 (tp) REVERT: E 152 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8200 (tm-30) REVERT: E 339 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.6896 (mpp) REVERT: E 388 GLN cc_start: 0.8358 (tp40) cc_final: 0.8047 (tp-100) REVERT: E 515 MET cc_start: 0.7358 (tpp) cc_final: 0.6670 (tpp) REVERT: E 602 MET cc_start: 0.8529 (pmm) cc_final: 0.8216 (pmm) REVERT: E 609 GLN cc_start: 0.8673 (tp-100) cc_final: 0.8368 (tp40) REVERT: E 627 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6201 (mmp80) REVERT: E 653 GLU cc_start: 0.7184 (mp0) cc_final: 0.6934 (mp0) REVERT: E 655 MET cc_start: 0.7370 (tpp) cc_final: 0.6962 (tpp) REVERT: F 21 ARG cc_start: 0.7321 (ttt180) cc_final: 0.6583 (mmt90) REVERT: F 81 ILE cc_start: 0.8799 (tt) cc_final: 0.8552 (tp) REVERT: F 223 MET cc_start: 0.8676 (mmp) cc_final: 0.8443 (mmp) REVERT: F 233 ASP cc_start: 0.8070 (m-30) cc_final: 0.7467 (m-30) REVERT: F 307 ASP cc_start: 0.7903 (t0) cc_final: 0.7525 (t0) REVERT: F 416 ASN cc_start: 0.7791 (t0) cc_final: 0.7543 (t0) REVERT: F 423 ILE cc_start: 0.9526 (mt) cc_final: 0.9308 (mm) REVERT: F 515 MET cc_start: 0.7687 (tpp) cc_final: 0.6926 (tpp) REVERT: F 543 SER cc_start: 0.9262 (m) cc_final: 0.8656 (p) REVERT: F 655 MET cc_start: 0.8290 (tpt) cc_final: 0.7962 (tpp) REVERT: F 674 ASP cc_start: 0.6886 (t0) cc_final: 0.6475 (t0) REVERT: F 677 LYS cc_start: 0.7673 (mttt) cc_final: 0.7271 (tptt) REVERT: F 681 LYS cc_start: 0.8293 (mtpt) cc_final: 0.7992 (mtpp) REVERT: F 694 MET cc_start: 0.8075 (mtp) cc_final: 0.7729 (mtt) outliers start: 95 outliers final: 76 residues processed: 574 average time/residue: 0.4845 time to fit residues: 454.8230 Evaluate side-chains 575 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 491 time to evaluate : 4.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 698 ARG Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 533 GLU Chi-restraints excluded: chain E residue 534 THR Chi-restraints excluded: chain E residue 615 GLU Chi-restraints excluded: chain E residue 621 THR Chi-restraints excluded: chain E residue 627 ARG Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain F residue 534 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 624 ILE Chi-restraints excluded: chain F residue 627 ARG Chi-restraints excluded: chain F residue 672 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 0.8980 chunk 421 optimal weight: 1.9990 chunk 257 optimal weight: 0.8980 chunk 200 optimal weight: 7.9990 chunk 293 optimal weight: 0.0870 chunk 442 optimal weight: 3.9990 chunk 407 optimal weight: 0.9980 chunk 352 optimal weight: 0.0270 chunk 36 optimal weight: 1.9990 chunk 272 optimal weight: 5.9990 chunk 215 optimal weight: 0.3980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN B 478 ASN B 688 GLN B 706 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN C 418 GLN C 688 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 688 GLN ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN E 478 ASN ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 ASN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 37068 Z= 0.151 Angle : 0.577 12.203 50310 Z= 0.287 Chirality : 0.042 0.173 5526 Planarity : 0.003 0.035 6336 Dihedral : 7.885 106.680 5304 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.82 % Allowed : 16.69 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 4458 helix: 0.78 (0.12), residues: 2190 sheet: -0.13 (0.32), residues: 306 loop : -0.53 (0.15), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 728 HIS 0.003 0.000 HIS C 724 PHE 0.015 0.001 PHE B 634 TYR 0.019 0.001 TYR F 726 ARG 0.004 0.000 ARG F 698 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8916 Ramachandran restraints generated. 4458 Oldfield, 0 Emsley, 4458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 553 time to evaluate : 4.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7432 (ttt180) cc_final: 0.6439 (mmt90) REVERT: A 26 CYS cc_start: 0.7452 (m) cc_final: 0.7185 (m) REVERT: A 81 ILE cc_start: 0.8880 (tt) cc_final: 0.8671 (tp) REVERT: A 307 ASP cc_start: 0.8180 (t0) cc_final: 0.7686 (t0) REVERT: A 405 MET cc_start: 0.7656 (mtp) cc_final: 0.7436 (mtp) REVERT: A 515 MET cc_start: 0.7843 (tpp) cc_final: 0.6791 (tpp) REVERT: A 540 LEU cc_start: 0.8933 (mm) cc_final: 0.8626 (mt) REVERT: A 543 SER cc_start: 0.9398 (m) cc_final: 0.8814 (p) REVERT: A 674 ASP cc_start: 0.7111 (t0) cc_final: 0.6829 (t0) REVERT: A 677 LYS cc_start: 0.8033 (mttt) cc_final: 0.7636 (tptt) REVERT: A 681 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7761 (mtpt) REVERT: A 689 LYS cc_start: 0.8370 (mttt) cc_final: 0.7646 (mmtm) REVERT: A 708 LEU cc_start: 0.8152 (mp) cc_final: 0.7811 (mp) REVERT: A 726 TYR cc_start: 0.8282 (t80) cc_final: 0.7728 (t80) REVERT: B 12 ARG cc_start: 0.6730 (mmt180) cc_final: 0.6354 (mmt180) REVERT: B 21 ARG cc_start: 0.7588 (ttt180) cc_final: 0.6840 (mmt-90) REVERT: B 416 ASN cc_start: 0.7678 (t0) cc_final: 0.7472 (t0) REVERT: B 515 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.6721 (tpp) REVERT: B 517 TYR cc_start: 0.7658 (m-80) cc_final: 0.7442 (m-80) REVERT: B 609 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8396 (tp40) REVERT: C 14 MET cc_start: 0.7653 (mpp) cc_final: 0.7230 (mpp) REVERT: C 21 ARG cc_start: 0.7516 (ttt180) cc_final: 0.6550 (mmt180) REVERT: C 23 GLN cc_start: 0.8417 (tt0) cc_final: 0.7950 (pt0) REVERT: C 81 ILE cc_start: 0.8744 (tt) cc_final: 0.8488 (tp) REVERT: C 172 MET cc_start: 0.6916 (tpp) cc_final: 0.6275 (tpp) REVERT: C 339 MET cc_start: 0.7710 (ttp) cc_final: 0.7383 (ptm) REVERT: C 416 ASN cc_start: 0.7798 (t0) cc_final: 0.7535 (t0) REVERT: C 515 MET cc_start: 0.7953 (mmm) cc_final: 0.7523 (tpp) REVERT: C 570 MET cc_start: 0.7005 (mtt) cc_final: 0.6772 (mtm) REVERT: C 577 ASP cc_start: 0.8317 (t0) cc_final: 0.8103 (t0) REVERT: C 655 MET cc_start: 0.8566 (tpt) cc_final: 0.8224 (tpp) REVERT: C 681 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7147 (mtmt) REVERT: C 690 THR cc_start: 0.7270 (p) cc_final: 0.6999 (t) REVERT: C 694 MET cc_start: 0.7669 (mtp) cc_final: 0.7261 (mtt) REVERT: C 708 LEU cc_start: 0.7954 (tp) cc_final: 0.7514 (mp) REVERT: C 726 TYR cc_start: 0.8649 (t80) cc_final: 0.8172 (t80) REVERT: D 21 ARG cc_start: 0.7342 (ttt180) cc_final: 0.6263 (mmt180) REVERT: D 23 GLN cc_start: 0.8158 (tt0) cc_final: 0.7737 (pt0) REVERT: D 57 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: D 59 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7844 (tt) REVERT: D 172 MET cc_start: 0.7004 (tpp) cc_final: 0.6320 (tpp) REVERT: D 199 THR cc_start: 0.8069 (p) cc_final: 0.7840 (p) REVERT: D 339 MET cc_start: 0.7788 (ttp) cc_final: 0.7265 (ptm) REVERT: D 515 MET cc_start: 0.7900 (mmm) cc_final: 0.7626 (mmt) REVERT: D 570 MET cc_start: 0.7043 (mtt) cc_final: 0.6813 (mtm) REVERT: D 655 MET cc_start: 0.8303 (tpt) cc_final: 0.8041 (tpp) REVERT: D 681 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7194 (ptmt) REVERT: D 694 MET cc_start: 0.7876 (mtp) cc_final: 0.7542 (mtt) REVERT: D 708 LEU cc_start: 0.8041 (tp) cc_final: 0.7417 (mp) REVERT: D 736 MET cc_start: 0.7921 (tmm) cc_final: 0.7712 (tmm) REVERT: E 21 ARG cc_start: 0.7638 (ttt180) cc_final: 0.6716 (mmt-90) REVERT: E 152 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8542 (tm-30) REVERT: E 388 GLN cc_start: 0.8185 (tp40) cc_final: 0.7854 (tp-100) REVERT: E 515 MET cc_start: 0.7149 (tpp) cc_final: 0.6213 (tpp) REVERT: E 517 TYR cc_start: 0.7706 (m-80) cc_final: 0.7172 (m-80) REVERT: E 627 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.6218 (mmp80) REVERT: E 655 MET cc_start: 0.7059 (tpp) cc_final: 0.6721 (tpp) REVERT: E 689 LYS cc_start: 0.8154 (mttt) cc_final: 0.7900 (mmtp) REVERT: F 21 ARG cc_start: 0.7188 (ttt180) cc_final: 0.6583 (mmt90) REVERT: F 81 ILE cc_start: 0.8847 (tt) cc_final: 0.8646 (tp) REVERT: F 307 ASP cc_start: 0.7881 (t0) cc_final: 0.7483 (t0) REVERT: F 515 MET cc_start: 0.7573 (tpp) cc_final: 0.6508 (tpp) REVERT: F 543 SER cc_start: 0.9183 (m) cc_final: 0.8610 (p) REVERT: F 655 MET cc_start: 0.8286 (tpt) cc_final: 0.7916 (tpp) REVERT: F 674 ASP cc_start: 0.6957 (t0) cc_final: 0.6722 (t0) REVERT: F 677 LYS cc_start: 0.7984 (mttt) cc_final: 0.7468 (tptt) REVERT: F 681 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7730 (mtpt) REVERT: F 689 LYS cc_start: 0.8352 (mttt) cc_final: 0.7785 (mmtm) REVERT: F 694 MET cc_start: 0.7937 (mtp) cc_final: 0.7681 (mtt) outliers start: 71 outliers final: 53 residues processed: 603 average time/residue: 0.4921 time to fit residues: 482.0895 Evaluate side-chains 546 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 489 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 698 ARG Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 533 GLU Chi-restraints excluded: chain E residue 621 THR Chi-restraints excluded: chain E residue 627 ARG Chi-restraints excluded: chain E residue 698 ARG Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 624 ILE Chi-restraints excluded: chain F residue 672 ILE Chi-restraints excluded: chain F residue 692 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 4.9990 chunk 375 optimal weight: 0.0670 chunk 107 optimal weight: 1.9990 chunk 324 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 352 optimal weight: 3.9990 chunk 147 optimal weight: 0.0770 chunk 362 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN C 288 GLN C 418 GLN C 730 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.110451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.097713 restraints weight = 78609.879| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.92 r_work: 0.3373 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 37068 Z= 0.159 Angle : 0.581 11.527 50310 Z= 0.289 Chirality : 0.043 0.180 5526 Planarity : 0.003 0.033 6336 Dihedral : 7.794 109.230 5304 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.69 % Allowed : 17.20 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.13), residues: 4458 helix: 0.85 (0.12), residues: 2184 sheet: -0.03 (0.32), residues: 306 loop : -0.45 (0.15), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 728 HIS 0.003 0.000 HIS C 724 PHE 0.019 0.001 PHE D 701 TYR 0.027 0.001 TYR F 517 ARG 0.006 0.000 ARG E 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9529.31 seconds wall clock time: 173 minutes 29.59 seconds (10409.59 seconds total)