Starting phenix.real_space_refine on Tue Apr 9 00:55:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x59_22046/04_2024/6x59_22046.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x59_22046/04_2024/6x59_22046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x59_22046/04_2024/6x59_22046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x59_22046/04_2024/6x59_22046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x59_22046/04_2024/6x59_22046.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x59_22046/04_2024/6x59_22046.pdb" } resolution = 2.98 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 288 5.49 5 S 23 5.16 5 C 8541 2.51 5 N 2764 2.21 5 O 3346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "K ASP 148": "OD1" <-> "OD2" Residue "K ASP 155": "OD1" <-> "OD2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "K GLU 193": "OE1" <-> "OE2" Residue "K TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 213": "OD1" <-> "OD2" Residue "K GLU 219": "OE1" <-> "OE2" Residue "K PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 241": "NH1" <-> "NH2" Residue "K ARG 244": "NH1" <-> "NH2" Residue "K GLU 253": "OE1" <-> "OE2" Residue "K GLU 272": "OE1" <-> "OE2" Residue "K GLU 276": "OE1" <-> "OE2" Residue "K ASP 279": "OD1" <-> "OD2" Residue "K GLU 285": "OE1" <-> "OE2" Residue "K ARG 299": "NH1" <-> "NH2" Residue "K ASP 307": "OD1" <-> "OD2" Residue "K ARG 341": "NH1" <-> "NH2" Residue "K ARG 342": "NH1" <-> "NH2" Residue "K GLU 343": "OE1" <-> "OE2" Residue "K ASP 354": "OD1" <-> "OD2" Residue "K GLU 361": "OE1" <-> "OE2" Residue "K GLU 371": "OE1" <-> "OE2" Residue "K GLU 386": "OE1" <-> "OE2" Residue "K GLU 406": "OE1" <-> "OE2" Residue "K ASP 416": "OD1" <-> "OD2" Residue "K PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 434": "OD1" <-> "OD2" Residue "K ASP 437": "OD1" <-> "OD2" Residue "K GLU 458": "OE1" <-> "OE2" Residue "K GLU 463": "OE1" <-> "OE2" Residue "K ASP 466": "OD1" <-> "OD2" Residue "K GLU 487": "OE1" <-> "OE2" Residue "K TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 496": "OE1" <-> "OE2" Residue "K ASP 505": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14963 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 637 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 645 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2954 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2985 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2994 Unusual residues: {' ZN': 1} Classifications: {'peptide': 362, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 345, None: 1} Not linked: pdbres="LEU K 507 " pdbres=" ZN K 601 " List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13921 SG CYS K 384 111.467 51.256 37.583 1.00189.24 S Time building chain proxies: 8.28, per 1000 atoms: 0.55 Number of scatterers: 14963 At special positions: 0 Unit cell: (130.54, 115.56, 133.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 23 16.00 P 288 15.00 O 3346 8.00 N 2764 7.00 C 8541 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: 6.64 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 378 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 384 " 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 62.9% alpha, 8.1% beta 142 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 6.93 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.618A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.690A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.964A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.598A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.833A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.757A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.618A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.688A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.553A pdb=" N ARG F 36 " --> pdb=" O PRO F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.910A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.576A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.712A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 57 through 84 removed outlier: 3.544A pdb=" N ASN H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.906A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 185 removed outlier: 4.188A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS K 184 " --> pdb=" O ARG K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 250 No H-bonds generated for 'chain 'K' and resid 248 through 250' Processing helix chain 'K' and resid 258 through 276 Processing helix chain 'K' and resid 319 through 323 Processing helix chain 'K' and resid 333 through 342 removed outlier: 3.597A pdb=" N ARG K 337 " --> pdb=" O GLY K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 377 Processing helix chain 'K' and resid 393 through 412 Processing helix chain 'K' and resid 419 through 434 removed outlier: 4.348A pdb=" N VAL K 423 " --> pdb=" O CYS K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 440 Processing helix chain 'K' and resid 441 through 443 No H-bonds generated for 'chain 'K' and resid 441 through 443' Processing helix chain 'K' and resid 444 through 462 removed outlier: 3.682A pdb=" N THR K 462 " --> pdb=" O GLU K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 482 through 499 Processing helix chain 'K' and resid 501 through 506 removed outlier: 3.738A pdb=" N LYS K 506 " --> pdb=" O ILE K 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.703A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.197A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.610A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.814A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.192A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 192 through 195 removed outlier: 4.301A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL K 294 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR K 295 " --> pdb=" O GLU K 285 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 192 through 195 removed outlier: 4.301A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU K 310 " --> pdb=" O PRO K 349 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 223 through 227 Processing sheet with id=AB5, first strand: chain 'K' and resid 252 through 253 531 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 7.23 Time building geometry restraints manager: 7.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2820 1.33 - 1.45: 4792 1.45 - 1.57: 7600 1.57 - 1.69: 579 1.69 - 1.81: 38 Bond restraints: 15829 Sorted by residual: bond pdb=" C PHE K 501 " pdb=" O PHE K 501 " ideal model delta sigma weight residual 1.233 1.255 -0.022 4.80e-03 4.34e+04 2.18e+01 bond pdb=" CB LYS K 173 " pdb=" CG LYS K 173 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.76e+00 bond pdb=" CG LYS K 484 " pdb=" CD LYS K 484 " ideal model delta sigma weight residual 1.520 1.577 -0.057 3.00e-02 1.11e+03 3.64e+00 bond pdb=" CG LYS K 162 " pdb=" CD LYS K 162 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.79e+00 bond pdb=" CG LYS K 173 " pdb=" CD LYS K 173 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.47e+00 ... (remaining 15824 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.39: 1403 105.39 - 112.92: 8799 112.92 - 120.45: 7071 120.45 - 127.98: 4892 127.98 - 135.51: 426 Bond angle restraints: 22591 Sorted by residual: angle pdb=" N LYS K 160 " pdb=" CA LYS K 160 " pdb=" C LYS K 160 " ideal model delta sigma weight residual 111.02 97.86 13.16 1.22e+00 6.72e-01 1.16e+02 angle pdb=" CA TYR K 495 " pdb=" CB TYR K 495 " pdb=" CG TYR K 495 " ideal model delta sigma weight residual 113.90 125.36 -11.46 1.80e+00 3.09e-01 4.06e+01 angle pdb=" CA LEU K 159 " pdb=" CB LEU K 159 " pdb=" CG LEU K 159 " ideal model delta sigma weight residual 116.30 135.51 -19.21 3.50e+00 8.16e-02 3.01e+01 angle pdb=" CB LYS K 484 " pdb=" CG LYS K 484 " pdb=" CD LYS K 484 " ideal model delta sigma weight residual 111.30 122.94 -11.64 2.30e+00 1.89e-01 2.56e+01 angle pdb=" C LYS K 160 " pdb=" CA LYS K 160 " pdb=" CB LYS K 160 " ideal model delta sigma weight residual 110.92 118.74 -7.82 1.59e+00 3.96e-01 2.42e+01 ... (remaining 22586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 7173 35.50 - 71.00: 1625 71.00 - 106.50: 23 106.50 - 142.00: 1 142.00 - 177.49: 2 Dihedral angle restraints: 8824 sinusoidal: 5557 harmonic: 3267 Sorted by residual: dihedral pdb=" CA LYS K 353 " pdb=" C LYS K 353 " pdb=" N ASP K 354 " pdb=" CA ASP K 354 " ideal model delta harmonic sigma weight residual -180.00 -134.92 -45.08 0 5.00e+00 4.00e-02 8.13e+01 dihedral pdb=" CA LYS A 37 " pdb=" C LYS A 37 " pdb=" N PRO A 38 " pdb=" CA PRO A 38 " ideal model delta harmonic sigma weight residual 180.00 -152.81 -27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA LYS E 37 " pdb=" C LYS E 37 " pdb=" N PRO E 38 " pdb=" CA PRO E 38 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 8821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2439 0.096 - 0.192: 94 0.192 - 0.288: 5 0.288 - 0.384: 1 0.384 - 0.481: 1 Chirality restraints: 2540 Sorted by residual: chirality pdb=" CG LEU K 150 " pdb=" CB LEU K 150 " pdb=" CD1 LEU K 150 " pdb=" CD2 LEU K 150 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" CB VAL K 153 " pdb=" CA VAL K 153 " pdb=" CG1 VAL K 153 " pdb=" CG2 VAL K 153 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CG LEU K 157 " pdb=" CB LEU K 157 " pdb=" CD1 LEU K 157 " pdb=" CD2 LEU K 157 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2537 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP K 450 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" CG ASP K 450 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP K 450 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP K 450 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG K 158 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C ARG K 158 " 0.041 2.00e-02 2.50e+03 pdb=" O ARG K 158 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU K 159 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP K 318 " -0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO K 319 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO K 319 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 319 " -0.032 5.00e-02 4.00e+02 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 449 2.66 - 3.22: 12609 3.22 - 3.78: 26037 3.78 - 4.34: 36307 4.34 - 4.90: 51819 Nonbonded interactions: 127221 Sorted by model distance: nonbonded pdb=" O GLU K 487 " pdb=" OG SER K 490 " model vdw 2.103 2.440 nonbonded pdb=" O2 DC I 94 " pdb=" N2 DG J 52 " model vdw 2.147 2.496 nonbonded pdb=" ND2 ASN K 356 " pdb=" O PHE K 358 " model vdw 2.206 2.520 nonbonded pdb=" NH2 ARG E 69 " pdb=" OP2 DA I 90 " model vdw 2.239 2.520 nonbonded pdb=" O LEU K 297 " pdb=" NH2 ARG K 299 " model vdw 2.247 2.520 ... (remaining 127216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 102) } ncs_group { reference = (chain 'C' and resid 10 through 116) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 31 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 3.020 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 50.720 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 15829 Z= 0.329 Angle : 0.843 19.207 22591 Z= 0.482 Chirality : 0.045 0.481 2540 Planarity : 0.006 0.058 1858 Dihedral : 27.582 177.494 6712 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.15 % Favored : 93.67 % Rotamer: Outliers : 7.57 % Allowed : 20.12 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.07 (0.22), residues: 1105 helix: -0.61 (0.17), residues: 680 sheet: -1.51 (0.63), residues: 54 loop : -2.69 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 363 HIS 0.008 0.001 HIS B 75 PHE 0.013 0.002 PHE K 455 TYR 0.037 0.002 TYR K 403 ARG 0.012 0.001 ARG K 394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 204 time to evaluate : 1.182 Fit side-chains REVERT: A 37 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.5671 (tppt) REVERT: D 76 GLU cc_start: 0.8355 (tp30) cc_final: 0.8094 (tp30) REVERT: F 79 LYS cc_start: 0.8851 (mttt) cc_final: 0.8640 (mttm) REVERT: G 95 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8794 (tttm) REVERT: H 76 GLU cc_start: 0.8177 (tp30) cc_final: 0.7820 (tp30) REVERT: K 152 LYS cc_start: 0.8604 (pmtt) cc_final: 0.8314 (pmtt) REVERT: K 155 ASP cc_start: 0.8187 (t70) cc_final: 0.7945 (m-30) REVERT: K 194 GLN cc_start: 0.7657 (pp30) cc_final: 0.7231 (pp30) REVERT: K 226 GLN cc_start: 0.7337 (mp10) cc_final: 0.7070 (mm-40) REVERT: K 251 PHE cc_start: 0.7995 (m-10) cc_final: 0.7583 (m-10) REVERT: K 262 MET cc_start: 0.7834 (ptm) cc_final: 0.7400 (ptm) REVERT: K 326 LEU cc_start: 0.8897 (tp) cc_final: 0.8672 (tt) REVERT: K 335 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8301 (mppt) REVERT: K 339 ASN cc_start: 0.8327 (m110) cc_final: 0.8046 (m-40) REVERT: K 346 TYR cc_start: 0.8635 (m-80) cc_final: 0.8322 (m-80) REVERT: K 385 CYS cc_start: 0.4065 (OUTLIER) cc_final: 0.3219 (p) REVERT: K 403 TYR cc_start: 0.6831 (m-10) cc_final: 0.6116 (m-80) REVERT: K 427 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7980 (tp) REVERT: K 430 MET cc_start: 0.7777 (tmm) cc_final: 0.7453 (tmm) REVERT: K 432 THR cc_start: 0.6990 (t) cc_final: 0.6444 (m) REVERT: K 461 ARG cc_start: 0.8185 (tpp-160) cc_final: 0.7838 (tpm170) REVERT: K 468 TYR cc_start: 0.8432 (t80) cc_final: 0.8115 (t80) REVERT: K 482 ASP cc_start: 0.5477 (OUTLIER) cc_final: 0.5189 (p0) REVERT: K 484 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8485 (tmmt) outliers start: 73 outliers final: 27 residues processed: 261 average time/residue: 1.6887 time to fit residues: 473.7323 Evaluate side-chains 197 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 165 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 385 CYS Chi-restraints excluded: chain K residue 387 SER Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 427 ILE Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 482 ASP Chi-restraints excluded: chain K residue 483 ARG Chi-restraints excluded: chain K residue 484 LYS Chi-restraints excluded: chain K residue 501 PHE Chi-restraints excluded: chain K residue 507 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 24 GLN C 31 HIS C 73 ASN D 95 GLN E 68 GLN F 75 HIS F 93 GLN G 73 ASN G 89 ASN G 104 GLN H 49 HIS H 63 ASN H 84 ASN K 183 GLN K 194 GLN K 196 ASN K 226 GLN K 246 ASN K 300 ASN K 339 ASN ** K 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15829 Z= 0.191 Angle : 0.630 9.184 22591 Z= 0.361 Chirality : 0.036 0.157 2540 Planarity : 0.005 0.047 1858 Dihedral : 29.651 178.818 4458 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 5.19 % Allowed : 23.55 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1105 helix: 0.99 (0.19), residues: 696 sheet: -0.77 (0.65), residues: 53 loop : -2.20 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 363 HIS 0.005 0.001 HIS K 378 PHE 0.015 0.001 PHE K 412 TYR 0.022 0.002 TYR K 403 ARG 0.006 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 186 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9040 (mt) REVERT: E 56 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8732 (ttpp) REVERT: E 59 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: F 95 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.6933 (mtp-110) REVERT: H 76 GLU cc_start: 0.8234 (tp30) cc_final: 0.7868 (tp30) REVERT: K 152 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8398 (pptt) REVERT: K 155 ASP cc_start: 0.8177 (t70) cc_final: 0.7905 (m-30) REVERT: K 182 MET cc_start: 0.7100 (mmp) cc_final: 0.6834 (mtm) REVERT: K 224 GLU cc_start: 0.6695 (tt0) cc_final: 0.6444 (tt0) REVERT: K 226 GLN cc_start: 0.7398 (mp-120) cc_final: 0.7023 (mm-40) REVERT: K 251 PHE cc_start: 0.8013 (m-10) cc_final: 0.7485 (m-10) REVERT: K 253 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6385 (pt0) REVERT: K 262 MET cc_start: 0.7756 (ptm) cc_final: 0.7097 (ptm) REVERT: K 300 ASN cc_start: 0.5002 (OUTLIER) cc_final: 0.4473 (t0) REVERT: K 326 LEU cc_start: 0.8840 (tp) cc_final: 0.8576 (tt) REVERT: K 339 ASN cc_start: 0.8394 (m-40) cc_final: 0.8093 (m-40) REVERT: K 346 TYR cc_start: 0.8309 (m-80) cc_final: 0.8033 (m-80) REVERT: K 361 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6665 (mm-30) REVERT: K 385 CYS cc_start: 0.4161 (OUTLIER) cc_final: 0.3492 (p) REVERT: K 401 MET cc_start: 0.6775 (tpt) cc_final: 0.6335 (tpp) REVERT: K 403 TYR cc_start: 0.6917 (m-10) cc_final: 0.6377 (m-80) REVERT: K 413 GLN cc_start: 0.6272 (OUTLIER) cc_final: 0.5448 (pp30) REVERT: K 428 PHE cc_start: 0.8042 (m-10) cc_final: 0.7841 (m-10) REVERT: K 461 ARG cc_start: 0.8314 (tpp-160) cc_final: 0.7823 (mmp-170) REVERT: K 464 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6422 (pptt) REVERT: K 481 ILE cc_start: 0.5500 (OUTLIER) cc_final: 0.5214 (tp) REVERT: K 482 ASP cc_start: 0.5376 (OUTLIER) cc_final: 0.5139 (p0) outliers start: 50 outliers final: 12 residues processed: 222 average time/residue: 1.7741 time to fit residues: 422.5462 Evaluate side-chains 190 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 152 LYS Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 361 GLU Chi-restraints excluded: chain K residue 385 CYS Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 413 GLN Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain K residue 438 SER Chi-restraints excluded: chain K residue 464 LYS Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 482 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 30.0000 chunk 133 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 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 39 HIS C 73 ASN E 68 GLN G 24 GLN G 104 GLN H 95 GLN ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** K 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15829 Z= 0.235 Angle : 0.631 12.026 22591 Z= 0.360 Chirality : 0.037 0.144 2540 Planarity : 0.005 0.054 1858 Dihedral : 29.691 179.551 4416 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.77 % Allowed : 25.41 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1105 helix: 1.44 (0.20), residues: 693 sheet: -0.56 (0.70), residues: 50 loop : -1.98 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 363 HIS 0.004 0.001 HIS B 75 PHE 0.012 0.001 PHE K 476 TYR 0.016 0.001 TYR K 403 ARG 0.009 0.000 ARG K 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: B 49 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9069 (mp) REVERT: B 84 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.8028 (mmm) REVERT: C 92 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: D 93 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: E 59 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8138 (pm20) REVERT: F 95 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.6951 (mtp-110) REVERT: G 73 ASN cc_start: 0.8249 (t0) cc_final: 0.7939 (t160) REVERT: H 76 GLU cc_start: 0.8220 (tp30) cc_final: 0.7846 (tp30) REVERT: K 152 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8356 (pptt) REVERT: K 155 ASP cc_start: 0.8179 (t70) cc_final: 0.7894 (m-30) REVERT: K 226 GLN cc_start: 0.7249 (mp-120) cc_final: 0.6905 (mm-40) REVERT: K 251 PHE cc_start: 0.8032 (m-10) cc_final: 0.7398 (m-10) REVERT: K 262 MET cc_start: 0.7845 (ptm) cc_final: 0.7336 (ptm) REVERT: K 300 ASN cc_start: 0.4746 (OUTLIER) cc_final: 0.4324 (t0) REVERT: K 324 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7881 (tp30) REVERT: K 326 LEU cc_start: 0.8773 (tp) cc_final: 0.8505 (tt) REVERT: K 339 ASN cc_start: 0.8286 (m-40) cc_final: 0.7994 (m-40) REVERT: K 361 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6534 (mm-30) REVERT: K 401 MET cc_start: 0.7028 (tpt) cc_final: 0.6515 (tpp) REVERT: K 403 TYR cc_start: 0.6984 (m-10) cc_final: 0.6457 (m-80) REVERT: K 413 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6218 (mp-120) REVERT: K 461 ARG cc_start: 0.8313 (tpp-160) cc_final: 0.7825 (mmp-170) REVERT: K 464 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.6415 (pptt) REVERT: K 481 ILE cc_start: 0.5301 (OUTLIER) cc_final: 0.4987 (tp) REVERT: K 482 ASP cc_start: 0.5521 (OUTLIER) cc_final: 0.5244 (p0) outliers start: 46 outliers final: 16 residues processed: 206 average time/residue: 1.8226 time to fit residues: 402.3531 Evaluate side-chains 193 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain K residue 152 LYS Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 361 GLU Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 413 GLN Chi-restraints excluded: chain K residue 464 LYS Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 482 ASP Chi-restraints excluded: chain K residue 501 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 131 optimal weight: 0.0170 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN E 39 HIS E 68 GLN G 24 GLN G 104 GLN ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15829 Z= 0.189 Angle : 0.597 8.769 22591 Z= 0.343 Chirality : 0.036 0.149 2540 Planarity : 0.004 0.045 1858 Dihedral : 29.595 179.444 4415 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.56 % Allowed : 25.93 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1105 helix: 1.78 (0.20), residues: 693 sheet: -0.42 (0.68), residues: 53 loop : -1.86 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP K 331 HIS 0.004 0.001 HIS K 378 PHE 0.017 0.001 PHE K 358 TYR 0.015 0.001 TYR K 403 ARG 0.010 0.000 ARG K 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 172 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9079 (mp) REVERT: B 84 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.8061 (mmm) REVERT: C 92 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7332 (mt-10) REVERT: D 51 ASP cc_start: 0.7621 (p0) cc_final: 0.7260 (p0) REVERT: D 76 GLU cc_start: 0.8415 (tp30) cc_final: 0.8185 (tp30) REVERT: D 93 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: E 59 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: F 95 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.6920 (mtp-110) REVERT: G 73 ASN cc_start: 0.8299 (t0) cc_final: 0.7895 (t0) REVERT: H 76 GLU cc_start: 0.8220 (tp30) cc_final: 0.7933 (tp30) REVERT: K 152 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8359 (pptt) REVERT: K 155 ASP cc_start: 0.8197 (t70) cc_final: 0.7958 (m-30) REVERT: K 226 GLN cc_start: 0.7206 (mp-120) cc_final: 0.6969 (mm-40) REVERT: K 251 PHE cc_start: 0.8018 (m-10) cc_final: 0.7390 (m-10) REVERT: K 262 MET cc_start: 0.7829 (ptm) cc_final: 0.7316 (ptm) REVERT: K 324 GLU cc_start: 0.8086 (tp30) cc_final: 0.7757 (tp30) REVERT: K 326 LEU cc_start: 0.8709 (tp) cc_final: 0.8488 (tt) REVERT: K 339 ASN cc_start: 0.8281 (m-40) cc_final: 0.8006 (m-40) REVERT: K 361 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6446 (mm-30) REVERT: K 401 MET cc_start: 0.7312 (tpt) cc_final: 0.6773 (tpp) REVERT: K 403 TYR cc_start: 0.7164 (m-80) cc_final: 0.6582 (m-80) REVERT: K 430 MET cc_start: 0.7971 (tmm) cc_final: 0.7524 (tmm) REVERT: K 461 ARG cc_start: 0.8315 (tpp-160) cc_final: 0.7891 (mmp-170) REVERT: K 481 ILE cc_start: 0.5392 (OUTLIER) cc_final: 0.5094 (tp) REVERT: K 482 ASP cc_start: 0.5548 (OUTLIER) cc_final: 0.5281 (p0) outliers start: 44 outliers final: 17 residues processed: 199 average time/residue: 1.8516 time to fit residues: 394.8132 Evaluate side-chains 195 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 152 LYS Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 361 GLU Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 482 ASP Chi-restraints excluded: chain K residue 501 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 24 GLN G 104 GLN K 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15829 Z= 0.257 Angle : 0.606 8.782 22591 Z= 0.348 Chirality : 0.037 0.143 2540 Planarity : 0.004 0.045 1858 Dihedral : 29.649 178.342 4415 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.39 % Allowed : 26.24 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1105 helix: 1.78 (0.20), residues: 693 sheet: -0.32 (0.68), residues: 53 loop : -1.79 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 363 HIS 0.005 0.001 HIS A 39 PHE 0.011 0.001 PHE K 455 TYR 0.023 0.001 TYR K 468 ARG 0.006 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 169 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7241 (mtp85) REVERT: B 49 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9104 (mp) REVERT: C 92 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7372 (mt-10) REVERT: D 51 ASP cc_start: 0.7692 (p0) cc_final: 0.7350 (p0) REVERT: D 93 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: E 59 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8144 (pm20) REVERT: F 95 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.6953 (mtp-110) REVERT: G 11 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6880 (mmm-85) REVERT: G 73 ASN cc_start: 0.8388 (t0) cc_final: 0.7906 (t0) REVERT: H 76 GLU cc_start: 0.8220 (tp30) cc_final: 0.7927 (tp30) REVERT: K 155 ASP cc_start: 0.8190 (t70) cc_final: 0.7972 (m-30) REVERT: K 251 PHE cc_start: 0.8004 (m-10) cc_final: 0.7341 (m-10) REVERT: K 262 MET cc_start: 0.7865 (ptm) cc_final: 0.7308 (ptm) REVERT: K 300 ASN cc_start: 0.4185 (OUTLIER) cc_final: 0.3904 (t0) REVERT: K 324 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7853 (tp30) REVERT: K 339 ASN cc_start: 0.8302 (m-40) cc_final: 0.8029 (m-40) REVERT: K 401 MET cc_start: 0.7259 (tpt) cc_final: 0.6875 (tpp) REVERT: K 403 TYR cc_start: 0.7138 (m-80) cc_final: 0.6590 (m-80) REVERT: K 430 MET cc_start: 0.8051 (tmm) cc_final: 0.7677 (tmm) REVERT: K 461 ARG cc_start: 0.8302 (tpp-160) cc_final: 0.7864 (mmp-170) REVERT: K 481 ILE cc_start: 0.5506 (OUTLIER) cc_final: 0.5012 (tp) REVERT: K 482 ASP cc_start: 0.5528 (OUTLIER) cc_final: 0.5235 (p0) outliers start: 52 outliers final: 26 residues processed: 202 average time/residue: 1.9243 time to fit residues: 415.1797 Evaluate side-chains 201 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 369 HIS Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 482 ASP Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 501 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 24 GLN G 104 GLN K 194 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15829 Z= 0.224 Angle : 0.608 15.990 22591 Z= 0.344 Chirality : 0.036 0.155 2540 Planarity : 0.005 0.071 1858 Dihedral : 29.619 178.039 4415 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.36 % Allowed : 27.49 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1105 helix: 1.89 (0.20), residues: 692 sheet: -0.16 (0.72), residues: 53 loop : -1.75 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 331 HIS 0.005 0.001 HIS A 39 PHE 0.010 0.001 PHE K 455 TYR 0.011 0.001 TYR K 403 ARG 0.013 0.000 ARG K 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.7208 (mtp85) REVERT: B 45 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8349 (mtp180) REVERT: B 49 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9094 (mp) REVERT: C 92 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: D 51 ASP cc_start: 0.7763 (p0) cc_final: 0.7431 (p0) REVERT: D 93 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: E 56 LYS cc_start: 0.9016 (ttpp) cc_final: 0.8581 (ttpp) REVERT: E 59 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: F 95 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.6944 (mtp-110) REVERT: G 11 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6780 (mmm-85) REVERT: G 15 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8699 (ttpt) REVERT: G 73 ASN cc_start: 0.8363 (t0) cc_final: 0.7856 (t0) REVERT: H 76 GLU cc_start: 0.8218 (tp30) cc_final: 0.7931 (tp30) REVERT: K 251 PHE cc_start: 0.8026 (m-10) cc_final: 0.7304 (m-10) REVERT: K 262 MET cc_start: 0.7838 (ptm) cc_final: 0.7300 (ptm) REVERT: K 300 ASN cc_start: 0.4249 (OUTLIER) cc_final: 0.4028 (t0) REVERT: K 324 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7860 (tp30) REVERT: K 335 LYS cc_start: 0.8598 (mppt) cc_final: 0.8375 (mppt) REVERT: K 339 ASN cc_start: 0.8302 (m-40) cc_final: 0.8033 (m-40) REVERT: K 401 MET cc_start: 0.7333 (tpt) cc_final: 0.6969 (tpp) REVERT: K 403 TYR cc_start: 0.7079 (m-80) cc_final: 0.6555 (m-80) REVERT: K 430 MET cc_start: 0.8030 (tmm) cc_final: 0.7647 (tmm) REVERT: K 461 ARG cc_start: 0.8287 (tpp-160) cc_final: 0.7855 (mmp-170) REVERT: K 481 ILE cc_start: 0.5444 (OUTLIER) cc_final: 0.5037 (tp) REVERT: K 482 ASP cc_start: 0.5437 (OUTLIER) cc_final: 0.5179 (p0) outliers start: 42 outliers final: 20 residues processed: 198 average time/residue: 1.9218 time to fit residues: 405.9656 Evaluate side-chains 199 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 482 ASP Chi-restraints excluded: chain K residue 501 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 110 optimal weight: 0.0980 chunk 73 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN E 68 GLN G 24 GLN G 104 GLN K 194 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 15829 Z= 0.386 Angle : 0.659 10.567 22591 Z= 0.372 Chirality : 0.041 0.142 2540 Planarity : 0.005 0.045 1858 Dihedral : 29.767 177.183 4415 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.08 % Allowed : 26.14 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1105 helix: 1.62 (0.20), residues: 692 sheet: -0.25 (0.72), residues: 55 loop : -1.94 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 363 HIS 0.007 0.001 HIS A 39 PHE 0.011 0.002 PHE K 358 TYR 0.011 0.002 TYR A 54 ARG 0.009 0.001 ARG K 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 172 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7219 (mtp85) REVERT: B 49 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9113 (mp) REVERT: C 91 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7691 (tp30) REVERT: C 92 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7397 (mt-10) REVERT: D 51 ASP cc_start: 0.7841 (p0) cc_final: 0.7535 (p0) REVERT: D 93 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: E 59 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: F 95 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7045 (mtp-110) REVERT: G 11 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7267 (mmm-85) REVERT: G 15 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8771 (ttpt) REVERT: G 56 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: G 73 ASN cc_start: 0.8416 (t0) cc_final: 0.7881 (t0) REVERT: H 76 GLU cc_start: 0.8166 (tp30) cc_final: 0.7810 (tp30) REVERT: K 202 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6379 (pm20) REVERT: K 251 PHE cc_start: 0.7916 (m-10) cc_final: 0.7319 (m-10) REVERT: K 262 MET cc_start: 0.7915 (ptm) cc_final: 0.7372 (ptm) REVERT: K 300 ASN cc_start: 0.4711 (OUTLIER) cc_final: 0.4195 (t0) REVERT: K 324 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7890 (tp30) REVERT: K 401 MET cc_start: 0.7323 (tpt) cc_final: 0.6916 (tpp) REVERT: K 403 TYR cc_start: 0.7162 (m-80) cc_final: 0.6653 (m-80) REVERT: K 430 MET cc_start: 0.8015 (tmm) cc_final: 0.7680 (tmm) REVERT: K 461 ARG cc_start: 0.8307 (tpp-160) cc_final: 0.7847 (mmp-170) REVERT: K 481 ILE cc_start: 0.5458 (OUTLIER) cc_final: 0.5030 (tp) REVERT: K 482 ASP cc_start: 0.5247 (OUTLIER) cc_final: 0.4993 (p0) outliers start: 49 outliers final: 25 residues processed: 201 average time/residue: 1.8818 time to fit residues: 404.4163 Evaluate side-chains 207 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 167 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 369 HIS Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 482 ASP Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 501 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 24 GLN K 194 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15829 Z= 0.288 Angle : 0.636 14.064 22591 Z= 0.360 Chirality : 0.038 0.144 2540 Planarity : 0.005 0.045 1858 Dihedral : 29.766 177.385 4415 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 5.08 % Allowed : 26.87 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1105 helix: 1.69 (0.20), residues: 692 sheet: -0.24 (0.74), residues: 55 loop : -1.92 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 331 HIS 0.005 0.001 HIS A 39 PHE 0.013 0.002 PHE K 476 TYR 0.014 0.002 TYR K 468 ARG 0.008 0.000 ARG K 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 172 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.7218 (mtp85) REVERT: B 49 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9100 (mp) REVERT: C 91 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7659 (tp30) REVERT: C 92 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: D 51 ASP cc_start: 0.7840 (p0) cc_final: 0.7542 (p0) REVERT: D 93 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: E 56 LYS cc_start: 0.9028 (ttpp) cc_final: 0.8606 (ttpp) REVERT: E 59 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8185 (pm20) REVERT: F 95 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.6993 (mtp-110) REVERT: G 11 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7209 (mmm-85) REVERT: G 15 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8771 (ttpt) REVERT: G 56 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: G 73 ASN cc_start: 0.8417 (t0) cc_final: 0.7889 (t0) REVERT: H 63 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8637 (m-40) REVERT: H 76 GLU cc_start: 0.8127 (tp30) cc_final: 0.7795 (tp30) REVERT: K 202 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6461 (pm20) REVERT: K 251 PHE cc_start: 0.7861 (m-10) cc_final: 0.7300 (m-10) REVERT: K 262 MET cc_start: 0.7914 (ptm) cc_final: 0.7368 (ptm) REVERT: K 324 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: K 339 ASN cc_start: 0.8290 (m-40) cc_final: 0.8008 (m-40) REVERT: K 361 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6388 (mm-30) REVERT: K 401 MET cc_start: 0.7332 (tpt) cc_final: 0.6924 (tpp) REVERT: K 403 TYR cc_start: 0.7162 (m-80) cc_final: 0.6638 (m-80) REVERT: K 430 MET cc_start: 0.8037 (tmm) cc_final: 0.7695 (tmm) REVERT: K 461 ARG cc_start: 0.8300 (tpp-160) cc_final: 0.7861 (mmp-170) REVERT: K 481 ILE cc_start: 0.5604 (OUTLIER) cc_final: 0.5189 (tp) REVERT: K 482 ASP cc_start: 0.5246 (OUTLIER) cc_final: 0.4983 (p0) outliers start: 49 outliers final: 25 residues processed: 203 average time/residue: 1.9116 time to fit residues: 414.8305 Evaluate side-chains 211 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 170 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 361 GLU Chi-restraints excluded: chain K residue 369 HIS Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 482 ASP Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 501 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 115 optimal weight: 0.0370 chunk 121 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 overall best weight: 2.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 24 GLN G 104 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN K 329 GLN ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15829 Z= 0.307 Angle : 0.635 10.918 22591 Z= 0.360 Chirality : 0.039 0.144 2540 Planarity : 0.005 0.045 1858 Dihedral : 29.748 177.024 4415 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.19 % Allowed : 27.39 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1105 helix: 1.70 (0.20), residues: 692 sheet: -0.29 (0.75), residues: 55 loop : -1.91 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 431 HIS 0.006 0.001 HIS A 39 PHE 0.012 0.001 PHE K 476 TYR 0.010 0.002 TYR D 40 ARG 0.012 0.001 ARG K 244 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 171 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.7233 (mtp85) REVERT: B 49 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9101 (mp) REVERT: C 91 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7654 (tp30) REVERT: D 51 ASP cc_start: 0.7882 (p0) cc_final: 0.7595 (p0) REVERT: D 93 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: E 56 LYS cc_start: 0.9035 (ttpp) cc_final: 0.8611 (ttpp) REVERT: E 59 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8168 (pm20) REVERT: F 95 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7014 (mtp-110) REVERT: G 11 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7166 (mmm-85) REVERT: G 15 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8726 (ttpt) REVERT: G 56 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: G 73 ASN cc_start: 0.8453 (t0) cc_final: 0.7932 (t0) REVERT: H 63 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8658 (m-40) REVERT: H 76 GLU cc_start: 0.8115 (tp30) cc_final: 0.7771 (tp30) REVERT: K 202 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6515 (pm20) REVERT: K 251 PHE cc_start: 0.7888 (m-10) cc_final: 0.7338 (m-10) REVERT: K 262 MET cc_start: 0.7903 (ptm) cc_final: 0.7351 (ptm) REVERT: K 300 ASN cc_start: 0.4665 (OUTLIER) cc_final: 0.4266 (t0) REVERT: K 324 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7807 (tp30) REVERT: K 329 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7311 (pm20) REVERT: K 361 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6347 (mm-30) REVERT: K 403 TYR cc_start: 0.7165 (m-80) cc_final: 0.6670 (m-80) REVERT: K 430 MET cc_start: 0.8045 (tmm) cc_final: 0.7702 (tmm) REVERT: K 461 ARG cc_start: 0.8302 (tpp-160) cc_final: 0.7888 (mmp-170) REVERT: K 481 ILE cc_start: 0.5490 (OUTLIER) cc_final: 0.5024 (tp) REVERT: K 482 ASP cc_start: 0.5290 (OUTLIER) cc_final: 0.4962 (p0) outliers start: 50 outliers final: 27 residues processed: 203 average time/residue: 1.9319 time to fit residues: 418.0347 Evaluate side-chains 209 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 165 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 295 THR Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 329 GLN Chi-restraints excluded: chain K residue 361 GLU Chi-restraints excluded: chain K residue 369 HIS Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 482 ASP Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 501 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 24 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.230 15829 Z= 0.331 Angle : 0.881 59.191 22591 Z= 0.540 Chirality : 0.038 0.235 2540 Planarity : 0.006 0.160 1858 Dihedral : 29.751 177.069 4415 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.56 % Allowed : 28.22 % Favored : 67.22 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1105 helix: 1.71 (0.20), residues: 692 sheet: -0.33 (0.74), residues: 55 loop : -1.91 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 431 HIS 0.006 0.001 HIS A 39 PHE 0.010 0.001 PHE K 476 TYR 0.010 0.001 TYR D 40 ARG 0.016 0.000 ARG K 244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 166 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7231 (mtp85) REVERT: B 49 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9100 (mp) REVERT: C 91 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7652 (tp30) REVERT: D 51 ASP cc_start: 0.7874 (p0) cc_final: 0.7608 (p0) REVERT: D 93 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: E 56 LYS cc_start: 0.9033 (ttpp) cc_final: 0.8612 (ttpp) REVERT: E 59 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: F 95 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7016 (mtp-110) REVERT: G 11 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7165 (mmm-85) REVERT: G 15 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8726 (ttpt) REVERT: G 56 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: G 73 ASN cc_start: 0.8450 (t0) cc_final: 0.7927 (t0) REVERT: H 63 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8650 (m-40) REVERT: H 76 GLU cc_start: 0.8113 (tp30) cc_final: 0.7769 (tp30) REVERT: K 202 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6464 (pm20) REVERT: K 251 PHE cc_start: 0.7885 (m-10) cc_final: 0.7337 (m-10) REVERT: K 262 MET cc_start: 0.7903 (ptm) cc_final: 0.7351 (ptm) REVERT: K 324 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7807 (tp30) REVERT: K 339 ASN cc_start: 0.8322 (m-40) cc_final: 0.8051 (m-40) REVERT: K 361 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6344 (mm-30) REVERT: K 403 TYR cc_start: 0.7187 (m-80) cc_final: 0.6789 (m-80) REVERT: K 430 MET cc_start: 0.8046 (tmm) cc_final: 0.7703 (tmm) REVERT: K 461 ARG cc_start: 0.8313 (tpp-160) cc_final: 0.7889 (mmp-170) REVERT: K 481 ILE cc_start: 0.5482 (OUTLIER) cc_final: 0.5036 (tp) REVERT: K 482 ASP cc_start: 0.5188 (OUTLIER) cc_final: 0.4938 (p0) outliers start: 44 outliers final: 26 residues processed: 194 average time/residue: 1.9182 time to fit residues: 397.3471 Evaluate side-chains 207 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 166 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 295 THR Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 361 GLU Chi-restraints excluded: chain K residue 369 HIS Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 414 GLU Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 482 ASP Chi-restraints excluded: chain K residue 501 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 24 GLN ** K 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.138120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096204 restraints weight = 21581.767| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.39 r_work: 0.2974 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.230 15829 Z= 0.331 Angle : 0.881 59.191 22591 Z= 0.540 Chirality : 0.038 0.235 2540 Planarity : 0.006 0.160 1858 Dihedral : 29.751 177.069 4415 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.36 % Allowed : 28.42 % Favored : 67.22 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1105 helix: 1.71 (0.20), residues: 692 sheet: -0.33 (0.74), residues: 55 loop : -1.91 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 431 HIS 0.006 0.001 HIS A 39 PHE 0.010 0.001 PHE K 476 TYR 0.010 0.001 TYR D 40 ARG 0.016 0.000 ARG K 244 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6188.10 seconds wall clock time: 114 minutes 27.04 seconds (6867.04 seconds total)