Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 01:59:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/04_2023/6of2_20040_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/04_2023/6of2_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_20040/04_2023/6of2_20040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/04_2023/6of2_20040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/04_2023/6of2_20040_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/04_2023/6of2_20040_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 6.24, per 1000 atoms: 0.56 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 1.5 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: 1.14 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: 3.38 Time building geometry restraints manager: 4.69 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: 6572 32.46 - 64.92: 182 64.92 - 97.38: 4 97.38 - 129.84: 0 129.84 - 162.30: 2 Dihedral angle restraints: 6760 sinusoidal: 2668 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 6757 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: 0.820 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: 3.540 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 30.380 Find NCS groups from input model: 0.600 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.140 ------------------------------------------------------------------------------- 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 : 14.632 162.297 4108 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 % 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 *********************** 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 : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 378 average time/residue: 0.9604 time to fit residues: 399.0530 Evaluate side-chains 214 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 211 time to evaluate : 1.257 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 2 average time/residue: 0.1451 time to fit residues: 2.3656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 1.9990 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: 0.9980 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: 0.4450 ------------------------------------------------------------------------------- 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 D 21 GLN D 143 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: 0.6608 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 11362 Z= 0.236 Angle : 0.831 10.098 15516 Z= 0.401 Chirality : 0.045 0.173 1738 Planarity : 0.007 0.058 1980 Dihedral : 8.814 164.986 1546 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer Outliers : 4.07 % 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: -1.27 (0.22), residues: 1382 helix: 1.97 (0.21), residues: 472 sheet: -1.03 (0.32), residues: 222 loop : -3.00 (0.21), residues: 688 *********************** 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 310 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 262 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 20 residues processed: 286 average time/residue: 0.8011 time to fit residues: 256.6792 Evaluate side-chains 245 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 225 time to evaluate : 1.257 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 9 residues processed: 13 average time/residue: 0.1419 time to fit residues: 4.6595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 0.0980 chunk 137 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN B 246 ASN B 327 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN D 21 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 120 ASN E 246 ASN E 334 HIS ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 11362 Z= 0.252 Angle : 0.784 10.343 15516 Z= 0.377 Chirality : 0.043 0.158 1738 Planarity : 0.006 0.051 1980 Dihedral : 8.629 163.431 1546 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer Outliers : 4.92 % 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: -0.54 (0.23), residues: 1382 helix: 2.40 (0.22), residues: 474 sheet: -0.80 (0.34), residues: 196 loop : -2.32 (0.23), residues: 712 *********************** 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 299 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 241 time to evaluate : 1.300 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 21 residues processed: 280 average time/residue: 0.8140 time to fit residues: 254.7272 Evaluate side-chains 218 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 197 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 9 average time/residue: 0.1331 time to fit residues: 3.8238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 0.0770 chunk 135 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS B 171 HIS ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 246 ASN E 334 HIS ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 11362 Z= 0.244 Angle : 0.774 14.897 15516 Z= 0.363 Chirality : 0.044 0.215 1738 Planarity : 0.006 0.050 1980 Dihedral : 8.424 162.064 1546 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 5.59 % 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: -0.39 (0.23), residues: 1382 helix: 2.35 (0.22), residues: 474 sheet: -0.53 (0.35), residues: 218 loop : -2.19 (0.23), residues: 690 *********************** 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 315 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 249 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 21 residues processed: 297 average time/residue: 0.9482 time to fit residues: 310.3583 Evaluate side-chains 237 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 216 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 0.5215 time to fit residues: 4.2884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 115 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 327 ASN ** 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: 0.7714 moved from start: 0.7836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 11362 Z= 0.239 Angle : 0.719 11.820 15516 Z= 0.344 Chirality : 0.043 0.152 1738 Planarity : 0.006 0.049 1980 Dihedral : 8.220 159.492 1546 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer Outliers : 5.08 % 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: -0.20 (0.23), residues: 1382 helix: 2.45 (0.23), residues: 476 sheet: -0.40 (0.36), residues: 200 loop : -2.01 (0.23), residues: 706 *********************** 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 303 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 243 time to evaluate : 1.324 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 27 residues processed: 285 average time/residue: 0.9899 time to fit residues: 309.8182 Evaluate side-chains 246 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 219 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 6 average time/residue: 0.1560 time to fit residues: 3.3337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 0.0980 chunk 11 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 GLN B 388 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.8579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11362 Z= 0.218 Angle : 0.723 12.994 15516 Z= 0.340 Chirality : 0.043 0.206 1738 Planarity : 0.006 0.046 1980 Dihedral : 8.166 159.163 1546 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer Outliers : 4.49 % 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: -0.04 (0.23), residues: 1382 helix: 2.61 (0.23), residues: 466 sheet: -0.42 (0.36), residues: 202 loop : -1.83 (0.23), residues: 714 *********************** 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 285 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 232 time to evaluate : 1.359 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 30 residues processed: 271 average time/residue: 0.9772 time to fit residues: 291.4921 Evaluate side-chains 235 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 1.745 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 25 residues processed: 5 average time/residue: 0.1745 time to fit residues: 3.2410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 0.0970 chunk 83 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.8983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 11362 Z= 0.188 Angle : 0.696 11.196 15516 Z= 0.330 Chirality : 0.042 0.199 1738 Planarity : 0.005 0.045 1980 Dihedral : 8.033 158.569 1546 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer Outliers : 3.90 % 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: 2.75 (0.23), residues: 464 sheet: -0.37 (0.35), residues: 202 loop : -1.63 (0.23), residues: 716 *********************** 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 261 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 215 time to evaluate : 1.197 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 21 residues processed: 247 average time/residue: 0.9691 time to fit residues: 264.2265 Evaluate side-chains 218 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 197 time to evaluate : 1.384 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.1853 time to fit residues: 2.3688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 40 optimal weight: 0.2980 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 0.0060 chunk 122 optimal weight: 0.8980 chunk 129 optimal weight: 0.0980 overall best weight: 0.2796 ------------------------------------------------------------------------------- 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** E 122 GLN E 309 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.9187 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= 0.177 Angle : 0.692 11.586 15516 Z= 0.324 Chirality : 0.042 0.218 1738 Planarity : 0.006 0.078 1980 Dihedral : 7.942 158.660 1546 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 3.56 % 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: 0.25 (0.23), residues: 1382 helix: 2.78 (0.23), residues: 468 sheet: -0.28 (0.36), residues: 192 loop : -1.59 (0.23), residues: 722 *********************** 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 260 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 218 time to evaluate : 1.349 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 28 residues processed: 249 average time/residue: 1.0290 time to fit residues: 281.9265 Evaluate side-chains 218 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 21 residues processed: 7 average time/residue: 0.1937 time to fit residues: 3.7136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 132 optimal weight: 0.0010 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.9469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 11362 Z= 0.185 Angle : 0.692 10.182 15516 Z= 0.330 Chirality : 0.042 0.194 1738 Planarity : 0.006 0.071 1980 Dihedral : 7.851 158.362 1546 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer Outliers : 2.63 % 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: 0.28 (0.24), residues: 1382 helix: 2.80 (0.24), residues: 468 sheet: -0.47 (0.33), residues: 234 loop : -1.55 (0.24), residues: 680 *********************** 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 230 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 1.276 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 23 residues processed: 223 average time/residue: 0.9803 time to fit residues: 242.3815 Evaluate side-chains 203 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 1.379 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.2027 time to fit residues: 2.6901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.1980 chunk 63 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 111 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** E 122 GLN E 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.9890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 11362 Z= 0.203 Angle : 0.713 10.946 15516 Z= 0.336 Chirality : 0.042 0.182 1738 Planarity : 0.006 0.067 1980 Dihedral : 7.819 157.740 1546 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 2.29 % 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: 0.33 (0.23), residues: 1382 helix: 2.76 (0.24), residues: 466 sheet: -0.22 (0.36), residues: 192 loop : -1.47 (0.23), residues: 724 ********************** 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 226 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 199 time to evaluate : 1.327 Fit side-chains outliers start: 27 outliers final: 23 residues processed: 222 average time/residue: 0.9729 time to fit residues: 238.7687 Evaluate side-chains 198 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.1886 time to fit residues: 2.5810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 388 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN E 625 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.091552 restraints weight = 17679.253| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.17 r_work: 0.3117 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 1.0170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 11362 Z= 0.219 Angle : 0.713 10.359 15516 Z= 0.338 Chirality : 0.042 0.190 1738 Planarity : 0.006 0.065 1980 Dihedral : 7.806 157.253 1546 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer Outliers : 2.63 % 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: 0.24 (0.23), residues: 1382 helix: 2.46 (0.24), residues: 480 sheet: -0.33 (0.36), residues: 194 loop : -1.42 (0.24), residues: 708 =============================================================================== Job complete usr+sys time: 4541.33 seconds wall clock time: 80 minutes 58.68 seconds (4858.68 seconds total)