Starting phenix.real_space_refine on Sun Mar 17 11:06:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/03_2024/6voy_21301.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/03_2024/6voy_21301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/03_2024/6voy_21301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/03_2024/6voy_21301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/03_2024/6voy_21301.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voy_21301/03_2024/6voy_21301.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 178 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 10706 2.51 5 N 3072 2.21 5 O 3540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 31": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 47": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ARG 47": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E GLU 276": "OE1" <-> "OE2" Residue "E GLU 310": "OE1" <-> "OE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F GLU 78": "OE1" <-> "OE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "F GLU 307": "OE1" <-> "OE2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "F GLU 344": "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: 17556 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2200 Classifications: {'peptide': 276} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 257} Chain: "B" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2058 Classifications: {'peptide': 259} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 242} Chain breaks: 1 Chain: "C" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2200 Classifications: {'peptide': 276} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 257} Chain: "D" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2058 Classifications: {'peptide': 259} Link IDs: {'CIS': 2, 'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "E" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2676 Classifications: {'peptide': 327} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 304} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2676 Classifications: {'peptide': 327} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 304} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 966 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "J" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 504 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "K" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 371 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "L" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 966 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "M" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 504 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "N" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 371 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 246 SG CYS A 33 63.285 78.778 64.823 1.00116.78 S ATOM 267 SG CYS A 36 64.894 75.597 65.874 1.00 99.36 S ATOM 2439 SG CYS B 33 137.488 80.123 80.291 1.00299.42 S ATOM 2460 SG CYS B 36 138.441 77.611 78.802 1.00269.90 S ATOM 4504 SG CYS C 33 105.877 38.294 66.337 1.00107.32 S ATOM 4525 SG CYS C 36 104.269 41.389 64.821 1.00 95.45 S ATOM 6697 SG CYS D 33 31.902 36.894 81.648 1.00337.40 S ATOM 6718 SG CYS D 36 30.371 38.588 79.947 1.00308.22 S Time building chain proxies: 9.41, per 1000 atoms: 0.54 Number of scatterers: 17556 At special positions: 0 Unit cell: (170.62, 115.236, 139.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 54 16.00 P 178 15.00 Mg 2 11.99 O 3540 8.00 N 3072 7.00 C 10706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.87 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 10 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 6 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 36 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 33 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 10 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 6 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 33 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 36 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 6 " pdb="ZN ZN C 301 " - pdb=" ND1 HIS C 10 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 33 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 36 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 10 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 6 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 36 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 33 " Number of angles added : 7 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 8 sheets defined 51.7% alpha, 4.1% beta 82 base pairs and 123 stacking pairs defined. Time for finding SS restraints: 6.54 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 96 through 108 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 148 through 151 Processing helix chain 'A' and resid 152 through 172 Processing helix chain 'A' and resid 179 through 191 Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 209 through 212 Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 16 through 20 Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 96 through 110 Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 151 through 171 Processing helix chain 'B' and resid 179 through 190 Processing helix chain 'B' and resid 201 through 207 Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 12 through 20 Processing helix chain 'C' and resid 22 through 30 Processing helix chain 'C' and resid 33 through 39 Processing helix chain 'C' and resid 96 through 108 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 127 through 136 Processing helix chain 'C' and resid 148 through 151 Processing helix chain 'C' and resid 152 through 172 Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 209 through 212 Processing helix chain 'C' and resid 267 through 271 Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 22 through 32 Processing helix chain 'D' and resid 96 through 110 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 127 through 135 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 151 through 171 Processing helix chain 'D' and resid 179 through 190 Processing helix chain 'D' and resid 201 through 206 Processing helix chain 'E' and resid 38 through 48 Processing helix chain 'E' and resid 63 through 83 Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 91 through 104 Processing helix chain 'E' and resid 130 through 146 Processing helix chain 'E' and resid 151 through 156 Processing helix chain 'E' and resid 160 through 169 Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 175 through 193 Processing helix chain 'E' and resid 194 through 213 Processing helix chain 'E' and resid 221 through 234 Processing helix chain 'E' and resid 241 through 251 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 259 through 262 Processing helix chain 'E' and resid 263 through 276 Processing helix chain 'E' and resid 277 through 286 Proline residue: E 284 - end of helix Processing helix chain 'E' and resid 287 through 292 Processing helix chain 'E' and resid 298 through 310 Processing helix chain 'E' and resid 320 through 332 removed outlier: 4.731A pdb=" N GLU E 325 " --> pdb=" O VAL E 321 " (cutoff:3.500A) Proline residue: E 326 - end of helix removed outlier: 3.696A pdb=" N GLN E 330 " --> pdb=" O PRO E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 346 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 63 through 83 Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 91 through 104 Processing helix chain 'F' and resid 130 through 146 Processing helix chain 'F' and resid 151 through 156 Processing helix chain 'F' and resid 160 through 169 Processing helix chain 'F' and resid 170 through 173 Processing helix chain 'F' and resid 175 through 193 Processing helix chain 'F' and resid 194 through 213 Processing helix chain 'F' and resid 221 through 234 Processing helix chain 'F' and resid 241 through 251 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 259 through 262 Processing helix chain 'F' and resid 263 through 276 Processing helix chain 'F' and resid 277 through 286 Proline residue: F 284 - end of helix Processing helix chain 'F' and resid 287 through 292 Processing helix chain 'F' and resid 298 through 310 Processing helix chain 'F' and resid 320 through 332 removed outlier: 4.702A pdb=" N GLU F 325 " --> pdb=" O VAL F 321 " (cutoff:3.500A) Proline residue: F 326 - end of helix removed outlier: 3.701A pdb=" N GLN F 330 " --> pdb=" O PRO F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 346 Processing helix chain 'F' and resid 353 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 230 Processing sheet with id=AA3, first strand: chain 'A' and resid 254 through 258 Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 65 Processing sheet with id=AA5, first strand: chain 'B' and resid 228 through 230 removed outlier: 4.195A pdb=" N GLN B 244 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N PHE B 230 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLY B 242 " --> pdb=" O PHE B 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 61 through 66 Processing sheet with id=AA7, first strand: chain 'D' and resid 62 through 65 Processing sheet with id=AA8, first strand: chain 'D' and resid 116 through 117 589 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 198 hydrogen bonds 392 hydrogen bond angles 0 basepair planarities 82 basepair parallelities 123 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 8.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3018 1.32 - 1.45: 5935 1.45 - 1.58: 9006 1.58 - 1.70: 347 1.70 - 1.83: 80 Bond restraints: 18386 Sorted by residual: bond pdb=" CG PRO D 243 " pdb=" CD PRO D 243 " ideal model delta sigma weight residual 1.503 1.348 0.155 3.40e-02 8.65e+02 2.09e+01 bond pdb=" CB TRP A 240 " pdb=" CG TRP A 240 " ideal model delta sigma weight residual 1.498 1.362 0.136 3.10e-02 1.04e+03 1.94e+01 bond pdb=" CB TRP C 60 " pdb=" CG TRP C 60 " ideal model delta sigma weight residual 1.498 1.368 0.130 3.10e-02 1.04e+03 1.76e+01 bond pdb=" CB ASN B 118 " pdb=" CG ASN B 118 " ideal model delta sigma weight residual 1.516 1.419 0.097 2.50e-02 1.60e+03 1.52e+01 bond pdb=" CB TRP C 240 " pdb=" CG TRP C 240 " ideal model delta sigma weight residual 1.498 1.388 0.110 3.10e-02 1.04e+03 1.25e+01 ... (remaining 18381 not shown) Histogram of bond angle deviations from ideal: 78.86 - 93.21: 2 93.21 - 107.56: 2489 107.56 - 121.91: 19516 121.91 - 136.26: 3760 136.26 - 150.62: 1 Bond angle restraints: 25768 Sorted by residual: angle pdb=" N PHE A 230 " pdb=" CA PHE A 230 " pdb=" CB PHE A 230 " ideal model delta sigma weight residual 110.63 78.86 31.77 1.94e+00 2.66e-01 2.68e+02 angle pdb=" C TRP D 227 " pdb=" N TYR D 228 " pdb=" CA TYR D 228 " ideal model delta sigma weight residual 121.70 150.62 -28.92 1.80e+00 3.09e-01 2.58e+02 angle pdb=" N PHE C 230 " pdb=" CA PHE C 230 " pdb=" C PHE C 230 " ideal model delta sigma weight residual 112.12 132.09 -19.97 1.34e+00 5.57e-01 2.22e+02 angle pdb=" N PHE A 230 " pdb=" CA PHE A 230 " pdb=" C PHE A 230 " ideal model delta sigma weight residual 112.12 131.73 -19.61 1.34e+00 5.57e-01 2.14e+02 angle pdb=" N PHE C 230 " pdb=" CA PHE C 230 " pdb=" CB PHE C 230 " ideal model delta sigma weight residual 110.63 83.38 27.25 1.94e+00 2.66e-01 1.97e+02 ... (remaining 25763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 9409 35.22 - 70.43: 1023 70.43 - 105.65: 52 105.65 - 140.86: 5 140.86 - 176.08: 9 Dihedral angle restraints: 10498 sinusoidal: 5394 harmonic: 5104 Sorted by residual: dihedral pdb=" CA GLU E 276 " pdb=" C GLU E 276 " pdb=" N LYS E 277 " pdb=" CA LYS E 277 " ideal model delta harmonic sigma weight residual -180.00 -49.46 -130.54 0 5.00e+00 4.00e-02 6.82e+02 dihedral pdb=" CA GLU F 276 " pdb=" C GLU F 276 " pdb=" N LYS F 277 " pdb=" CA LYS F 277 " ideal model delta harmonic sigma weight residual -180.00 -50.02 -129.98 0 5.00e+00 4.00e-02 6.76e+02 dihedral pdb=" CA GLN A 244 " pdb=" C GLN A 244 " pdb=" N GLU A 245 " pdb=" CA GLU A 245 " ideal model delta harmonic sigma weight residual -180.00 -83.94 -96.06 0 5.00e+00 4.00e-02 3.69e+02 ... (remaining 10495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 2853 0.336 - 0.672: 23 0.672 - 1.009: 4 1.009 - 1.345: 1 1.345 - 1.681: 1 Chirality restraints: 2882 Sorted by residual: chirality pdb=" CA TYR D 228 " pdb=" N TYR D 228 " pdb=" C TYR D 228 " pdb=" CB TYR D 228 " both_signs ideal model delta sigma weight residual False 2.51 0.83 1.68 2.00e-01 2.50e+01 7.06e+01 chirality pdb=" CA PRO C 243 " pdb=" N PRO C 243 " pdb=" C PRO C 243 " pdb=" CB PRO C 243 " both_signs ideal model delta sigma weight residual False 2.72 1.71 1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" CA PRO A 243 " pdb=" N PRO A 243 " pdb=" C PRO A 243 " pdb=" CB PRO A 243 " both_signs ideal model delta sigma weight residual False 2.72 1.72 1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 2879 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 153 " 0.043 2.00e-02 2.50e+03 8.63e-02 7.45e+01 pdb=" C GLY B 153 " -0.149 2.00e-02 2.50e+03 pdb=" O GLY B 153 " 0.056 2.00e-02 2.50e+03 pdb=" N LEU B 154 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 132 " -0.041 2.00e-02 2.50e+03 8.00e-02 6.40e+01 pdb=" C PRO F 132 " 0.138 2.00e-02 2.50e+03 pdb=" O PRO F 132 " -0.051 2.00e-02 2.50e+03 pdb=" N HIS F 133 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 132 " 0.041 2.00e-02 2.50e+03 8.00e-02 6.39e+01 pdb=" C PRO E 132 " -0.138 2.00e-02 2.50e+03 pdb=" O PRO E 132 " 0.051 2.00e-02 2.50e+03 pdb=" N HIS E 133 " 0.047 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.25: 47 2.25 - 2.91: 8538 2.91 - 3.57: 28016 3.57 - 4.24: 42570 4.24 - 4.90: 62808 Nonbonded interactions: 141979 Sorted by model distance: nonbonded pdb=" O TRP A 60 " pdb=" O VAL A 80 " model vdw 1.583 3.040 nonbonded pdb=" CD2 HIS B 6 " pdb=" CD2 HIS B 10 " model vdw 1.769 3.480 nonbonded pdb=" O GLY C 122 " pdb=" N TYR C 125 " model vdw 1.971 2.520 nonbonded pdb=" OD2 ASP A 63 " pdb="MG MG A 302 " model vdw 1.992 2.170 nonbonded pdb=" NE2 GLN A 44 " pdb=" OP1 DT J 10 " model vdw 2.005 2.520 ... (remaining 141974 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 1 through 37 or resid 53 through 274)) selection = (chain 'B' and resid 1 through 274) selection = (chain 'C' and (resid 1 through 37 or resid 53 through 274)) selection = (chain 'D' and resid 1 through 274) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 4.950 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 54.530 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.155 18386 Z= 0.778 Angle : 1.522 31.766 25768 Z= 0.887 Chirality : 0.100 1.681 2882 Planarity : 0.013 0.095 2630 Dihedral : 24.618 176.075 7174 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 35.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.46 % Allowed : 13.41 % Favored : 86.12 % Cbeta Deviations : 1.81 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.96 % Twisted General : 1.49 % 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: -6.32 (0.14), residues: 1700 helix: -4.02 (0.11), residues: 784 sheet: -3.45 (0.47), residues: 100 loop : -4.53 (0.16), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP A 227 HIS 0.052 0.003 HIS B 10 PHE 0.031 0.003 PHE A 230 TYR 0.058 0.004 TYR D 228 ARG 0.010 0.001 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 433 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.9000 (p0) cc_final: 0.8451 (p0) REVERT: A 179 ASP cc_start: 0.8924 (p0) cc_final: 0.8463 (p0) REVERT: A 238 ARG cc_start: 0.8415 (tpm170) cc_final: 0.8169 (mmm160) REVERT: A 248 GLN cc_start: 0.8186 (tp40) cc_final: 0.7964 (tm-30) REVERT: A 249 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 129 ASP cc_start: 0.9192 (m-30) cc_final: 0.8846 (m-30) REVERT: B 241 LYS cc_start: 0.9315 (mppt) cc_final: 0.8819 (mtmm) REVERT: C 133 MET cc_start: 0.8332 (tpp) cc_final: 0.8113 (tpp) REVERT: C 173 LYS cc_start: 0.9056 (mtpp) cc_final: 0.8728 (mtpp) REVERT: C 175 ASP cc_start: 0.8880 (p0) cc_final: 0.8493 (p0) REVERT: D 99 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8752 (mm-30) REVERT: D 111 LEU cc_start: 0.7730 (mt) cc_final: 0.7509 (mt) REVERT: D 175 ASP cc_start: 0.9008 (p0) cc_final: 0.8694 (p0) REVERT: E 141 PHE cc_start: 0.9401 (t80) cc_final: 0.9068 (t80) REVERT: E 143 ARG cc_start: 0.8673 (tmt170) cc_final: 0.8287 (tmt170) REVERT: E 183 LYS cc_start: 0.9509 (ttmt) cc_final: 0.9216 (ttmt) REVERT: E 223 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: E 226 GLU cc_start: 0.9417 (mp0) cc_final: 0.9044 (mp0) REVERT: F 183 LYS cc_start: 0.9382 (ttmt) cc_final: 0.8906 (ttmt) REVERT: F 223 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: F 226 GLU cc_start: 0.9314 (mp0) cc_final: 0.8967 (mp0) outliers start: 7 outliers final: 0 residues processed: 437 average time/residue: 0.3090 time to fit residues: 195.4542 Evaluate side-chains 371 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 369 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain F residue 223 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 165 optimal weight: 0.0010 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN A 132 ASN A 141 HIS ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 204 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN A 226 HIS A 236 ASN B 34 HIS B 141 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 ASN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN D 61 GLN ** D 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 224 GLN ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 133 HIS E 187 HIS E 205 ASN E 233 ASN E 306 ASN E 330 GLN F 48 GLN F 85 ASN F 187 HIS F 205 ASN F 233 ASN F 306 ASN F 330 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 18386 Z= 0.420 Angle : 0.963 16.845 25768 Z= 0.520 Chirality : 0.053 0.464 2882 Planarity : 0.007 0.069 2630 Dihedral : 28.367 176.691 3850 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 24.68 Ramachandran Plot: Outliers : 0.76 % Allowed : 16.59 % Favored : 82.65 % Rotamer: Outliers : 3.92 % Allowed : 22.64 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.93 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.18), residues: 1700 helix: -2.05 (0.16), residues: 766 sheet: -2.96 (0.43), residues: 110 loop : -3.80 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP F 131 HIS 0.014 0.002 HIS B 10 PHE 0.021 0.003 PHE D 170 TYR 0.035 0.003 TYR E 209 ARG 0.009 0.001 ARG F 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 414 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8954 (p0) cc_final: 0.8477 (p0) REVERT: A 179 ASP cc_start: 0.8887 (p0) cc_final: 0.8408 (p0) REVERT: A 245 GLU cc_start: 0.8771 (pm20) cc_final: 0.8435 (pm20) REVERT: A 249 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7613 (tm-30) REVERT: B 94 LYS cc_start: 0.8422 (mmmt) cc_final: 0.7989 (mttp) REVERT: B 139 ILE cc_start: 0.9491 (mm) cc_final: 0.9242 (mm) REVERT: B 229 TYR cc_start: 0.8745 (m-10) cc_final: 0.8198 (m-10) REVERT: B 241 LYS cc_start: 0.9315 (mppt) cc_final: 0.9084 (mppt) REVERT: B 245 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8091 (mm-30) REVERT: C 63 ASP cc_start: 0.8379 (t0) cc_final: 0.8122 (t0) REVERT: C 99 GLU cc_start: 0.8550 (tp30) cc_final: 0.8309 (tp30) REVERT: C 133 MET cc_start: 0.8255 (tpp) cc_final: 0.8025 (tpp) REVERT: C 175 ASP cc_start: 0.8931 (p0) cc_final: 0.8619 (p0) REVERT: C 186 LEU cc_start: 0.9445 (tt) cc_final: 0.9221 (tp) REVERT: D 99 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8827 (mm-30) REVERT: D 116 TYR cc_start: 0.8534 (m-80) cc_final: 0.8269 (m-80) REVERT: E 70 ARG cc_start: 0.8868 (ttm-80) cc_final: 0.8532 (tpp-160) REVERT: E 103 MET cc_start: 0.8626 (pmm) cc_final: 0.8357 (pmm) REVERT: E 141 PHE cc_start: 0.9302 (t80) cc_final: 0.9054 (t80) REVERT: E 203 GLN cc_start: 0.9563 (tp-100) cc_final: 0.9160 (mm-40) REVERT: E 266 GLN cc_start: 0.8275 (pm20) cc_final: 0.7888 (pm20) REVERT: E 307 GLU cc_start: 0.9226 (tp30) cc_final: 0.8909 (tp30) REVERT: F 70 ARG cc_start: 0.8849 (ttm-80) cc_final: 0.8378 (tpp80) REVERT: F 103 MET cc_start: 0.8628 (pmm) cc_final: 0.8396 (pmm) REVERT: F 203 GLN cc_start: 0.9549 (tp-100) cc_final: 0.9138 (mm-40) REVERT: F 307 GLU cc_start: 0.9279 (tp30) cc_final: 0.8971 (tp30) outliers start: 59 outliers final: 43 residues processed: 439 average time/residue: 0.2794 time to fit residues: 184.6701 Evaluate side-chains 427 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 384 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 268 TRP Chi-restraints excluded: chain E residue 49 CYS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 217 HIS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 270 CYS Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 49 CYS Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 45 optimal weight: 0.0570 chunk 165 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 overall best weight: 2.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 159 ASN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 HIS ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 226 HIS ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18386 Z= 0.298 Angle : 0.863 15.213 25768 Z= 0.464 Chirality : 0.049 0.405 2882 Planarity : 0.005 0.049 2630 Dihedral : 28.140 177.807 3844 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.47 % Favored : 87.18 % Rotamer: Outliers : 5.98 % Allowed : 22.97 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.19), residues: 1700 helix: -1.14 (0.17), residues: 782 sheet: -2.55 (0.45), residues: 108 loop : -3.67 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 268 HIS 0.011 0.001 HIS D 207 PHE 0.020 0.002 PHE B 170 TYR 0.036 0.002 TYR E 209 ARG 0.005 0.001 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 416 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.8675 (pm20) cc_final: 0.8271 (pp30) REVERT: A 106 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8457 (tm-30) REVERT: A 175 ASP cc_start: 0.8874 (p0) cc_final: 0.8346 (p0) REVERT: A 179 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8235 (p0) REVERT: A 245 GLU cc_start: 0.8766 (pm20) cc_final: 0.8494 (pm20) REVERT: A 249 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 131 LEU cc_start: 0.9329 (pp) cc_final: 0.9114 (pp) REVERT: B 178 MET cc_start: 0.7868 (mpp) cc_final: 0.7340 (tpp) REVERT: B 229 TYR cc_start: 0.8748 (m-10) cc_final: 0.8236 (m-10) REVERT: B 239 GLN cc_start: 0.7283 (mp10) cc_final: 0.7030 (mp10) REVERT: C 13 GLN cc_start: 0.8928 (pm20) cc_final: 0.8395 (pp30) REVERT: C 133 MET cc_start: 0.8206 (tpp) cc_final: 0.7986 (tpp) REVERT: C 172 ASP cc_start: 0.8357 (t0) cc_final: 0.8049 (t0) REVERT: C 175 ASP cc_start: 0.8877 (p0) cc_final: 0.8506 (p0) REVERT: C 199 HIS cc_start: 0.8420 (m-70) cc_final: 0.8183 (m-70) REVERT: C 228 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.8003 (p90) REVERT: D 99 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8757 (mm-30) REVERT: D 116 TYR cc_start: 0.8528 (m-80) cc_final: 0.8274 (m-80) REVERT: D 200 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8753 (mmmm) REVERT: E 70 ARG cc_start: 0.8911 (ttm-80) cc_final: 0.8497 (tpp-160) REVERT: E 87 ILE cc_start: 0.6273 (OUTLIER) cc_final: 0.5861 (mt) REVERT: E 141 PHE cc_start: 0.9329 (t80) cc_final: 0.8978 (t80) REVERT: E 203 GLN cc_start: 0.9556 (tp-100) cc_final: 0.9117 (mm-40) REVERT: E 263 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8237 (p90) REVERT: E 266 GLN cc_start: 0.8313 (pm20) cc_final: 0.7882 (pm20) REVERT: E 267 LEU cc_start: 0.9038 (pp) cc_final: 0.8322 (pp) REVERT: F 70 ARG cc_start: 0.8840 (ttm-80) cc_final: 0.8339 (tpp80) REVERT: F 87 ILE cc_start: 0.6375 (OUTLIER) cc_final: 0.5996 (mt) REVERT: F 213 TYR cc_start: 0.7800 (m-80) cc_final: 0.7520 (m-80) outliers start: 90 outliers final: 53 residues processed: 458 average time/residue: 0.2865 time to fit residues: 194.7516 Evaluate side-chains 441 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 383 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 227 TRP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 49 CYS Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 217 HIS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain F residue 49 CYS Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 79 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 47 optimal weight: 30.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 ASN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN F 38 GLN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 18386 Z= 0.339 Angle : 0.853 13.765 25768 Z= 0.458 Chirality : 0.048 0.371 2882 Planarity : 0.005 0.045 2630 Dihedral : 28.003 178.310 3844 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.76 % Favored : 84.88 % Rotamer: Outliers : 6.84 % Allowed : 24.77 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.19), residues: 1700 helix: -0.85 (0.18), residues: 796 sheet: -2.42 (0.46), residues: 108 loop : -3.68 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 268 HIS 0.010 0.002 HIS D 207 PHE 0.024 0.002 PHE B 170 TYR 0.022 0.002 TYR D 228 ARG 0.004 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 393 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8509 (tm-30) REVERT: A 175 ASP cc_start: 0.8862 (p0) cc_final: 0.8462 (p0) REVERT: A 179 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8339 (p0) REVERT: A 245 GLU cc_start: 0.8801 (pm20) cc_final: 0.8479 (pm20) REVERT: B 128 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8042 (tm-30) REVERT: B 131 LEU cc_start: 0.9331 (pp) cc_final: 0.9006 (pp) REVERT: B 178 MET cc_start: 0.7952 (mpp) cc_final: 0.7227 (tpp) REVERT: B 229 TYR cc_start: 0.8814 (m-10) cc_final: 0.8256 (m-10) REVERT: C 51 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7066 (pmt-80) REVERT: C 63 ASP cc_start: 0.8069 (t0) cc_final: 0.7755 (t0) REVERT: C 133 MET cc_start: 0.8150 (tpp) cc_final: 0.7938 (tpp) REVERT: C 172 ASP cc_start: 0.8423 (t0) cc_final: 0.8091 (t0) REVERT: C 175 ASP cc_start: 0.8844 (p0) cc_final: 0.8489 (p0) REVERT: C 178 MET cc_start: 0.8040 (tpp) cc_final: 0.7827 (tpp) REVERT: C 228 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.7775 (p90) REVERT: D 99 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8738 (mm-30) REVERT: D 116 TYR cc_start: 0.8532 (m-80) cc_final: 0.8263 (m-80) REVERT: D 226 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.6291 (m-70) REVERT: E 39 GLU cc_start: 0.7841 (pm20) cc_final: 0.7626 (pm20) REVERT: E 70 ARG cc_start: 0.8965 (ttm-80) cc_final: 0.8462 (tpt170) REVERT: E 87 ILE cc_start: 0.6317 (OUTLIER) cc_final: 0.5899 (mt) REVERT: E 141 PHE cc_start: 0.9353 (t80) cc_final: 0.8929 (t80) REVERT: E 203 GLN cc_start: 0.9514 (tp-100) cc_final: 0.9050 (mm-40) REVERT: E 263 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8336 (p90) REVERT: E 266 GLN cc_start: 0.8338 (pm20) cc_final: 0.7987 (pm20) REVERT: E 267 LEU cc_start: 0.9047 (pp) cc_final: 0.8338 (pp) REVERT: E 276 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8191 (pp20) REVERT: E 320 PHE cc_start: 0.7005 (t80) cc_final: 0.6805 (t80) REVERT: F 70 ARG cc_start: 0.8836 (ttm-80) cc_final: 0.8355 (tpp-160) REVERT: F 87 ILE cc_start: 0.6450 (OUTLIER) cc_final: 0.6086 (mt) REVERT: F 165 LEU cc_start: 0.9242 (mt) cc_final: 0.8972 (mt) REVERT: F 175 ASP cc_start: 0.8089 (t0) cc_final: 0.7837 (t0) REVERT: F 203 GLN cc_start: 0.9554 (tp-100) cc_final: 0.9015 (mm-40) REVERT: F 276 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8379 (pp20) outliers start: 103 outliers final: 70 residues processed: 452 average time/residue: 0.2759 time to fit residues: 187.6728 Evaluate side-chains 451 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 373 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 227 TRP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 268 TRP Chi-restraints excluded: chain E residue 49 CYS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 49 CYS Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 0.0970 chunk 157 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 overall best weight: 2.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 GLN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN F 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18386 Z= 0.275 Angle : 0.835 13.809 25768 Z= 0.444 Chirality : 0.048 0.343 2882 Planarity : 0.005 0.045 2630 Dihedral : 27.863 178.029 3844 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.82 % Favored : 86.88 % Rotamer: Outliers : 8.03 % Allowed : 25.37 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.20), residues: 1700 helix: -0.57 (0.18), residues: 782 sheet: -2.67 (0.41), residues: 130 loop : -3.53 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 268 HIS 0.010 0.001 HIS D 207 PHE 0.024 0.002 PHE B 170 TYR 0.034 0.002 TYR F 209 ARG 0.006 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 402 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8937 (pp20) cc_final: 0.8701 (pp20) REVERT: A 42 GLN cc_start: 0.7145 (tm-30) cc_final: 0.6725 (mm-40) REVERT: A 106 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8467 (tm-30) REVERT: A 175 ASP cc_start: 0.8744 (p0) cc_final: 0.8313 (p0) REVERT: A 179 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8150 (p0) REVERT: A 245 GLU cc_start: 0.8787 (pm20) cc_final: 0.8468 (pm20) REVERT: B 128 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: B 131 LEU cc_start: 0.9313 (pp) cc_final: 0.8954 (pp) REVERT: B 142 THR cc_start: 0.8485 (m) cc_final: 0.8280 (p) REVERT: B 178 MET cc_start: 0.7925 (mpp) cc_final: 0.7133 (tpp) REVERT: B 229 TYR cc_start: 0.8791 (m-10) cc_final: 0.8213 (m-10) REVERT: C 13 GLN cc_start: 0.8894 (pm20) cc_final: 0.8574 (pp30) REVERT: C 51 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7044 (pmt-80) REVERT: C 133 MET cc_start: 0.8200 (tpp) cc_final: 0.7968 (tpp) REVERT: C 172 ASP cc_start: 0.8365 (t0) cc_final: 0.8030 (t0) REVERT: C 175 ASP cc_start: 0.8789 (p0) cc_final: 0.8426 (p0) REVERT: C 178 MET cc_start: 0.7950 (tpp) cc_final: 0.7710 (tpp) REVERT: C 199 HIS cc_start: 0.8500 (m-70) cc_final: 0.8225 (m-70) REVERT: C 228 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7692 (p90) REVERT: C 238 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.5876 (mmm160) REVERT: D 99 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8711 (mm-30) REVERT: D 116 TYR cc_start: 0.8515 (m-80) cc_final: 0.8248 (m-80) REVERT: D 170 PHE cc_start: 0.8247 (p90) cc_final: 0.7965 (p90) REVERT: D 226 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.5985 (m-70) REVERT: E 70 ARG cc_start: 0.8961 (ttm-80) cc_final: 0.8464 (tpt170) REVERT: E 87 ILE cc_start: 0.6269 (OUTLIER) cc_final: 0.5864 (mt) REVERT: E 169 GLU cc_start: 0.8830 (tp30) cc_final: 0.8540 (mp0) REVERT: E 178 GLU cc_start: 0.9088 (pp20) cc_final: 0.8872 (pp20) REVERT: E 263 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.8396 (p90) REVERT: E 266 GLN cc_start: 0.8450 (pm20) cc_final: 0.8046 (pm20) REVERT: E 267 LEU cc_start: 0.9042 (pp) cc_final: 0.8389 (pp) REVERT: E 276 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8448 (pp20) REVERT: F 70 ARG cc_start: 0.8854 (ttm-80) cc_final: 0.8361 (tpp-160) REVERT: F 87 ILE cc_start: 0.6281 (OUTLIER) cc_final: 0.5860 (mt) REVERT: F 276 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8430 (pp20) outliers start: 121 outliers final: 74 residues processed: 470 average time/residue: 0.2710 time to fit residues: 192.7607 Evaluate side-chains 467 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 384 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 227 TRP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 268 TRP Chi-restraints excluded: chain E residue 49 CYS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 49 CYS Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 103 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.0980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 233 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18386 Z= 0.247 Angle : 0.831 13.820 25768 Z= 0.438 Chirality : 0.048 0.442 2882 Planarity : 0.005 0.045 2630 Dihedral : 27.673 177.813 3844 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.29 % Allowed : 13.18 % Favored : 86.53 % Rotamer: Outliers : 6.31 % Allowed : 28.22 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.20), residues: 1700 helix: -0.47 (0.18), residues: 782 sheet: -2.40 (0.41), residues: 132 loop : -3.41 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 268 HIS 0.009 0.001 HIS D 207 PHE 0.026 0.002 PHE B 170 TYR 0.031 0.002 TYR E 209 ARG 0.009 0.001 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 417 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8925 (pp20) cc_final: 0.8660 (pp20) REVERT: A 42 GLN cc_start: 0.7040 (tm-30) cc_final: 0.6787 (mm-40) REVERT: A 106 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8472 (tm-30) REVERT: A 175 ASP cc_start: 0.8741 (p0) cc_final: 0.8320 (p0) REVERT: A 179 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8069 (p0) REVERT: A 245 GLU cc_start: 0.8728 (pm20) cc_final: 0.8403 (pm20) REVERT: B 128 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8294 (tm-30) REVERT: B 131 LEU cc_start: 0.9283 (pp) cc_final: 0.9070 (mm) REVERT: B 178 MET cc_start: 0.7870 (mpp) cc_final: 0.7153 (tpp) REVERT: B 229 TYR cc_start: 0.8771 (m-10) cc_final: 0.8193 (m-10) REVERT: B 245 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8029 (mm-30) REVERT: C 13 GLN cc_start: 0.8876 (pm20) cc_final: 0.8649 (pp30) REVERT: C 51 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6925 (pmt-80) REVERT: C 106 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8494 (tm-30) REVERT: C 133 MET cc_start: 0.8156 (tpp) cc_final: 0.7929 (tpp) REVERT: C 172 ASP cc_start: 0.8316 (t0) cc_final: 0.7969 (t0) REVERT: C 175 ASP cc_start: 0.8747 (p0) cc_final: 0.8376 (p0) REVERT: C 199 HIS cc_start: 0.8539 (m-70) cc_final: 0.8311 (m-70) REVERT: C 228 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.7558 (p90) REVERT: C 238 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.6021 (mmm160) REVERT: D 99 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8701 (mm-30) REVERT: D 116 TYR cc_start: 0.8505 (m-80) cc_final: 0.8243 (m-80) REVERT: D 226 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.5360 (m-70) REVERT: E 39 GLU cc_start: 0.7498 (pm20) cc_final: 0.7294 (tm-30) REVERT: E 70 ARG cc_start: 0.8936 (ttm-80) cc_final: 0.8480 (tpt170) REVERT: E 213 TYR cc_start: 0.7595 (m-80) cc_final: 0.7222 (m-80) REVERT: E 263 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.8432 (p90) REVERT: E 266 GLN cc_start: 0.8444 (pm20) cc_final: 0.8117 (pm20) REVERT: E 267 LEU cc_start: 0.9044 (pp) cc_final: 0.8329 (pp) REVERT: E 276 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8495 (pp20) REVERT: F 70 ARG cc_start: 0.8880 (ttm-80) cc_final: 0.8427 (tpp-160) REVERT: F 87 ILE cc_start: 0.6323 (OUTLIER) cc_final: 0.5936 (mt) REVERT: F 276 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8496 (pp20) outliers start: 95 outliers final: 70 residues processed: 465 average time/residue: 0.2741 time to fit residues: 190.8403 Evaluate side-chains 462 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 384 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 99 optimal weight: 0.0770 chunk 148 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 109 optimal weight: 30.0000 chunk 106 optimal weight: 30.0000 chunk 80 optimal weight: 0.0470 overall best weight: 1.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN F 233 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18386 Z= 0.245 Angle : 0.842 13.854 25768 Z= 0.439 Chirality : 0.048 0.434 2882 Planarity : 0.005 0.046 2630 Dihedral : 27.523 177.752 3844 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.29 % Allowed : 13.06 % Favored : 86.65 % Rotamer: Outliers : 6.31 % Allowed : 29.88 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.20), residues: 1700 helix: -0.41 (0.18), residues: 794 sheet: -2.40 (0.41), residues: 128 loop : -3.37 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 268 HIS 0.008 0.001 HIS D 207 PHE 0.035 0.002 PHE E 304 TYR 0.027 0.002 TYR F 209 ARG 0.008 0.001 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 410 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8885 (pp20) cc_final: 0.8612 (pp20) REVERT: A 106 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8468 (tm-30) REVERT: A 175 ASP cc_start: 0.8706 (p0) cc_final: 0.8285 (p0) REVERT: A 179 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8038 (p0) REVERT: A 245 GLU cc_start: 0.8721 (pm20) cc_final: 0.8389 (pm20) REVERT: A 273 ARG cc_start: 0.6914 (ttt90) cc_final: 0.6503 (ttt-90) REVERT: B 128 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8407 (tm-30) REVERT: B 131 LEU cc_start: 0.9298 (pp) cc_final: 0.9094 (mm) REVERT: B 175 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.7723 (p0) REVERT: B 178 MET cc_start: 0.7860 (mpp) cc_final: 0.7030 (tpp) REVERT: C 92 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6567 (ttpp) REVERT: C 106 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8469 (tm-30) REVERT: C 133 MET cc_start: 0.8169 (tpp) cc_final: 0.7932 (tpp) REVERT: C 175 ASP cc_start: 0.8718 (p0) cc_final: 0.8349 (p0) REVERT: C 199 HIS cc_start: 0.8538 (m-70) cc_final: 0.8298 (m-70) REVERT: C 228 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7558 (p90) REVERT: C 238 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.6075 (mmm160) REVERT: C 249 GLU cc_start: 0.8672 (tp30) cc_final: 0.8413 (tp30) REVERT: D 99 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8671 (mm-30) REVERT: D 116 TYR cc_start: 0.8509 (m-80) cc_final: 0.8252 (m-80) REVERT: D 170 PHE cc_start: 0.8121 (p90) cc_final: 0.7879 (p90) REVERT: D 200 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8468 (mmmt) REVERT: E 70 ARG cc_start: 0.8908 (ttm-80) cc_final: 0.8461 (tpt170) REVERT: E 87 ILE cc_start: 0.6264 (OUTLIER) cc_final: 0.5870 (mt) REVERT: E 169 GLU cc_start: 0.8899 (tp30) cc_final: 0.8619 (mm-30) REVERT: E 263 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.8456 (p90) REVERT: E 266 GLN cc_start: 0.8461 (pm20) cc_final: 0.8103 (pm20) REVERT: E 267 LEU cc_start: 0.9008 (pp) cc_final: 0.8273 (pp) REVERT: E 276 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8553 (pp20) REVERT: F 70 ARG cc_start: 0.8873 (ttm-80) cc_final: 0.8459 (tpp-160) REVERT: F 87 ILE cc_start: 0.6280 (OUTLIER) cc_final: 0.5901 (mt) REVERT: F 241 GLU cc_start: 0.9071 (mp0) cc_final: 0.8857 (mm-30) REVERT: F 276 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8528 (pp20) REVERT: F 293 TRP cc_start: 0.8083 (t-100) cc_final: 0.7792 (t-100) outliers start: 95 outliers final: 78 residues processed: 454 average time/residue: 0.2756 time to fit residues: 188.7568 Evaluate side-chains 483 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 396 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 49 CYS Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 264 HIS Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 49 CYS Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN F 233 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18386 Z= 0.287 Angle : 0.858 13.606 25768 Z= 0.447 Chirality : 0.049 0.425 2882 Planarity : 0.005 0.046 2630 Dihedral : 27.478 177.959 3844 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.76 % Favored : 86.00 % Rotamer: Outliers : 6.44 % Allowed : 29.95 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.20), residues: 1700 helix: -0.32 (0.18), residues: 790 sheet: -1.69 (0.48), residues: 108 loop : -3.45 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 227 HIS 0.009 0.001 HIS D 207 PHE 0.031 0.002 PHE E 304 TYR 0.023 0.002 TYR F 209 ARG 0.009 0.001 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 406 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8928 (pp20) cc_final: 0.8639 (pp20) REVERT: A 106 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8507 (tm-30) REVERT: A 175 ASP cc_start: 0.8705 (p0) cc_final: 0.8295 (p0) REVERT: A 179 ASP cc_start: 0.8762 (p0) cc_final: 0.8131 (p0) REVERT: A 245 GLU cc_start: 0.8798 (pm20) cc_final: 0.8406 (pm20) REVERT: B 64 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8820 (mt) REVERT: B 128 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8449 (tm-30) REVERT: B 131 LEU cc_start: 0.9287 (pp) cc_final: 0.9086 (mm) REVERT: B 175 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.7744 (p0) REVERT: B 178 MET cc_start: 0.7894 (mpp) cc_final: 0.7069 (tpp) REVERT: B 245 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8069 (mm-30) REVERT: C 51 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6886 (pmt-80) REVERT: C 92 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6706 (ttpp) REVERT: C 106 GLN cc_start: 0.9015 (tm-30) cc_final: 0.8504 (tm-30) REVERT: C 133 MET cc_start: 0.8144 (tpp) cc_final: 0.7919 (tpp) REVERT: C 175 ASP cc_start: 0.8733 (p0) cc_final: 0.8381 (p0) REVERT: C 199 HIS cc_start: 0.8566 (m-70) cc_final: 0.8330 (m-70) REVERT: C 228 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7578 (p90) REVERT: C 238 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.6258 (mmm160) REVERT: D 99 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8686 (mm-30) REVERT: D 116 TYR cc_start: 0.8538 (m-80) cc_final: 0.8293 (m-80) REVERT: D 170 PHE cc_start: 0.8185 (p90) cc_final: 0.7922 (p90) REVERT: E 39 GLU cc_start: 0.8364 (tt0) cc_final: 0.8095 (pm20) REVERT: E 70 ARG cc_start: 0.8934 (ttm-80) cc_final: 0.8519 (tpp-160) REVERT: E 87 ILE cc_start: 0.6211 (OUTLIER) cc_final: 0.5762 (mt) REVERT: E 169 GLU cc_start: 0.8876 (tp30) cc_final: 0.8381 (mp0) REVERT: E 208 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.9184 (m-10) REVERT: E 263 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.8417 (p90) REVERT: E 266 GLN cc_start: 0.8468 (pm20) cc_final: 0.8146 (pm20) REVERT: E 267 LEU cc_start: 0.9038 (pp) cc_final: 0.8267 (pp) REVERT: E 276 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8551 (pp20) REVERT: F 70 ARG cc_start: 0.8881 (ttm-80) cc_final: 0.8448 (tpp-160) REVERT: F 87 ILE cc_start: 0.6219 (OUTLIER) cc_final: 0.5838 (mt) REVERT: F 208 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.9157 (m-10) REVERT: F 241 GLU cc_start: 0.9099 (mp0) cc_final: 0.8880 (mm-30) REVERT: F 276 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8550 (pp20) REVERT: F 293 TRP cc_start: 0.8226 (t-100) cc_final: 0.7712 (t-100) REVERT: F 314 VAL cc_start: 0.7233 (OUTLIER) cc_final: 0.6899 (t) outliers start: 97 outliers final: 75 residues processed: 461 average time/residue: 0.2743 time to fit residues: 190.6899 Evaluate side-chains 477 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 389 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 49 CYS Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 264 HIS Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN E 233 ASN F 203 GLN F 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18386 Z= 0.306 Angle : 0.881 16.169 25768 Z= 0.456 Chirality : 0.050 0.403 2882 Planarity : 0.005 0.050 2630 Dihedral : 27.454 177.838 3844 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.29 % Allowed : 14.06 % Favored : 85.65 % Rotamer: Outliers : 6.71 % Allowed : 30.01 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.20), residues: 1700 helix: -0.36 (0.18), residues: 806 sheet: -1.56 (0.52), residues: 94 loop : -3.41 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 268 HIS 0.011 0.001 HIS D 207 PHE 0.026 0.002 PHE F 304 TYR 0.021 0.002 TYR D 228 ARG 0.015 0.001 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 400 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8960 (pp20) cc_final: 0.8650 (pp20) REVERT: A 106 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8505 (tm-30) REVERT: A 175 ASP cc_start: 0.8701 (p0) cc_final: 0.8290 (p0) REVERT: A 179 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8154 (p0) REVERT: A 245 GLU cc_start: 0.8822 (pm20) cc_final: 0.8435 (pm20) REVERT: B 64 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8799 (mt) REVERT: B 128 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8427 (tm-30) REVERT: B 175 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.7741 (p0) REVERT: B 178 MET cc_start: 0.7971 (mpp) cc_final: 0.7187 (tpp) REVERT: B 245 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 51 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6887 (pmt-80) REVERT: C 92 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6835 (ttpp) REVERT: C 133 MET cc_start: 0.8143 (tpp) cc_final: 0.7931 (tpp) REVERT: C 175 ASP cc_start: 0.8746 (p0) cc_final: 0.8394 (p0) REVERT: C 228 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7640 (p90) REVERT: C 238 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.6282 (mmm160) REVERT: C 266 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9153 (mt) REVERT: D 99 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8720 (mm-30) REVERT: D 116 TYR cc_start: 0.8542 (m-80) cc_final: 0.8253 (m-80) REVERT: D 170 PHE cc_start: 0.8180 (p90) cc_final: 0.7901 (p90) REVERT: D 200 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8364 (mmmt) REVERT: E 39 GLU cc_start: 0.8350 (tt0) cc_final: 0.8076 (pm20) REVERT: E 70 ARG cc_start: 0.8933 (ttm-80) cc_final: 0.8526 (tpp-160) REVERT: E 87 ILE cc_start: 0.6153 (OUTLIER) cc_final: 0.5711 (mt) REVERT: E 263 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.8404 (p90) REVERT: E 266 GLN cc_start: 0.8482 (pm20) cc_final: 0.8147 (pm20) REVERT: E 267 LEU cc_start: 0.9052 (pp) cc_final: 0.8300 (pp) REVERT: E 276 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8627 (pp20) REVERT: F 70 ARG cc_start: 0.8888 (ttm-80) cc_final: 0.8480 (tpp-160) REVERT: F 87 ILE cc_start: 0.6222 (OUTLIER) cc_final: 0.5853 (mt) REVERT: F 208 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.9142 (m-10) REVERT: F 241 GLU cc_start: 0.9116 (mp0) cc_final: 0.8882 (mm-30) REVERT: F 276 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8598 (pp20) REVERT: F 293 TRP cc_start: 0.8251 (t-100) cc_final: 0.7727 (t-100) REVERT: F 314 VAL cc_start: 0.7216 (OUTLIER) cc_final: 0.6926 (t) outliers start: 101 outliers final: 77 residues processed: 454 average time/residue: 0.2738 time to fit residues: 187.3364 Evaluate side-chains 483 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 392 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 49 CYS Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 264 HIS Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 181 optimal weight: 20.0000 chunk 166 optimal weight: 0.0670 chunk 144 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN E 203 GLN E 233 ASN F 203 GLN F 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18386 Z= 0.240 Angle : 0.886 13.692 25768 Z= 0.452 Chirality : 0.049 0.418 2882 Planarity : 0.005 0.058 2630 Dihedral : 27.273 177.077 3844 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.59 % Favored : 87.12 % Rotamer: Outliers : 5.18 % Allowed : 31.81 % Favored : 63.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.20), residues: 1700 helix: -0.33 (0.18), residues: 792 sheet: -1.33 (0.51), residues: 90 loop : -3.29 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 268 HIS 0.009 0.001 HIS D 207 PHE 0.024 0.002 PHE F 304 TYR 0.024 0.002 TYR F 209 ARG 0.018 0.001 ARG A 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 423 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8874 (pp20) cc_final: 0.8549 (pp20) REVERT: A 106 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8465 (tm-30) REVERT: A 175 ASP cc_start: 0.8648 (p0) cc_final: 0.8136 (p0) REVERT: A 179 ASP cc_start: 0.8697 (p0) cc_final: 0.8033 (p0) REVERT: A 245 GLU cc_start: 0.8775 (pm20) cc_final: 0.8433 (pm20) REVERT: B 64 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8849 (mt) REVERT: B 119 THR cc_start: 0.7637 (t) cc_final: 0.7303 (t) REVERT: B 178 MET cc_start: 0.7889 (mpp) cc_final: 0.7027 (tpp) REVERT: B 245 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7984 (mm-30) REVERT: C 51 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6791 (pmt-80) REVERT: C 92 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6563 (ttpp) REVERT: C 133 MET cc_start: 0.8200 (tpp) cc_final: 0.7973 (tpp) REVERT: C 175 ASP cc_start: 0.8658 (p0) cc_final: 0.8301 (p0) REVERT: C 228 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7513 (p90) REVERT: C 238 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.6287 (mmm160) REVERT: D 99 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8744 (mm-30) REVERT: D 116 TYR cc_start: 0.8515 (m-80) cc_final: 0.8234 (m-80) REVERT: D 170 PHE cc_start: 0.8074 (p90) cc_final: 0.7851 (p90) REVERT: D 200 LYS cc_start: 0.8769 (mmmm) cc_final: 0.8511 (mmmt) REVERT: E 70 ARG cc_start: 0.8934 (ttm-80) cc_final: 0.8501 (tpt170) REVERT: E 87 ILE cc_start: 0.6190 (OUTLIER) cc_final: 0.5749 (mt) REVERT: E 199 TYR cc_start: 0.9481 (t80) cc_final: 0.8798 (t80) REVERT: E 208 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.9185 (m-10) REVERT: E 263 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8457 (p90) REVERT: E 266 GLN cc_start: 0.8484 (pm20) cc_final: 0.8125 (pm20) REVERT: E 267 LEU cc_start: 0.9033 (pp) cc_final: 0.8268 (pp) REVERT: F 70 ARG cc_start: 0.8922 (ttm-80) cc_final: 0.8430 (tpp-160) REVERT: F 87 ILE cc_start: 0.6256 (OUTLIER) cc_final: 0.5882 (mt) REVERT: F 208 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.9188 (m-10) REVERT: F 241 GLU cc_start: 0.9116 (mp0) cc_final: 0.8904 (mm-30) REVERT: F 273 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8552 (tp-100) REVERT: F 276 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8718 (pp20) REVERT: F 293 TRP cc_start: 0.8234 (t-100) cc_final: 0.7725 (t-100) REVERT: F 314 VAL cc_start: 0.7200 (OUTLIER) cc_final: 0.6954 (t) outliers start: 78 outliers final: 61 residues processed: 456 average time/residue: 0.2788 time to fit residues: 190.5291 Evaluate side-chains 476 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 404 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 255 HIS Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 264 HIS Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 314 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 133 optimal weight: 50.0000 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN F 203 GLN F 233 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.181327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.127535 restraints weight = 37591.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.131001 restraints weight = 17395.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.133138 restraints weight = 11367.350| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.264 18386 Z= 0.373 Angle : 1.011 59.178 25768 Z= 0.545 Chirality : 0.051 0.905 2882 Planarity : 0.005 0.058 2630 Dihedral : 27.273 177.072 3844 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.71 % Favored : 87.00 % Rotamer: Outliers : 5.05 % Allowed : 32.14 % Favored : 62.82 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.20), residues: 1700 helix: -0.35 (0.18), residues: 794 sheet: -1.32 (0.51), residues: 90 loop : -3.29 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 268 HIS 0.009 0.001 HIS D 207 PHE 0.023 0.002 PHE E 171 TYR 0.073 0.002 TYR E 199 ARG 0.024 0.001 ARG A 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4078.07 seconds wall clock time: 74 minutes 13.51 seconds (4453.51 seconds total)