Starting phenix.real_space_refine (version: dev) on Mon Dec 12 16:16:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/12_2022/6of2_20040_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/12_2022/6of2_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_20040/12_2022/6of2_20040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/12_2022/6of2_20040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/12_2022/6of2_20040_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of2_20040/12_2022/6of2_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 Convert atoms to be neutral 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 6.67, per 1000 atoms: 0.60 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: 4.81 Conformation dependent library (CDL) restraints added in 1.6 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: 1.19 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: 3.30 Time building geometry restraints manager: 5.08 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 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. 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: 0.530 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: 3.810 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.080 Process input model: 31.630 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 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 : 8.89 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 : 1.324 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: 0.8538 time to fit residues: 356.0526 Evaluate side-chains 214 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 211 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 2 average time/residue: 0.1331 time to fit residues: 2.1469 ------------------------------------------------------------------------------- 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: 0.0670 chunk 81 optimal weight: 0.2980 chunk 127 optimal weight: 0.8980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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: 0.6871 moved from start: 0.3395 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= 0.245 Angle : 0.844 10.765 15516 Z= 0.406 Chirality : 0.045 0.176 1738 Planarity : 0.007 0.081 1980 Dihedral : 8.900 165.656 1546 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer Outliers : 4.15 % 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: -1.18 (0.22), residues: 1382 helix: 2.06 (0.21), residues: 472 sheet: -1.02 (0.32), residues: 222 loop : -2.95 (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 316 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 267 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 19 residues processed: 292 average time/residue: 0.7535 time to fit residues: 247.4830 Evaluate side-chains 247 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 228 time to evaluate : 1.331 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 9 residues processed: 12 average time/residue: 0.1450 time to fit residues: 4.4874 ------------------------------------------------------------------------------- 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: 0.5980 chunk 127 optimal weight: 0.1980 chunk 137 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 480 GLN D 21 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 171 HIS E 246 ASN E 334 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 11362 Z= 0.233 Angle : 0.764 10.917 15516 Z= 0.364 Chirality : 0.042 0.150 1738 Planarity : 0.006 0.047 1980 Dihedral : 8.588 164.051 1546 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % 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: -0.55 (0.23), residues: 1382 helix: 2.47 (0.22), residues: 474 sheet: -1.25 (0.31), residues: 232 loop : -2.26 (0.24), residues: 676 *********************** 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 292 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 234 time to evaluate : 1.344 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 26 residues processed: 274 average time/residue: 0.8009 time to fit residues: 245.2325 Evaluate side-chains 218 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 1.334 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 18 residues processed: 10 average time/residue: 0.1434 time to fit residues: 4.1581 ------------------------------------------------------------------------------- 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: 0.0870 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 0.0980 chunk 135 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN B 454 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN E 246 ASN E 334 HIS ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.7964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 11362 Z= 0.314 Angle : 0.834 15.978 15516 Z= 0.404 Chirality : 0.047 0.237 1738 Planarity : 0.007 0.064 1980 Dihedral : 8.553 161.700 1546 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer Outliers : 6.02 % 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: -0.65 (0.23), residues: 1382 helix: 2.02 (0.22), residues: 462 sheet: -1.22 (0.32), residues: 222 loop : -1.95 (0.23), residues: 698 *********************** 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 378 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 307 time to evaluate : 1.287 Fit side-chains revert: symmetry clash outliers start: 71 outliers final: 19 residues processed: 350 average time/residue: 0.8893 time to fit residues: 343.3407 Evaluate side-chains 248 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 229 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 5 average time/residue: 0.4292 time to fit residues: 4.3778 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 GLN D 21 GLN D 62 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.9054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 11362 Z= 0.262 Angle : 0.746 12.988 15516 Z= 0.354 Chirality : 0.044 0.163 1738 Planarity : 0.006 0.056 1980 Dihedral : 8.260 158.615 1546 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % 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: -0.38 (0.23), residues: 1382 helix: 2.32 (0.23), residues: 468 sheet: -0.81 (0.31), residues: 242 loop : -2.02 (0.24), residues: 672 *********************** 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 298 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 238 time to evaluate : 1.274 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 28 residues processed: 280 average time/residue: 0.8894 time to fit residues: 275.2967 Evaluate side-chains 227 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 23 residues processed: 5 average time/residue: 0.4165 time to fit residues: 4.3341 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 112 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN E 388 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.9489 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= 0.213 Angle : 0.697 11.322 15516 Z= 0.332 Chirality : 0.042 0.177 1738 Planarity : 0.006 0.051 1980 Dihedral : 8.112 157.565 1546 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 5.17 % 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: -0.14 (0.23), residues: 1382 helix: 2.46 (0.23), residues: 466 sheet: -0.55 (0.32), residues: 232 loop : -1.86 (0.24), residues: 684 *********************** 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 280 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 219 time to evaluate : 1.292 Fit side-chains outliers start: 61 outliers final: 35 residues processed: 258 average time/residue: 0.8897 time to fit residues: 254.1116 Evaluate side-chains 227 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 192 time to evaluate : 1.242 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 27 residues processed: 8 average time/residue: 0.8290 time to fit residues: 9.1648 ------------------------------------------------------------------------------- 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: 0.9980 chunk 77 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN D 62 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.9839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11362 Z= 0.211 Angle : 0.696 10.747 15516 Z= 0.331 Chirality : 0.042 0.168 1738 Planarity : 0.006 0.072 1980 Dihedral : 7.980 156.786 1546 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer Outliers : 4.41 % 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: 2.50 (0.23), residues: 468 sheet: -0.53 (0.32), residues: 232 loop : -1.74 (0.24), residues: 682 *********************** 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 252 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 200 time to evaluate : 1.224 Fit side-chains outliers start: 52 outliers final: 29 residues processed: 241 average time/residue: 0.9028 time to fit residues: 240.5597 Evaluate side-chains 215 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 186 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 3 average time/residue: 0.6109 time to fit residues: 3.7880 ------------------------------------------------------------------------------- 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: 0.9980 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN D 62 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 1.0054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 11362 Z= 0.204 Angle : 0.686 11.235 15516 Z= 0.328 Chirality : 0.042 0.165 1738 Planarity : 0.006 0.071 1980 Dihedral : 7.919 156.171 1546 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer Outliers : 3.47 % 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: 0.09 (0.23), residues: 1382 helix: 2.62 (0.23), residues: 466 sheet: -0.52 (0.32), residues: 232 loop : -1.65 (0.24), residues: 684 *********************** 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 233 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 192 time to evaluate : 1.160 Fit side-chains outliers start: 41 outliers final: 29 residues processed: 229 average time/residue: 0.8934 time to fit residues: 226.2968 Evaluate side-chains 215 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 186 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 4 average time/residue: 0.4765 time to fit residues: 4.0859 ------------------------------------------------------------------------------- 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: 2.9990 chunk 125 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 0.0870 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 132 optimal weight: 0.0370 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 1.0249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11362 Z= 0.181 Angle : 0.687 11.964 15516 Z= 0.327 Chirality : 0.041 0.167 1738 Planarity : 0.006 0.067 1980 Dihedral : 7.836 155.543 1546 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer Outliers : 2.88 % 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: 0.23 (0.23), residues: 1382 helix: 2.75 (0.24), residues: 466 sheet: -0.48 (0.32), residues: 232 loop : -1.57 (0.24), residues: 684 *********************** 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 223 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 189 time to evaluate : 1.342 Fit side-chains outliers start: 34 outliers final: 25 residues processed: 220 average time/residue: 0.8920 time to fit residues: 217.4643 Evaluate side-chains 200 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 175 time to evaluate : 1.160 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 0.1470 time to fit residues: 2.1868 ------------------------------------------------------------------------------- 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: 4.9990 chunk 63 optimal weight: 0.0970 chunk 92 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 11 optimal weight: 0.0370 chunk 85 optimal weight: 0.0050 chunk 68 optimal weight: 0.0060 chunk 88 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.8288 ------------------------------------------------------------------------------- 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 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN E 388 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 1.0493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 11362 Z= 0.227 Angle : 0.707 12.257 15516 Z= 0.339 Chirality : 0.043 0.537 1738 Planarity : 0.006 0.065 1980 Dihedral : 7.815 155.188 1546 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer Outliers : 2.71 % 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: 0.22 (0.23), residues: 1382 helix: 2.63 (0.24), residues: 466 sheet: -0.45 (0.32), residues: 232 loop : -1.50 (0.24), residues: 684 ********************** 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 215 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 1.307 Fit side-chains outliers start: 32 outliers final: 24 residues processed: 212 average time/residue: 0.8806 time to fit residues: 207.5622 Evaluate side-chains 200 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 3 average time/residue: 0.5065 time to fit residues: 3.6020 ------------------------------------------------------------------------------- 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: 2.9990 chunk 102 optimal weight: 0.7980 chunk 16 optimal weight: 0.0070 chunk 30 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 46 optimal weight: 0.0060 chunk 114 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4814 ------------------------------------------------------------------------------- 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 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.112900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.091101 restraints weight = 17763.938| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.15 r_work: 0.3114 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 1.0633 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= 0.186 Angle : 0.689 12.110 15516 Z= 0.329 Chirality : 0.042 0.430 1738 Planarity : 0.006 0.062 1980 Dihedral : 7.733 154.487 1546 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1382 helix: 2.78 (0.24), residues: 462 sheet: -0.47 (0.32), residues: 232 loop : -1.43 (0.25), residues: 688 =============================================================================== Job complete usr+sys time: 4180.56 seconds wall clock time: 74 minutes 42.09 seconds (4482.09 seconds total)