Starting phenix.real_space_refine on Fri Mar 15 08:10:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/03_2024/6of2_20040_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/03_2024/6of2_20040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/03_2024/6of2_20040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/03_2024/6of2_20040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/03_2024/6of2_20040_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/03_2024/6of2_20040_updated.pdb" } resolution = 2.9 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= 0.005 sd= 0.705 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 7048 2.51 5 N 1930 2.21 5 O 2020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11062 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1451 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4048 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 52, 'TRANS': 475} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1451 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4048 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 52, 'TRANS': 475} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.39, per 1000 atoms: 0.58 Number of scatterers: 11062 At special positions: 0 Unit cell: (145.8, 87.48, 90.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 6 15.00 Mg 2 11.99 O 2020 8.00 N 1930 7.00 C 7048 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: 4.34 Conformation dependent library (CDL) restraints added in 2.0 seconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 10 sheets defined 35.2% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 24 through 27 No H-bonds generated for 'chain 'A' and resid 24 through 27' Processing helix chain 'A' and resid 41 through 63 Processing helix chain 'A' and resid 68 through 83 Processing helix chain 'A' and resid 94 through 114 Processing helix chain 'A' and resid 124 through 131 Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'B' and resid 196 through 206 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 243 through 258 removed outlier: 3.880A pdb=" N ARG B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 368 through 386 Processing helix chain 'B' and resid 404 through 416 Processing helix chain 'B' and resid 430 through 443 removed outlier: 3.642A pdb=" N SER B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 483 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.160A pdb=" N SER B 540 " --> pdb=" O PRO B 536 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 Processing helix chain 'B' and resid 677 through 690 removed outlier: 3.855A pdb=" N VAL B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 684 " --> pdb=" O TYR B 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 22 Processing helix chain 'D' and resid 24 through 27 No H-bonds generated for 'chain 'D' and resid 24 through 27' Processing helix chain 'D' and resid 41 through 63 Processing helix chain 'D' and resid 68 through 83 Processing helix chain 'D' and resid 94 through 114 Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 152 through 169 Processing helix chain 'D' and resid 171 through 174 Processing helix chain 'E' and resid 196 through 206 Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 243 through 258 removed outlier: 3.880A pdb=" N ARG E 258 " --> pdb=" O THR E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 287 Processing helix chain 'E' and resid 331 through 333 No H-bonds generated for 'chain 'E' and resid 331 through 333' Processing helix chain 'E' and resid 368 through 386 Processing helix chain 'E' and resid 404 through 416 Processing helix chain 'E' and resid 430 through 443 removed outlier: 3.642A pdb=" N SER E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 483 Processing helix chain 'E' and resid 536 through 543 removed outlier: 4.160A pdb=" N SER E 540 " --> pdb=" O PRO E 536 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP E 541 " --> pdb=" O GLU E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 659 Processing helix chain 'E' and resid 677 through 690 removed outlier: 3.855A pdb=" N VAL E 681 " --> pdb=" O THR E 677 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY E 683 " --> pdb=" O ALA E 679 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU E 684 " --> pdb=" O TYR E 680 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 122 through 125 removed outlier: 6.752A pdb=" N GLU B 190 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL B 149 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 192 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL B 147 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 143 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 137 through 139 Processing sheet with id= C, first strand: chain 'B' and resid 447 through 450 removed outlier: 6.927A pdb=" N LEU B 393 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE B 266 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 395 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET B 301 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASN B 396 " --> pdb=" O MET B 301 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU B 303 " --> pdb=" O ASN B 396 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 355 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS B 322 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N THR B 353 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 511 through 514 Processing sheet with id= E, first strand: chain 'B' and resid 551 through 553 Processing sheet with id= F, first strand: chain 'E' and resid 122 through 125 removed outlier: 6.752A pdb=" N GLU E 190 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL E 149 " --> pdb=" O GLU E 190 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU E 192 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL E 147 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY E 143 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 137 through 139 Processing sheet with id= H, first strand: chain 'E' and resid 447 through 450 removed outlier: 6.927A pdb=" N LEU E 393 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE E 266 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL E 395 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET E 301 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASN E 396 " --> pdb=" O MET E 301 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU E 303 " --> pdb=" O ASN E 396 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG E 355 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS E 322 " --> pdb=" O THR E 353 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N THR E 353 " --> pdb=" O LYS E 322 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 511 through 514 Processing sheet with id= J, first strand: chain 'E' and resid 551 through 553 444 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 3823 1.37 - 1.51: 3947 1.51 - 1.66: 3502 1.66 - 1.80: 76 1.80 - 1.94: 14 Bond restraints: 11362 Sorted by residual: bond pdb=" O3G AGS E 801 " pdb=" PG AGS E 801 " ideal model delta sigma weight residual 1.558 1.504 0.054 2.00e-02 2.50e+03 7.41e+00 bond pdb=" O3G AGS B 801 " pdb=" PG AGS B 801 " ideal model delta sigma weight residual 1.558 1.504 0.054 2.00e-02 2.50e+03 7.19e+00 bond pdb=" O2G AGS E 801 " pdb=" PG AGS E 801 " ideal model delta sigma weight residual 1.557 1.505 0.052 2.00e-02 2.50e+03 6.74e+00 bond pdb=" O2G AGS B 801 " pdb=" PG AGS B 801 " ideal model delta sigma weight residual 1.557 1.505 0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" O3B AGS E 801 " pdb=" PG AGS E 801 " ideal model delta sigma weight residual 1.559 1.605 -0.046 2.00e-02 2.50e+03 5.20e+00 ... (remaining 11357 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.49: 610 106.49 - 113.40: 6181 113.40 - 120.32: 3883 120.32 - 127.23: 4600 127.23 - 134.14: 242 Bond angle restraints: 15516 Sorted by residual: angle pdb=" N PRO E 455 " pdb=" CA PRO E 455 " pdb=" CB PRO E 455 " ideal model delta sigma weight residual 103.00 110.62 -7.62 1.10e+00 8.26e-01 4.79e+01 angle pdb=" N PRO B 455 " pdb=" CA PRO B 455 " pdb=" CB PRO B 455 " ideal model delta sigma weight residual 103.00 110.58 -7.58 1.10e+00 8.26e-01 4.74e+01 angle pdb=" C TYR E 225 " pdb=" N THR E 226 " pdb=" CA THR E 226 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C TYR B 225 " pdb=" N THR B 226 " pdb=" CA THR B 226 " ideal model delta sigma weight residual 121.54 130.12 -8.58 1.91e+00 2.74e-01 2.02e+01 angle pdb=" N ASN E 185 " pdb=" CA ASN E 185 " pdb=" C ASN E 185 " ideal model delta sigma weight residual 110.42 116.89 -6.47 1.46e+00 4.69e-01 1.96e+01 ... (remaining 15511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.46: 6592 32.46 - 64.92: 184 64.92 - 97.38: 4 97.38 - 129.84: 0 129.84 - 162.30: 2 Dihedral angle restraints: 6782 sinusoidal: 2690 harmonic: 4092 Sorted by residual: dihedral pdb=" CA ARG B 295 " pdb=" C ARG B 295 " pdb=" N SER B 296 " pdb=" CA SER B 296 " ideal model delta harmonic sigma weight residual 180.00 -130.21 -49.79 0 5.00e+00 4.00e-02 9.92e+01 dihedral pdb=" CA ARG E 295 " pdb=" C ARG E 295 " pdb=" N SER E 296 " pdb=" CA SER E 296 " ideal model delta harmonic sigma weight residual -180.00 -130.24 -49.76 0 5.00e+00 4.00e-02 9.90e+01 dihedral pdb=" O1A AGS E 801 " pdb=" O3A AGS E 801 " pdb=" PA AGS E 801 " pdb=" PB AGS E 801 " ideal model delta sinusoidal sigma weight residual -67.73 94.57 -162.30 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 6779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1202 0.047 - 0.094: 402 0.094 - 0.141: 114 0.141 - 0.188: 16 0.188 - 0.235: 4 Chirality restraints: 1738 Sorted by residual: chirality pdb=" CA PRO B 455 " pdb=" N PRO B 455 " pdb=" C PRO B 455 " pdb=" CB PRO B 455 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA PRO E 455 " pdb=" N PRO E 455 " pdb=" C PRO E 455 " pdb=" CB PRO E 455 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA PHE B 673 " pdb=" N PHE B 673 " pdb=" C PHE B 673 " pdb=" CB PHE B 673 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.25e-01 ... (remaining 1735 not shown) Planarity restraints: 1980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 451 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.71e+00 pdb=" N PRO E 452 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 452 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 452 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 451 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO B 452 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 452 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 452 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 486 " 0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO E 487 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 487 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 487 " 0.026 5.00e-02 4.00e+02 ... (remaining 1977 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 100 2.63 - 3.20: 10226 3.20 - 3.76: 15417 3.76 - 4.33: 20401 4.33 - 4.90: 35718 Nonbonded interactions: 81862 Sorted by model distance: nonbonded pdb=" O3G AGS B 801 " pdb="MG MG B 802 " model vdw 2.062 2.170 nonbonded pdb=" O3G AGS E 801 " pdb="MG MG E 802 " model vdw 2.063 2.170 nonbonded pdb=" OG SER E 275 " pdb="MG MG E 802 " model vdw 2.069 2.170 nonbonded pdb=" OG SER B 275 " pdb="MG MG B 802 " model vdw 2.070 2.170 nonbonded pdb=" O2B AGS E 801 " pdb="MG MG E 802 " model vdw 2.089 2.170 ... (remaining 81857 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.070 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.700 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 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 0.061 11362 Z= 0.397 Angle : 1.003 8.618 15516 Z= 0.536 Chirality : 0.051 0.235 1738 Planarity : 0.007 0.048 1980 Dihedral : 14.668 162.297 4130 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 2.17 % Allowed : 17.66 % Favored : 80.17 % Rotamer: Outliers : 1.02 % Allowed : 4.32 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.18), residues: 1382 helix: -2.03 (0.16), residues: 470 sheet: -1.32 (0.34), residues: 212 loop : -4.10 (0.19), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 297 HIS 0.005 0.001 HIS B 242 PHE 0.017 0.002 PHE E 139 TYR 0.022 0.002 TYR B 685 ARG 0.005 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 371 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 VAL cc_start: 0.6082 (t) cc_final: 0.5842 (t) REVERT: B 154 VAL cc_start: 0.4398 (OUTLIER) cc_final: 0.4036 (m) REVERT: B 483 PHE cc_start: 0.5060 (m-80) cc_final: 0.4434 (m-80) REVERT: E 154 VAL cc_start: 0.3642 (OUTLIER) cc_final: 0.3332 (m) REVERT: E 354 VAL cc_start: 0.6110 (t) cc_final: 0.5698 (t) outliers start: 12 outliers final: 3 residues processed: 378 average time/residue: 0.9273 time to fit residues: 385.7842 Evaluate side-chains 216 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 211 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 249 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.0270 chunk 109 optimal weight: 0.0270 chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 0.0040 chunk 81 optimal weight: 0.2980 chunk 127 optimal weight: 0.8980 overall best weight: 0.2508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 143 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 171 HIS B 174 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN B 480 GLN B 533 GLN B 644 ASN D 21 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN E 171 HIS E 174 HIS ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 HIS E 480 GLN E 533 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11362 Z= 0.212 Angle : 0.832 10.312 15516 Z= 0.399 Chirality : 0.044 0.175 1738 Planarity : 0.007 0.068 1980 Dihedral : 8.957 163.939 1576 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 3.64 % Allowed : 18.56 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.22), residues: 1382 helix: 2.08 (0.21), residues: 472 sheet: -0.99 (0.32), residues: 222 loop : -3.00 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 678 HIS 0.009 0.001 HIS E 484 PHE 0.032 0.002 PHE B 332 TYR 0.014 0.002 TYR B 381 ARG 0.008 0.001 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 251 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.5885 (OUTLIER) cc_final: 0.5619 (tt0) REVERT: A 75 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6815 (mm) REVERT: B 137 GLU cc_start: 0.6910 (pm20) cc_final: 0.6462 (pm20) REVERT: B 513 VAL cc_start: 0.6997 (t) cc_final: 0.6793 (p) REVERT: D 21 GLN cc_start: 0.5392 (OUTLIER) cc_final: 0.5107 (tt0) REVERT: D 23 TYR cc_start: 0.7397 (m-80) cc_final: 0.6416 (m-80) REVERT: D 75 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6820 (mm) REVERT: E 364 PRO cc_start: 0.5779 (Cg_exo) cc_final: 0.5515 (Cg_endo) REVERT: E 513 VAL cc_start: 0.7165 (t) cc_final: 0.6933 (p) outliers start: 43 outliers final: 17 residues processed: 274 average time/residue: 0.7693 time to fit residues: 236.7279 Evaluate side-chains 242 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 221 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 659 HIS Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 390 ASN Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 659 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 0.0980 chunk 137 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 246 ASN B 327 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN D 21 GLN D 143 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 334 HIS ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 11362 Z= 0.348 Angle : 0.813 10.731 15516 Z= 0.400 Chirality : 0.044 0.223 1738 Planarity : 0.006 0.048 1980 Dihedral : 8.779 162.278 1572 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 4.83 % Allowed : 19.49 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.75 (0.22), residues: 1382 helix: 2.24 (0.22), residues: 474 sheet: -1.29 (0.32), residues: 208 loop : -2.33 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.034 0.002 HIS B 174 PHE 0.023 0.002 PHE A 107 TYR 0.022 0.002 TYR E 145 ARG 0.008 0.001 ARG E 636 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 261 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5987 (tpp) cc_final: 0.4593 (mmt) REVERT: A 138 VAL cc_start: 0.8651 (t) cc_final: 0.8442 (t) REVERT: B 251 GLU cc_start: 0.7988 (tt0) cc_final: 0.7554 (pt0) REVERT: B 288 ASP cc_start: 0.7796 (p0) cc_final: 0.7591 (p0) REVERT: B 377 ASP cc_start: 0.6789 (t0) cc_final: 0.6497 (t0) REVERT: B 613 LEU cc_start: 0.8441 (pt) cc_final: 0.8081 (tp) REVERT: D 1 MET cc_start: 0.5329 (tpp) cc_final: 0.3417 (mmt) REVERT: D 23 TYR cc_start: 0.8212 (m-80) cc_final: 0.7149 (m-80) REVERT: E 131 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6845 (pp) REVERT: E 141 ILE cc_start: 0.8324 (mt) cc_final: 0.8053 (mp) REVERT: E 251 GLU cc_start: 0.8003 (tt0) cc_final: 0.7522 (pt0) REVERT: E 364 PRO cc_start: 0.6596 (Cg_exo) cc_final: 0.6388 (Cg_endo) REVERT: E 630 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7936 (p) outliers start: 57 outliers final: 20 residues processed: 303 average time/residue: 0.8445 time to fit residues: 284.4361 Evaluate side-chains 232 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 210 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 639 SER Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 390 ASN Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 630 VAL Chi-restraints excluded: chain E residue 653 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 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 21 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 ASN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 HIS ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 ASN E 689 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11362 Z= 0.237 Angle : 0.750 11.650 15516 Z= 0.351 Chirality : 0.043 0.216 1738 Planarity : 0.006 0.049 1980 Dihedral : 8.578 158.475 1570 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 5.00 % Allowed : 23.31 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.38 (0.23), residues: 1382 helix: 2.57 (0.22), residues: 464 sheet: -1.07 (0.31), residues: 230 loop : -2.08 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 500 HIS 0.012 0.001 HIS E 174 PHE 0.017 0.002 PHE A 107 TYR 0.023 0.002 TYR D 170 ARG 0.007 0.001 ARG E 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 248 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8599 (tt0) cc_final: 0.8267 (tp40) REVERT: B 139 PHE cc_start: 0.7424 (m-80) cc_final: 0.7091 (m-80) REVERT: B 151 GLN cc_start: 0.7441 (tt0) cc_final: 0.7078 (tt0) REVERT: B 251 GLU cc_start: 0.8014 (tt0) cc_final: 0.7599 (pt0) REVERT: B 477 MET cc_start: 0.8282 (mtm) cc_final: 0.7774 (mtt) REVERT: B 485 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8293 (tp) REVERT: B 525 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7858 (tp) REVERT: B 548 MET cc_start: 0.7942 (mtp) cc_final: 0.7568 (mtp) REVERT: B 613 LEU cc_start: 0.8592 (pt) cc_final: 0.8154 (tp) REVERT: D 62 GLN cc_start: 0.8632 (tp40) cc_final: 0.8404 (tp40) REVERT: E 251 GLU cc_start: 0.8078 (tt0) cc_final: 0.7612 (pt0) REVERT: E 320 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6890 (pp) REVERT: E 364 PRO cc_start: 0.7127 (Cg_exo) cc_final: 0.6927 (Cg_endo) REVERT: E 389 GLU cc_start: 0.7356 (pt0) cc_final: 0.6492 (pp20) REVERT: E 525 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7480 (tp) REVERT: E 548 MET cc_start: 0.7847 (mtp) cc_final: 0.7593 (mtp) REVERT: E 644 ASN cc_start: 0.7144 (m110) cc_final: 0.6813 (m110) outliers start: 59 outliers final: 21 residues processed: 289 average time/residue: 0.9344 time to fit residues: 297.7413 Evaluate side-chains 244 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 219 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 639 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 390 ASN Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 450 MET Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain E residue 653 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 55 optimal weight: 0.0570 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.7082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11362 Z= 0.191 Angle : 0.692 11.876 15516 Z= 0.326 Chirality : 0.042 0.168 1738 Planarity : 0.005 0.045 1980 Dihedral : 8.305 155.665 1568 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 4.49 % Allowed : 25.34 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1382 helix: 2.57 (0.23), residues: 474 sheet: -1.00 (0.32), residues: 230 loop : -1.88 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 500 HIS 0.007 0.001 HIS E 174 PHE 0.017 0.002 PHE E 312 TYR 0.013 0.001 TYR D 170 ARG 0.009 0.001 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 237 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8563 (tt0) cc_final: 0.8361 (tt0) REVERT: B 131 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7097 (pp) REVERT: B 151 GLN cc_start: 0.7539 (tt0) cc_final: 0.7236 (tt0) REVERT: B 251 GLU cc_start: 0.8043 (tt0) cc_final: 0.7635 (pt0) REVERT: B 300 VAL cc_start: 0.8122 (t) cc_final: 0.7862 (p) REVERT: B 388 GLN cc_start: 0.7870 (mp10) cc_final: 0.7632 (mt0) REVERT: B 525 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8111 (tp) REVERT: B 534 TYR cc_start: 0.7563 (m-80) cc_final: 0.6833 (t80) REVERT: B 551 VAL cc_start: 0.8441 (m) cc_final: 0.8217 (p) REVERT: B 613 LEU cc_start: 0.8692 (pt) cc_final: 0.8216 (tp) REVERT: D 62 GLN cc_start: 0.8671 (tp40) cc_final: 0.8356 (tp40) REVERT: E 251 GLU cc_start: 0.8109 (tt0) cc_final: 0.7616 (pt0) REVERT: E 300 VAL cc_start: 0.8038 (t) cc_final: 0.7786 (p) REVERT: E 389 GLU cc_start: 0.7430 (pt0) cc_final: 0.6627 (pp20) REVERT: E 525 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7757 (tp) REVERT: E 534 TYR cc_start: 0.7563 (m-80) cc_final: 0.7156 (t80) outliers start: 53 outliers final: 23 residues processed: 273 average time/residue: 0.9252 time to fit residues: 277.6863 Evaluate side-chains 243 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 217 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 639 SER Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 390 ASN Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 450 MET Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 646 GLU Chi-restraints excluded: chain E residue 653 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 0.0040 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.8800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11362 Z= 0.254 Angle : 0.753 15.851 15516 Z= 0.356 Chirality : 0.044 0.164 1738 Planarity : 0.006 0.058 1980 Dihedral : 8.137 153.076 1568 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.83 % Allowed : 26.44 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.23), residues: 1382 helix: 2.54 (0.23), residues: 468 sheet: -1.08 (0.31), residues: 230 loop : -1.71 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 214 HIS 0.007 0.001 HIS E 174 PHE 0.026 0.002 PHE E 312 TYR 0.038 0.003 TYR B 225 ARG 0.013 0.001 ARG E 560 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 254 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: B 131 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7340 (pp) REVERT: B 151 GLN cc_start: 0.7720 (tt0) cc_final: 0.7166 (tt0) REVERT: B 251 GLU cc_start: 0.8081 (tt0) cc_final: 0.7735 (tm-30) REVERT: B 377 ASP cc_start: 0.7947 (t70) cc_final: 0.7479 (t70) REVERT: B 384 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7271 (ttp-110) REVERT: B 546 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8018 (mmm) REVERT: D 62 GLN cc_start: 0.8690 (tp40) cc_final: 0.8352 (tp40) REVERT: E 251 GLU cc_start: 0.8138 (tt0) cc_final: 0.7764 (tm-30) REVERT: E 321 THR cc_start: 0.8653 (m) cc_final: 0.8382 (p) REVERT: E 377 ASP cc_start: 0.7955 (t70) cc_final: 0.7644 (t70) REVERT: E 384 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7224 (ttp-110) REVERT: E 485 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8838 (tp) outliers start: 57 outliers final: 19 residues processed: 297 average time/residue: 0.9437 time to fit residues: 308.7934 Evaluate side-chains 222 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 198 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 639 SER Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 390 ASN Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 646 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 134 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 0.0270 chunk 83 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.9234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11362 Z= 0.185 Angle : 0.704 11.734 15516 Z= 0.333 Chirality : 0.042 0.141 1738 Planarity : 0.006 0.072 1980 Dihedral : 7.950 149.855 1568 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.15 % Allowed : 29.83 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.02 (0.23), residues: 1382 helix: 2.75 (0.23), residues: 466 sheet: -1.04 (0.31), residues: 230 loop : -1.66 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 678 HIS 0.005 0.001 HIS E 174 PHE 0.025 0.001 PHE E 312 TYR 0.015 0.002 TYR E 626 ARG 0.018 0.001 ARG B 560 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 217 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8654 (tt0) cc_final: 0.8415 (tt0) REVERT: B 151 GLN cc_start: 0.7653 (tt0) cc_final: 0.7297 (tt0) REVERT: B 251 GLU cc_start: 0.8078 (tt0) cc_final: 0.7725 (tm-30) REVERT: B 309 GLN cc_start: 0.8018 (tt0) cc_final: 0.7801 (mt0) REVERT: B 312 PHE cc_start: 0.8624 (m-80) cc_final: 0.8294 (m-80) REVERT: B 328 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8962 (mt) REVERT: B 548 MET cc_start: 0.8508 (mtp) cc_final: 0.8283 (mtp) REVERT: D 62 GLN cc_start: 0.8548 (tp40) cc_final: 0.8257 (tp40) REVERT: E 133 THR cc_start: 0.7620 (OUTLIER) cc_final: 0.6925 (t) REVERT: E 251 GLU cc_start: 0.8119 (tt0) cc_final: 0.7849 (pt0) REVERT: E 623 SER cc_start: 0.8895 (t) cc_final: 0.8530 (p) outliers start: 49 outliers final: 19 residues processed: 255 average time/residue: 0.9673 time to fit residues: 271.2441 Evaluate side-chains 217 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 390 ASN Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain E residue 639 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.0030 chunk 66 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 106 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.9518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11362 Z= 0.191 Angle : 0.706 11.985 15516 Z= 0.330 Chirality : 0.041 0.132 1738 Planarity : 0.006 0.070 1980 Dihedral : 7.830 150.247 1568 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.22 % Allowed : 31.10 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.19 (0.23), residues: 1382 helix: 2.81 (0.23), residues: 466 sheet: -0.60 (0.32), residues: 242 loop : -1.64 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 214 HIS 0.005 0.001 HIS E 174 PHE 0.029 0.001 PHE E 312 TYR 0.022 0.002 TYR B 382 ARG 0.009 0.001 ARG E 560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 208 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8608 (tp40) cc_final: 0.8391 (tt0) REVERT: B 151 GLN cc_start: 0.7750 (tt0) cc_final: 0.7407 (tt0) REVERT: B 251 GLU cc_start: 0.8063 (tt0) cc_final: 0.7719 (tm-30) REVERT: B 312 PHE cc_start: 0.8642 (m-80) cc_final: 0.8312 (m-80) REVERT: B 557 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6715 (pp20) REVERT: B 644 ASN cc_start: 0.7366 (m-40) cc_final: 0.6969 (p0) REVERT: D 62 GLN cc_start: 0.8509 (tp40) cc_final: 0.8229 (tp40) REVERT: D 129 LYS cc_start: 0.8336 (tttt) cc_final: 0.8125 (ttpp) REVERT: E 133 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.6862 (t) REVERT: E 251 GLU cc_start: 0.8092 (tt0) cc_final: 0.7804 (pt0) REVERT: E 485 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8767 (tp) REVERT: E 623 SER cc_start: 0.8871 (t) cc_final: 0.8467 (p) outliers start: 38 outliers final: 22 residues processed: 240 average time/residue: 0.9325 time to fit residues: 246.3282 Evaluate side-chains 214 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 189 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 390 ASN Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 639 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.9980 chunk 125 optimal weight: 0.0040 chunk 129 optimal weight: 0.9990 chunk 75 optimal weight: 0.0070 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 132 optimal weight: 0.0060 overall best weight: 0.3626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 HIS E 122 GLN E 388 GLN ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.9754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11362 Z= 0.172 Angle : 0.696 11.945 15516 Z= 0.325 Chirality : 0.040 0.143 1738 Planarity : 0.006 0.068 1980 Dihedral : 7.673 148.921 1568 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.88 % Allowed : 32.46 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.31 (0.23), residues: 1382 helix: 2.90 (0.23), residues: 466 sheet: -0.49 (0.34), residues: 200 loop : -1.53 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.005 0.001 HIS E 174 PHE 0.032 0.001 PHE E 312 TYR 0.019 0.001 TYR E 382 ARG 0.009 0.001 ARG E 560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 204 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8536 (tp40) cc_final: 0.8299 (tt0) REVERT: A 129 LYS cc_start: 0.8629 (tppt) cc_final: 0.8357 (tmmm) REVERT: B 151 GLN cc_start: 0.7800 (tt0) cc_final: 0.7508 (tt0) REVERT: B 251 GLU cc_start: 0.8098 (tt0) cc_final: 0.7730 (tm-30) REVERT: B 312 PHE cc_start: 0.8634 (m-80) cc_final: 0.8250 (m-80) REVERT: B 313 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8306 (m) REVERT: B 377 ASP cc_start: 0.7987 (t70) cc_final: 0.7725 (t70) REVERT: B 557 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6823 (pp20) REVERT: B 623 SER cc_start: 0.8823 (t) cc_final: 0.8598 (t) REVERT: B 644 ASN cc_start: 0.7288 (m-40) cc_final: 0.6953 (p0) REVERT: D 129 LYS cc_start: 0.8360 (tttt) cc_final: 0.8136 (ttpp) REVERT: E 251 GLU cc_start: 0.8089 (tt0) cc_final: 0.7843 (pt0) REVERT: E 420 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: E 485 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8711 (mt) REVERT: E 623 SER cc_start: 0.8857 (t) cc_final: 0.8652 (t) outliers start: 34 outliers final: 20 residues processed: 232 average time/residue: 0.9513 time to fit residues: 243.5398 Evaluate side-chains 211 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 639 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 128 optimal weight: 0.0970 chunk 111 optimal weight: 4.9990 chunk 11 optimal weight: 0.0050 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 0.0980 chunk 88 optimal weight: 7.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN E 388 GLN ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.9892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11362 Z= 0.173 Angle : 0.692 12.234 15516 Z= 0.324 Chirality : 0.040 0.137 1738 Planarity : 0.006 0.064 1980 Dihedral : 7.582 148.929 1568 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.46 % Allowed : 32.80 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.23), residues: 1382 helix: 2.90 (0.23), residues: 468 sheet: -0.30 (0.35), residues: 190 loop : -1.45 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 400 HIS 0.005 0.001 HIS E 174 PHE 0.037 0.001 PHE E 312 TYR 0.020 0.001 TYR E 382 ARG 0.009 0.001 ARG E 560 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 199 time to evaluate : 1.272 Fit side-chains REVERT: A 129 LYS cc_start: 0.8598 (tppt) cc_final: 0.8331 (ttpp) REVERT: B 151 GLN cc_start: 0.7881 (tt0) cc_final: 0.7533 (tt0) REVERT: B 251 GLU cc_start: 0.8072 (tt0) cc_final: 0.7700 (tm-30) REVERT: B 312 PHE cc_start: 0.8617 (m-80) cc_final: 0.8225 (m-80) REVERT: B 313 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8317 (m) REVERT: B 377 ASP cc_start: 0.8027 (t70) cc_final: 0.7759 (t70) REVERT: B 401 ILE cc_start: 0.8601 (pt) cc_final: 0.8377 (pt) REVERT: B 557 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6944 (pp20) REVERT: B 623 SER cc_start: 0.8812 (t) cc_final: 0.8577 (t) REVERT: B 644 ASN cc_start: 0.7298 (m-40) cc_final: 0.6967 (p0) REVERT: D 129 LYS cc_start: 0.8401 (tttt) cc_final: 0.8137 (ttpp) REVERT: E 122 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6735 (tt0) REVERT: E 251 GLU cc_start: 0.8086 (tt0) cc_final: 0.7793 (tm-30) REVERT: E 309 GLN cc_start: 0.8155 (mt0) cc_final: 0.7944 (mm110) REVERT: E 485 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8768 (mt) REVERT: E 557 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6999 (pp20) REVERT: E 623 SER cc_start: 0.8845 (t) cc_final: 0.8626 (t) outliers start: 29 outliers final: 17 residues processed: 222 average time/residue: 1.0066 time to fit residues: 245.9361 Evaluate side-chains 201 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 179 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 557 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 16 optimal weight: 0.0050 chunk 30 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 0.0030 chunk 114 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN ** E 454 GLN ** 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 = 0.3604 r_free = 0.3604 target = 0.115566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.093432 restraints weight = 17572.588| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.20 r_work: 0.3149 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.9908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 11362 Z= 0.273 Angle : 0.924 59.196 15516 Z= 0.494 Chirality : 0.046 0.878 1738 Planarity : 0.006 0.063 1980 Dihedral : 7.591 148.928 1568 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.46 % Allowed : 33.39 % Favored : 64.15 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.23), residues: 1382 helix: 2.90 (0.23), residues: 468 sheet: -0.31 (0.35), residues: 190 loop : -1.45 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 500 HIS 0.005 0.001 HIS E 532 PHE 0.035 0.001 PHE E 312 TYR 0.017 0.001 TYR B 626 ARG 0.008 0.000 ARG E 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4481.03 seconds wall clock time: 79 minutes 51.78 seconds (4791.78 seconds total)