Starting phenix.real_space_refine on Sat Mar 16 21:45:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upa_26659/03_2024/7upa_26659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upa_26659/03_2024/7upa_26659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upa_26659/03_2024/7upa_26659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upa_26659/03_2024/7upa_26659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upa_26659/03_2024/7upa_26659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upa_26659/03_2024/7upa_26659.pdb" } resolution = 2.5 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= 0.141 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 9940 2.51 5 N 2586 2.21 5 O 3132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 46": "OE1" <-> "OE2" Residue "L ASP 17": "OD1" <-> "OD2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 251": "OE1" <-> "OE2" Residue "D PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 251": "OE1" <-> "OE2" Residue "G ASP 252": "OD1" <-> "OD2" Residue "G GLU 287": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "E ASP 28": "OD1" <-> "OD2" Residue "E TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C ASP 97": "OD1" <-> "OD2" Residue "F ASP 17": "OD1" <-> "OD2" Residue "F ASP 28": "OD1" <-> "OD2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15745 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 924 Classifications: {'peptide': 118} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 102} Chain: "A" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3462 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 16, 'TRANS': 433} Chain breaks: 1 Chain: "D" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3446 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 16, 'TRANS': 430} Chain breaks: 1 Chain: "G" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3446 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 16, 'TRANS': 430} Chain breaks: 1 Chain: "B" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 924 Classifications: {'peptide': 118} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 102} Chain: "C" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 924 Classifications: {'peptide': 118} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 102} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.45, per 1000 atoms: 0.54 Number of scatterers: 15745 At special positions: 0 Unit cell: (145.2, 132, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 3132 8.00 N 2586 7.00 C 9940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.04 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 392 " distance=2.03 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS G 71 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS G 355 " - pdb=" SG CYS G 363 " distance=2.03 Simple disulfide: pdb=" SG CYS G 387 " - pdb=" SG CYS G 392 " distance=2.04 Simple disulfide: pdb=" SG CYS G 394 " - pdb=" SG CYS G 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.05 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 67 " " NAG A 502 " - " ASN A 99 " " NAG A 503 " - " ASN A 414 " " NAG A 504 " - " ASN A 464 " " NAG D 501 " - " ASN D 67 " " NAG D 502 " - " ASN D 99 " " NAG D 503 " - " ASN D 414 " " NAG D 504 " - " ASN D 464 " " NAG G 501 " - " ASN G 67 " " NAG G 502 " - " ASN G 99 " " NAG G 503 " - " ASN G 414 " " NAG G 504 " - " ASN G 464 " Time building additional restraints: 5.49 Conformation dependent library (CDL) restraints added in 3.0 seconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3754 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 21 sheets defined 30.5% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.851A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.836A pdb=" N LYS H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.828A pdb=" N SER H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.651A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'A' and resid 29 through 37 removed outlier: 3.644A pdb=" N LYS A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.896A pdb=" N CYS A 71 " --> pdb=" O MET A 68 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 68 through 72' Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.854A pdb=" N ASN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 3.953A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.952A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.601A pdb=" N SER A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 removed outlier: 3.611A pdb=" N ILE A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.918A pdb=" N THR A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 197 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 246 removed outlier: 4.002A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.639A pdb=" N CYS A 363 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.695A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 480 removed outlier: 3.838A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 37 removed outlier: 3.703A pdb=" N LYS D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 72 removed outlier: 3.750A pdb=" N SER D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLN D 70 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N CYS D 71 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 100 removed outlier: 3.938A pdb=" N ASN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 86 " --> pdb=" O ARG D 82 " (cutoff:3.500A) Proline residue: D 89 - end of helix removed outlier: 3.942A pdb=" N ILE D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN D 100 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 125 through 145 removed outlier: 4.374A pdb=" N LYS D 139 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASN D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP D 142 " --> pdb=" O MET D 138 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 175 through 182 removed outlier: 3.666A pdb=" N ILE D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 215 removed outlier: 4.006A pdb=" N THR D 195 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 238 through 246 removed outlier: 3.776A pdb=" N LEU D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 349 through 357 Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.648A pdb=" N CYS D 363 " --> pdb=" O THR D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 441 removed outlier: 3.741A pdb=" N GLU D 441 " --> pdb=" O TYR D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 480 removed outlier: 3.763A pdb=" N SER D 457 " --> pdb=" O LYS D 453 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 477 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 37 removed outlier: 3.683A pdb=" N LYS G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 removed outlier: 3.986A pdb=" N SER G 69 " --> pdb=" O SER G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 99 removed outlier: 3.587A pdb=" N ASN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY G 85 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Proline residue: G 89 - end of helix removed outlier: 3.814A pdb=" N ILE G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 Processing helix chain 'G' and resid 125 through 145 removed outlier: 4.389A pdb=" N LYS G 139 " --> pdb=" O TYR G 135 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASN G 140 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA G 141 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP G 142 " --> pdb=" O MET G 138 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN G 143 " --> pdb=" O LYS G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 153 Processing helix chain 'G' and resid 175 through 182 removed outlier: 3.626A pdb=" N ILE G 179 " --> pdb=" O LEU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 215 removed outlier: 3.692A pdb=" N THR G 195 " --> pdb=" O PRO G 191 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 238 through 246 removed outlier: 3.855A pdb=" N LEU G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 328 through 331 Processing helix chain 'G' and resid 349 through 357 Processing helix chain 'G' and resid 359 through 363 removed outlier: 3.554A pdb=" N CYS G 363 " --> pdb=" O THR G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 441 removed outlier: 3.740A pdb=" N GLU G 441 " --> pdb=" O TYR G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 480 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.862A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 3.731A pdb=" N LYS B 64 " --> pdb=" O GLN B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.707A pdb=" N SER B 87 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.706A pdb=" N ILE E 83 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.796A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.682A pdb=" N LYS C 64 " --> pdb=" O GLN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.730A pdb=" N SER C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.653A pdb=" N ASP F 82 " --> pdb=" O GLU F 79 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE F 83 " --> pdb=" O GLN F 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 56 through 59 current: chain 'H' and resid 100B through 103 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 100B through 103 current: chain 'A' and resid 168 through 173 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 168 through 173 current: chain 'A' and resid 263 through 270 removed outlier: 3.905A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 288 current: chain 'A' and resid 315 through 319 removed outlier: 6.483A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 322 through 326 current: chain 'A' and resid 337 through 340 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 44 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AA5, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.564A pdb=" N VAL A 113 " --> pdb=" O ILE G 426 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N SER G 428 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N MET A 115 " --> pdb=" O SER G 428 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN G 393 " --> pdb=" O VAL G 421 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG G 399 " --> pdb=" O CYS G 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA8, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA9, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.944A pdb=" N GLN A 393 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 38 through 60 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 38 through 60 current: chain 'D' and resid 167 through 173 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 167 through 173 current: chain 'D' and resid 263 through 270 removed outlier: 6.023A pdb=" N GLY D 264 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR D 281 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE D 266 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG D 279 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR D 268 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR D 275 " --> pdb=" O ASP D 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 275 through 288 current: chain 'D' and resid 315 through 319 removed outlier: 6.474A pdb=" N PHE D 315 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE D 326 " --> pdb=" O PHE D 315 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 322 through 326 current: chain 'D' and resid 337 through 340 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 337 through 340 current: chain 'C' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 59 current: chain 'C' and resid 100B through 103 Processing sheet with id=AB2, first strand: chain 'D' and resid 301 through 303 Processing sheet with id=AB3, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB4, first strand: chain 'D' and resid 399 through 400 removed outlier: 3.523A pdb=" N ARG D 399 " --> pdb=" O CYS D 394 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN D 393 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE D 426 " --> pdb=" O MET G 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 38 through 60 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 38 through 60 current: chain 'G' and resid 168 through 173 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 168 through 173 current: chain 'G' and resid 263 through 270 removed outlier: 5.971A pdb=" N GLY G 264 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TYR G 281 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE G 266 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG G 279 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR G 268 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR G 275 " --> pdb=" O ASP G 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 275 through 288 current: chain 'G' and resid 315 through 319 removed outlier: 6.486A pdb=" N PHE G 315 " --> pdb=" O ILE G 326 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE G 326 " --> pdb=" O PHE G 315 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 322 through 326 current: chain 'G' and resid 337 through 340 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 337 through 340 current: chain 'B' and resid 44 through 52 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 59 current: chain 'B' and resid 100B through 103 Processing sheet with id=AB6, first strand: chain 'G' and resid 301 through 302 Processing sheet with id=AB7, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.734A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 10 through 12 current: chain 'F' and resid 44 through 49 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 53 through 54 current: chain 'F' and resid 97 through 98 493 hydrogen bonds defined for protein. 1305 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: 4.87 Time building geometry restraints manager: 6.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5065 1.35 - 1.47: 3722 1.47 - 1.59: 7096 1.59 - 1.71: 0 1.71 - 1.83: 126 Bond restraints: 16009 Sorted by residual: bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C1 NAG A 502 " pdb=" O5 NAG A 502 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C1 NAG D 503 " pdb=" O5 NAG D 503 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG G 502 " pdb=" O5 NAG G 502 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 ... (remaining 16004 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.76: 266 105.76 - 112.83: 8684 112.83 - 119.90: 5280 119.90 - 126.97: 7374 126.97 - 134.03: 120 Bond angle restraints: 21724 Sorted by residual: angle pdb=" CG ARG A 399 " pdb=" CD ARG A 399 " pdb=" NE ARG A 399 " ideal model delta sigma weight residual 112.00 120.05 -8.05 2.20e+00 2.07e-01 1.34e+01 angle pdb=" CA GLU H 85 " pdb=" CB GLU H 85 " pdb=" CG GLU H 85 " ideal model delta sigma weight residual 114.10 121.40 -7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" CG ARG G 399 " pdb=" CD ARG G 399 " pdb=" NE ARG G 399 " ideal model delta sigma weight residual 112.00 119.74 -7.74 2.20e+00 2.07e-01 1.24e+01 angle pdb=" CB GLU H 85 " pdb=" CG GLU H 85 " pdb=" CD GLU H 85 " ideal model delta sigma weight residual 112.60 118.35 -5.75 1.70e+00 3.46e-01 1.14e+01 angle pdb=" CA GLU C 85 " pdb=" CB GLU C 85 " pdb=" CG GLU C 85 " ideal model delta sigma weight residual 114.10 120.57 -6.47 2.00e+00 2.50e-01 1.05e+01 ... (remaining 21719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8821 17.90 - 35.81: 760 35.81 - 53.71: 221 53.71 - 71.61: 45 71.61 - 89.52: 13 Dihedral angle restraints: 9860 sinusoidal: 4006 harmonic: 5854 Sorted by residual: dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -169.16 83.16 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS D 71 " pdb=" SG CYS D 71 " pdb=" SG CYS D 192 " pdb=" CB CYS D 192 " ideal model delta sinusoidal sigma weight residual -86.00 -164.95 78.95 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS A 387 " pdb=" SG CYS A 387 " pdb=" SG CYS A 392 " pdb=" CB CYS A 392 " ideal model delta sinusoidal sigma weight residual 93.00 43.70 49.30 1 1.00e+01 1.00e-02 3.34e+01 ... (remaining 9857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2123 0.061 - 0.121: 411 0.121 - 0.182: 53 0.182 - 0.243: 4 0.243 - 0.303: 1 Chirality restraints: 2592 Sorted by residual: chirality pdb=" C1 NAG D 502 " pdb=" ND2 ASN D 99 " pdb=" C2 NAG D 502 " pdb=" O5 NAG D 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C1 NAG G 501 " pdb=" ND2 ASN G 67 " pdb=" C2 NAG G 501 " pdb=" O5 NAG G 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CA ASN L 77 " pdb=" N ASN L 77 " pdb=" C ASN L 77 " pdb=" CB ASN L 77 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 2589 not shown) Planarity restraints: 2751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 336 " -0.155 9.50e-02 1.11e+02 7.02e-02 3.99e+00 pdb=" NE ARG G 336 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG G 336 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG G 336 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG G 336 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 85 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" CD GLU C 85 " 0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU C 85 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU C 85 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 399 " -0.153 9.50e-02 1.11e+02 6.91e-02 3.77e+00 pdb=" NE ARG D 399 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 399 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG D 399 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG D 399 " -0.000 2.00e-02 2.50e+03 ... (remaining 2748 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2052 2.76 - 3.30: 13544 3.30 - 3.83: 23921 3.83 - 4.37: 28183 4.37 - 4.90: 50626 Nonbonded interactions: 118326 Sorted by model distance: nonbonded pdb=" OD2 ASP B 72 " pdb=" OG SER B 75 " model vdw 2.227 2.440 nonbonded pdb=" OE1 GLU D 327 " pdb=" OG1 THR D 346 " model vdw 2.229 2.440 nonbonded pdb=" OE1 GLU G 327 " pdb=" OG1 THR G 346 " model vdw 2.251 2.440 nonbonded pdb=" N GLU A 251 " pdb=" OE1 GLU A 251 " model vdw 2.252 2.520 nonbonded pdb=" OE1 GLU A 327 " pdb=" OG1 THR A 346 " model vdw 2.261 2.440 ... (remaining 118321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 104 or resid 112 through 480 or resid 501 throu \ gh 504)) selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'L' } 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=0.00 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: 5.180 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: 0.010 Extract box with map and model: 17.610 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 41.830 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.100 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:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.003 0.042 16009 Z= 0.221 Angle : 0.645 8.316 21724 Z= 0.346 Chirality : 0.048 0.303 2592 Planarity : 0.005 0.070 2739 Dihedral : 14.864 89.515 6034 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.96 % Allowed : 11.80 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.34 (0.19), residues: 1992 helix: 1.88 (0.27), residues: 411 sheet: 0.74 (0.20), residues: 647 loop : -0.92 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 103 HIS 0.002 0.000 HIS D 29 PHE 0.009 0.001 PHE D 301 TYR 0.014 0.001 TYR D 473 ARG 0.017 0.001 ARG G 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.827 Fit side-chains REVERT: L 23 CYS cc_start: 0.6180 (t) cc_final: 0.5810 (t) REVERT: A 244 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7633 (mmt90) REVERT: E 24 ARG cc_start: 0.7133 (mtp-110) cc_final: 0.6579 (ttm110) REVERT: E 105 GLU cc_start: 0.7827 (pp20) cc_final: 0.7333 (pm20) outliers start: 17 outliers final: 15 residues processed: 180 average time/residue: 1.5974 time to fit residues: 311.8789 Evaluate side-chains 179 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain C residue 21 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 100 optimal weight: 0.0770 chunk 79 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 114 optimal weight: 0.3980 chunk 177 optimal weight: 3.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN E 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16009 Z= 0.154 Angle : 0.502 6.849 21724 Z= 0.272 Chirality : 0.045 0.292 2592 Planarity : 0.004 0.037 2739 Dihedral : 6.229 59.076 2435 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.37 % Allowed : 11.29 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.58 (0.19), residues: 1992 helix: 2.17 (0.27), residues: 419 sheet: 0.82 (0.21), residues: 645 loop : -0.78 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 103 HIS 0.001 0.000 HIS D 102 PHE 0.007 0.001 PHE E 87 TYR 0.012 0.001 TYR D 473 ARG 0.008 0.001 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 2.181 Fit side-chains revert: symmetry clash REVERT: H 72 ASP cc_start: 0.8110 (t0) cc_final: 0.7909 (t0) REVERT: H 95 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: L 23 CYS cc_start: 0.6035 (t) cc_final: 0.5384 (t) REVERT: D 322 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7943 (mm) REVERT: B 73 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8356 (mttt) REVERT: E 11 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8307 (tt) REVERT: E 105 GLU cc_start: 0.7656 (pp20) cc_final: 0.7240 (pm20) REVERT: F 77 ASN cc_start: 0.8230 (p0) cc_final: 0.7859 (p0) outliers start: 42 outliers final: 22 residues processed: 188 average time/residue: 1.5451 time to fit residues: 316.4545 Evaluate side-chains 190 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain G residue 71 CYS Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.0020 chunk 55 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 176 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN E 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16009 Z= 0.151 Angle : 0.491 6.879 21724 Z= 0.266 Chirality : 0.045 0.290 2592 Planarity : 0.004 0.039 2739 Dihedral : 5.693 57.453 2421 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.77 % Allowed : 11.80 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.63 (0.19), residues: 1992 helix: 2.35 (0.27), residues: 422 sheet: 0.75 (0.20), residues: 659 loop : -0.77 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 103 HIS 0.001 0.000 HIS G 102 PHE 0.008 0.001 PHE E 87 TYR 0.012 0.001 TYR D 473 ARG 0.009 0.001 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 167 time to evaluate : 2.173 Fit side-chains revert: symmetry clash REVERT: H 72 ASP cc_start: 0.8128 (t0) cc_final: 0.7887 (t0) REVERT: H 95 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: L 23 CYS cc_start: 0.6081 (t) cc_final: 0.5420 (t) REVERT: A 463 MET cc_start: 0.9042 (mtp) cc_final: 0.8805 (mtp) REVERT: D 322 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7976 (mm) REVERT: B 73 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8358 (mttt) REVERT: B 95 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: E 105 GLU cc_start: 0.7617 (pp20) cc_final: 0.7352 (pm20) REVERT: C 10 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: C 81 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: F 77 ASN cc_start: 0.8273 (p0) cc_final: 0.7943 (p0) outliers start: 49 outliers final: 23 residues processed: 195 average time/residue: 1.4835 time to fit residues: 315.7927 Evaluate side-chains 192 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain G residue 71 CYS Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain F residue 11 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 93 optimal weight: 0.0980 chunk 169 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN E 3 GLN C 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16009 Z= 0.174 Angle : 0.510 7.003 21724 Z= 0.277 Chirality : 0.046 0.285 2592 Planarity : 0.004 0.040 2739 Dihedral : 5.606 56.087 2419 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.11 % Allowed : 12.14 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.63 (0.19), residues: 1992 helix: 2.39 (0.27), residues: 421 sheet: 0.76 (0.21), residues: 644 loop : -0.78 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 103 HIS 0.001 0.000 HIS B 41 PHE 0.009 0.001 PHE E 87 TYR 0.012 0.001 TYR D 473 ARG 0.010 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 167 time to evaluate : 1.823 Fit side-chains revert: symmetry clash REVERT: H 95 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: L 23 CYS cc_start: 0.6056 (t) cc_final: 0.5408 (t) REVERT: A 322 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7693 (mm) REVERT: A 463 MET cc_start: 0.9024 (mtp) cc_final: 0.8813 (mtp) REVERT: D 70 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7226 (pt0) REVERT: D 322 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7989 (mm) REVERT: B 73 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8428 (mttt) REVERT: E 11 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8285 (tt) REVERT: E 105 GLU cc_start: 0.7623 (pp20) cc_final: 0.7350 (pm20) REVERT: C 10 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7590 (mm-30) REVERT: C 81 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: F 77 ASN cc_start: 0.8252 (p0) cc_final: 0.7912 (p0) outliers start: 55 outliers final: 30 residues processed: 203 average time/residue: 1.4921 time to fit residues: 330.3502 Evaluate side-chains 205 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain G residue 71 CYS Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 6 GLN B 61 GLN E 3 GLN C 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16009 Z= 0.278 Angle : 0.604 6.674 21724 Z= 0.328 Chirality : 0.048 0.276 2592 Planarity : 0.004 0.041 2739 Dihedral : 5.961 56.867 2419 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.27 % Allowed : 12.54 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1992 helix: 2.31 (0.27), residues: 418 sheet: 0.66 (0.21), residues: 629 loop : -0.96 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 103 HIS 0.002 0.001 HIS G 29 PHE 0.013 0.001 PHE E 87 TYR 0.014 0.002 TYR B 98 ARG 0.010 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 165 time to evaluate : 1.751 Fit side-chains revert: symmetry clash REVERT: L 23 CYS cc_start: 0.6290 (t) cc_final: 0.5607 (t) REVERT: A 244 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7604 (mmt90) REVERT: A 322 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7712 (mm) REVERT: A 463 MET cc_start: 0.9044 (mtp) cc_final: 0.8591 (mtm) REVERT: D 70 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7282 (pt0) REVERT: D 322 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7997 (mm) REVERT: B 73 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8501 (mttt) REVERT: B 95 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: E 11 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8301 (tt) REVERT: E 105 GLU cc_start: 0.7672 (pp20) cc_final: 0.7362 (pm20) REVERT: C 10 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: C 81 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: F 77 ASN cc_start: 0.8280 (p0) cc_final: 0.7869 (p0) outliers start: 58 outliers final: 33 residues processed: 201 average time/residue: 1.4977 time to fit residues: 328.0477 Evaluate side-chains 206 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 164 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain G residue 71 CYS Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 361 GLU Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 189 optimal weight: 0.5980 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 0.1980 chunk 99 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 61 GLN E 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16009 Z= 0.147 Angle : 0.497 5.118 21724 Z= 0.270 Chirality : 0.045 0.277 2592 Planarity : 0.004 0.042 2739 Dihedral : 5.579 53.537 2419 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.82 % Allowed : 13.50 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.19), residues: 1992 helix: 2.51 (0.27), residues: 418 sheet: 0.67 (0.21), residues: 649 loop : -0.89 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 103 HIS 0.001 0.000 HIS H 41 PHE 0.008 0.001 PHE E 49 TYR 0.012 0.001 TYR D 473 ARG 0.012 0.001 ARG G 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 168 time to evaluate : 1.928 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8141 (pt0) cc_final: 0.7482 (pp30) REVERT: L 23 CYS cc_start: 0.6072 (t) cc_final: 0.5455 (t) REVERT: A 244 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7712 (mmt180) REVERT: A 322 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7702 (mm) REVERT: A 463 MET cc_start: 0.9040 (mtp) cc_final: 0.8837 (mtp) REVERT: D 70 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: D 322 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7989 (mm) REVERT: G 361 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: B 73 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8341 (mttt) REVERT: B 95 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: E 11 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8278 (tt) REVERT: E 105 GLU cc_start: 0.7583 (pp20) cc_final: 0.7263 (pm20) REVERT: C 81 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: F 77 ASN cc_start: 0.8259 (p0) cc_final: 0.7962 (p0) outliers start: 50 outliers final: 30 residues processed: 200 average time/residue: 1.5143 time to fit residues: 330.0197 Evaluate side-chains 203 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 164 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain G residue 71 CYS Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 361 GLU Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain F residue 11 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN E 3 GLN C 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16009 Z= 0.275 Angle : 0.615 7.037 21724 Z= 0.332 Chirality : 0.048 0.282 2592 Planarity : 0.005 0.053 2739 Dihedral : 5.802 53.951 2417 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.33 % Allowed : 13.27 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1992 helix: 2.35 (0.27), residues: 418 sheet: 0.64 (0.21), residues: 623 loop : -0.98 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 103 HIS 0.002 0.001 HIS G 29 PHE 0.013 0.001 PHE E 87 TYR 0.014 0.002 TYR B 98 ARG 0.013 0.001 ARG G 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 166 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 10 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7689 (mt-10) REVERT: L 23 CYS cc_start: 0.6339 (t) cc_final: 0.5675 (t) REVERT: A 244 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7723 (mmt180) REVERT: A 322 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7716 (mm) REVERT: A 463 MET cc_start: 0.9055 (mtp) cc_final: 0.8631 (mtm) REVERT: D 322 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8003 (mm) REVERT: B 73 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8453 (mttt) REVERT: B 95 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: E 11 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8308 (tt) REVERT: E 105 GLU cc_start: 0.7664 (pp20) cc_final: 0.7348 (pm20) REVERT: C 10 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7539 (mm-30) REVERT: C 81 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: F 77 ASN cc_start: 0.8346 (p0) cc_final: 0.8116 (p0) REVERT: F 105 GLU cc_start: 0.7614 (pp20) cc_final: 0.7307 (pm20) outliers start: 59 outliers final: 36 residues processed: 204 average time/residue: 1.5202 time to fit residues: 338.2477 Evaluate side-chains 210 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 166 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain G residue 71 CYS Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 361 GLU Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN E 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16009 Z= 0.163 Angle : 0.518 6.121 21724 Z= 0.281 Chirality : 0.045 0.277 2592 Planarity : 0.004 0.055 2739 Dihedral : 5.509 51.174 2417 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.71 % Allowed : 13.55 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.46 (0.19), residues: 1992 helix: 2.50 (0.27), residues: 418 sheet: 0.68 (0.21), residues: 617 loop : -0.98 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 103 HIS 0.001 0.000 HIS H 41 PHE 0.008 0.001 PHE E 87 TYR 0.012 0.001 TYR D 473 ARG 0.014 0.001 ARG G 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 164 time to evaluate : 1.860 Fit side-chains revert: symmetry clash REVERT: L 23 CYS cc_start: 0.6181 (t) cc_final: 0.5562 (t) REVERT: A 244 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7685 (mmt180) REVERT: A 322 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7718 (mm) REVERT: A 463 MET cc_start: 0.9057 (mtp) cc_final: 0.8705 (mtm) REVERT: D 70 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7333 (pt0) REVERT: D 322 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7991 (mm) REVERT: G 361 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: B 73 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8368 (mttt) REVERT: E 11 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8256 (tt) REVERT: E 105 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: C 10 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7533 (mm-30) REVERT: C 81 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: F 77 ASN cc_start: 0.8282 (p0) cc_final: 0.8057 (p0) REVERT: F 105 GLU cc_start: 0.7607 (pp20) cc_final: 0.7366 (pm20) outliers start: 48 outliers final: 33 residues processed: 193 average time/residue: 1.5272 time to fit residues: 320.5678 Evaluate side-chains 207 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 164 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain G residue 71 CYS Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 361 GLU Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain F residue 11 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN E 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16009 Z= 0.284 Angle : 0.631 8.453 21724 Z= 0.339 Chirality : 0.049 0.286 2592 Planarity : 0.005 0.063 2739 Dihedral : 5.809 52.306 2417 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.94 % Allowed : 13.72 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.37 (0.19), residues: 1992 helix: 2.34 (0.26), residues: 418 sheet: 0.62 (0.21), residues: 603 loop : -0.97 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 103 HIS 0.004 0.001 HIS B 41 PHE 0.013 0.001 PHE E 87 TYR 0.014 0.002 TYR B 98 ARG 0.015 0.001 ARG G 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 165 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 23 CYS cc_start: 0.6217 (t) cc_final: 0.5556 (t) REVERT: A 244 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7719 (mmt180) REVERT: A 322 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7716 (mm) REVERT: A 463 MET cc_start: 0.9060 (mtp) cc_final: 0.8629 (mtm) REVERT: D 322 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8006 (mm) REVERT: B 43 LYS cc_start: 0.7596 (mmpt) cc_final: 0.7224 (mmmm) REVERT: B 73 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8456 (mttt) REVERT: E 11 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8312 (tt) REVERT: E 105 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: C 10 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7495 (mm-30) REVERT: C 81 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8189 (tt0) outliers start: 52 outliers final: 36 residues processed: 200 average time/residue: 1.5127 time to fit residues: 329.1053 Evaluate side-chains 209 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 165 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain G residue 71 CYS Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 361 GLU Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain F residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 113 optimal weight: 0.0170 chunk 88 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 195 optimal weight: 0.6980 chunk 179 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 120 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16009 Z= 0.157 Angle : 0.525 7.530 21724 Z= 0.282 Chirality : 0.045 0.280 2592 Planarity : 0.004 0.058 2739 Dihedral : 5.403 50.916 2417 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.37 % Allowed : 14.29 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 1992 helix: 2.55 (0.27), residues: 418 sheet: 0.67 (0.21), residues: 649 loop : -0.98 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 103 HIS 0.001 0.000 HIS B 41 PHE 0.008 0.001 PHE D 301 TYR 0.012 0.001 TYR D 473 ARG 0.014 0.001 ARG G 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 10 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7633 (mt-10) REVERT: L 23 CYS cc_start: 0.6167 (t) cc_final: 0.5569 (t) REVERT: A 244 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7682 (mmt180) REVERT: A 322 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7701 (mm) REVERT: A 463 MET cc_start: 0.9046 (mtp) cc_final: 0.8678 (mtm) REVERT: D 322 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8024 (mm) REVERT: G 361 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: B 43 LYS cc_start: 0.7412 (mmpt) cc_final: 0.6993 (mmmt) REVERT: B 73 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8362 (mttt) REVERT: E 11 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8294 (tt) REVERT: E 105 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7264 (pm20) REVERT: C 10 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: C 81 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8101 (tt0) outliers start: 42 outliers final: 29 residues processed: 193 average time/residue: 1.5526 time to fit residues: 326.3624 Evaluate side-chains 202 residues out of total 1771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 164 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain G residue 71 CYS Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 361 GLU Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain F residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN E 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.098015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.071241 restraints weight = 25434.698| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.74 r_work: 0.2874 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16009 Z= 0.314 Angle : 0.657 8.790 21724 Z= 0.353 Chirality : 0.049 0.294 2592 Planarity : 0.005 0.058 2739 Dihedral : 5.790 52.579 2416 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.88 % Allowed : 14.00 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.32 (0.19), residues: 1992 helix: 2.32 (0.26), residues: 418 sheet: 0.63 (0.21), residues: 588 loop : -1.01 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 103 HIS 0.002 0.001 HIS G 29 PHE 0.014 0.001 PHE E 87 TYR 0.016 0.002 TYR B 98 ARG 0.014 0.001 ARG G 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6027.03 seconds wall clock time: 107 minutes 11.04 seconds (6431.04 seconds total)