Starting phenix.real_space_refine (version: 1.19rc7) on Tue Jan 5 19:23:50 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/01_2021/6rjg_4904.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/01_2021/6rjg_4904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/01_2021/6rjg_4904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/01_2021/6rjg_4904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/01_2021/6rjg_4904.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/01_2021/6rjg_4904.pdb" } resolution = 3.2 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= 0.000 sd= 0.011 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 12220 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "B" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "C" Number of atoms: 6633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6633 Classifications: {'peptide': 814} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 794} Chain breaks: 5 Chain: "D" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1656 Classifications: {'RNA': 78} Modifications used: {'rna3p_pyr': 32, 'rna2p_pur': 3, 'rna3p_pur': 37, 'rna2p_pyr': 6} Link IDs: {'rna3p': 68, 'rna2p': 9} Chain breaks: 2 Chain: "E" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 646 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "G" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 273 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 7.10, per 1000 atoms: 0.58 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Number of scatterers: 12220 At special positions: 0 Unit cell: (121.793, 140.462, 111.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 123 15.00 O 2639 8.00 N 2103 7.00 C 7318 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 Amimo 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: 5.01 Conformation dependent library (CDL) restraints added in 1.6 seconds 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 47.7% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 removed outlier: 3.621A pdb=" N LYS A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.836A pdb=" N ASP A 24 " --> pdb=" O PHE A 21 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 26 " --> pdb=" O ASN A 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 27 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 28 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.675A pdb=" N LEU A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 81 removed outlier: 3.896A pdb=" N ASN A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 4.163A pdb=" N LYS A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.935A pdb=" N GLY A 146 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 147 " --> pdb=" O GLY A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 147' Processing helix chain 'A' and resid 167 through 178 removed outlier: 3.559A pdb=" N GLU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 19 removed outlier: 3.617A pdb=" N LYS B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 removed outlier: 3.833A pdb=" N TYR B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 43 removed outlier: 3.554A pdb=" N ASN B 43 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.688A pdb=" N LEU B 63 " --> pdb=" O MET B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 80 Processing helix chain 'B' and resid 82 through 89 removed outlier: 4.128A pdb=" N LYS B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 110 removed outlier: 3.716A pdb=" N TYR B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 110 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.759A pdb=" N ARG B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 73 removed outlier: 3.757A pdb=" N VAL C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 98 Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 134 through 145 removed outlier: 3.674A pdb=" N GLN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 185 through 204 removed outlier: 3.748A pdb=" N TYR C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.346A pdb=" N ILE C 254 " --> pdb=" O ASN C 250 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU C 255 " --> pdb=" O ILE C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 255' Processing helix chain 'C' and resid 272 through 285 removed outlier: 3.922A pdb=" N GLN C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 311 Processing helix chain 'C' and resid 315 through 328 removed outlier: 3.949A pdb=" N LEU C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 358 removed outlier: 3.755A pdb=" N THR C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 382 removed outlier: 3.521A pdb=" N ASN C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 396 removed outlier: 3.737A pdb=" N PHE C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 416 removed outlier: 3.644A pdb=" N ASN C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.832A pdb=" N PHE C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 436 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.801A pdb=" N LEU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 500 removed outlier: 3.568A pdb=" N ALA C 483 " --> pdb=" O ASN C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 705 Processing helix chain 'C' and resid 854 through 868 Processing helix chain 'C' and resid 869 through 872 removed outlier: 3.687A pdb=" N PHE C 872 " --> pdb=" O LYS C 869 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 869 through 872' Processing helix chain 'C' and resid 873 through 878 Processing helix chain 'C' and resid 878 through 892 removed outlier: 3.594A pdb=" N PHE C 882 " --> pdb=" O ASP C 878 " (cutoff:3.500A) Proline residue: C 888 - end of helix Processing helix chain 'C' and resid 910 through 918 Processing helix chain 'C' and resid 986 through 988 No H-bonds generated for 'chain 'C' and resid 986 through 988' Processing helix chain 'C' and resid 1000 through 1011 Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 122 removed outlier: 6.776A pdb=" N ILE A 115 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 136 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY A 117 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU A 134 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 119 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET A 121 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA A 130 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 122 removed outlier: 6.776A pdb=" N ILE A 115 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 136 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY A 117 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU A 134 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 119 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET A 121 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA A 130 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N TYR A 128 " --> pdb=" O ASP C 947 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N ILE C 827 " --> pdb=" O LYS C 848 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N LYS C 848 " --> pdb=" O ILE C 827 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA C 829 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THR C 843 " --> pdb=" O LYS C 941 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LYS C 941 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C 845 " --> pdb=" O ASP C 939 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 114 through 122 removed outlier: 7.535A pdb=" N MET B 121 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN B 131 " --> pdb=" O MET B 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 710 through 713 removed outlier: 3.919A pdb=" N HIS C 29 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N LEU C 809 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS C 30 " --> pdb=" O LEU C 809 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N SER C 811 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER C 32 " --> pdb=" O SER C 811 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 268 through 269 removed outlier: 3.586A pdb=" N ALA C 268 " --> pdb=" O HIS C 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 338 through 339 removed outlier: 3.805A pdb=" N ARG C 338 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 978 through 980 removed outlier: 7.039A pdb=" N LEU C 983 " --> pdb=" O TRP C 965 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 978 through 980 removed outlier: 3.561A pdb=" N PHE C1021 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE C 971 " --> pdb=" O PHE C1019 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE C1019 " --> pdb=" O PHE C 971 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 989 through 990 Processing sheet with id=AB1, first strand: chain 'C' and resid 1085 through 1088 removed outlier: 4.515A pdb=" N CYS C1085 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU C1057 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C1028 " --> pdb=" O VAL C1099 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1242 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: 3.78 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2561 1.33 - 1.45: 3525 1.45 - 1.57: 6301 1.57 - 1.70: 241 1.70 - 1.82: 69 Bond restraints: 12697 Sorted by residual: bond pdb=" CA ASN B 83 " pdb=" C ASN B 83 " ideal model delta sigma weight residual 1.522 1.558 -0.036 1.72e-02 3.38e+03 4.44e+00 bond pdb=" CB ARG C 267 " pdb=" CG ARG C 267 " ideal model delta sigma weight residual 1.520 1.457 0.063 3.00e-02 1.11e+03 4.37e+00 bond pdb=" CG LEU C 959 " pdb=" CD1 LEU C 959 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.34e+00 bond pdb=" CB LYS C1010 " pdb=" CG LYS C1010 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.29e+00 bond pdb=" CA GLU C 887 " pdb=" C GLU C 887 " ideal model delta sigma weight residual 1.520 1.540 -0.020 1.23e-02 6.61e+03 2.59e+00 ... (remaining 12692 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.52: 698 105.52 - 112.95: 6698 112.95 - 120.37: 5478 120.37 - 127.79: 4524 127.79 - 135.22: 228 Bond angle restraints: 17626 Sorted by residual: angle pdb=" CA TYR A 26 " pdb=" CB TYR A 26 " pdb=" CG TYR A 26 " ideal model delta sigma weight residual 113.90 122.15 -8.25 1.80e+00 3.09e-01 2.10e+01 angle pdb=" CA ILE C 436 " pdb=" C ILE C 436 " pdb=" N PRO C 437 " ideal model delta sigma weight residual 118.88 124.84 -5.96 1.54e+00 4.22e-01 1.50e+01 angle pdb=" C HIS C 705 " pdb=" N LYS C 706 " pdb=" CA LYS C 706 " ideal model delta sigma weight residual 122.36 127.36 -5.00 1.42e+00 4.96e-01 1.24e+01 angle pdb=" CA LYS C 706 " pdb=" CB LYS C 706 " pdb=" CG LYS C 706 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA GLU C1113 " pdb=" CB GLU C1113 " pdb=" CG GLU C1113 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 ... (remaining 17621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 6257 17.72 - 35.44: 785 35.44 - 53.16: 252 53.16 - 70.88: 48 70.88 - 88.60: 16 Dihedral angle restraints: 7358 sinusoidal: 3911 harmonic: 3447 Sorted by residual: dihedral pdb=" CA ILE C 334 " pdb=" C ILE C 334 " pdb=" N LYS C 335 " pdb=" CA LYS C 335 " ideal model delta harmonic sigma weight residual -180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA HIS C 348 " pdb=" C HIS C 348 " pdb=" N THR C 349 " pdb=" CA THR C 349 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA MET A 87 " pdb=" C MET A 87 " pdb=" N ASN A 88 " pdb=" CA ASN A 88 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 7355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1707 0.082 - 0.165: 236 0.165 - 0.247: 21 0.247 - 0.330: 3 0.330 - 0.412: 2 Chirality restraints: 1969 Sorted by residual: chirality pdb=" CB ILE B 48 " pdb=" CA ILE B 48 " pdb=" CG1 ILE B 48 " pdb=" CG2 ILE B 48 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB ILE A 48 " pdb=" CA ILE A 48 " pdb=" CG1 ILE A 48 " pdb=" CG2 ILE A 48 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CB ILE C 999 " pdb=" CA ILE C 999 " pdb=" CG1 ILE C 999 " pdb=" CG2 ILE C 999 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1966 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 260 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C THR C 260 " 0.053 2.00e-02 2.50e+03 pdb=" O THR C 260 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE C 261 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U D 7 " 0.034 2.00e-02 2.50e+03 2.05e-02 9.42e+00 pdb=" N1 U D 7 " -0.049 2.00e-02 2.50e+03 pdb=" C2 U D 7 " 0.007 2.00e-02 2.50e+03 pdb=" O2 U D 7 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U D 7 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U D 7 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U D 7 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U D 7 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U D 7 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 26 " -0.025 2.00e-02 2.50e+03 1.83e-02 6.72e+00 pdb=" CG TYR B 26 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B 26 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 26 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 26 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 26 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 26 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 26 " -0.001 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3449 2.82 - 3.34: 9658 3.34 - 3.86: 19991 3.86 - 4.38: 23532 4.38 - 4.90: 38482 Nonbonded interactions: 95112 Sorted by model distance: nonbonded pdb=" OD2 ASP C 878 " pdb=" OG1 THR C 881 " model vdw 2.297 2.440 nonbonded pdb=" OE2 GLU A 68 " pdb=" NZ LYS A 99 " model vdw 2.339 2.520 nonbonded pdb=" OE1 GLU B 135 " pdb=" NE2 GLN B 151 " model vdw 2.341 2.520 nonbonded pdb=" OG1 THR C 830 " pdb=" O LYS C 956 " model vdw 2.362 2.440 nonbonded pdb=" O ALA C 376 " pdb=" OG1 THR C 380 " model vdw 2.377 2.440 ... (remaining 95107 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 3012 12220 True True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 123 5.49 5 S 37 5.16 5 C 7318 2.51 5 N 2103 2.21 5 O 2639 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 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: 1.390 Set model interpretation parameters: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.110 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.060 Process input model: 35.920 Set up NCS constraints: 0.050 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:2.470 Internal consistency checks: 0.000 Total: 47.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.008 0.071 12697 Angle : 0.955 12.264 17626 Chirality : 0.059 0.412 1969 Planarity : 0.006 0.063 1818 Dihedral : 16.967 88.602 5152 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer Outliers : 0.10 % 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: -3.61 (0.18), residues: 1164 helix: -2.16 (0.17), residues: 504 sheet: -1.79 (0.34), residues: 143 loop : -2.74 (0.21), residues: 517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 200 time to evaluate : 1.296 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 200 average time/residue: 0.3100 time to fit residues: 64.0602 Evaluate side-chains 148 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.356 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1486 time to fit residues: 1.9094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 161 GLN A 177 ASN B 88 ASN B 177 ASN B 178 ASN C 85 ASN C 142 ASN C 227 HIS C 276 GLN C 505 ASN C 832 GLN C 855 GLN C 944 ASN C 945 HIS C1001 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.030 12697 Angle : 0.489 7.603 17626 Chirality : 0.036 0.161 1969 Planarity : 0.003 0.035 1818 Dihedral : 14.762 80.517 2673 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 0.10 % 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: -1.76 (0.21), residues: 1164 helix: 0.05 (0.21), residues: 510 sheet: -1.21 (0.37), residues: 135 loop : -2.45 (0.22), residues: 519 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 210 time to evaluate : 1.240 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 210 average time/residue: 0.2955 time to fit residues: 64.2110 Evaluate side-chains 156 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 116 optimal weight: 0.3980 chunk 125 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.044 12697 Angle : 0.608 11.211 17626 Chirality : 0.041 0.177 1969 Planarity : 0.004 0.036 1818 Dihedral : 15.074 82.138 2673 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 0.10 % 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: -1.24 (0.23), residues: 1164 helix: 0.65 (0.22), residues: 512 sheet: -1.09 (0.39), residues: 141 loop : -2.34 (0.23), residues: 511 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 177 time to evaluate : 1.343 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.2803 time to fit residues: 51.8652 Evaluate side-chains 148 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.405 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 61 optimal weight: 0.0050 chunk 110 optimal weight: 0.0020 chunk 33 optimal weight: 0.9990 overall best weight: 1.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN C 403 GLN ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.031 12697 Angle : 0.479 7.516 17626 Chirality : 0.036 0.219 1969 Planarity : 0.003 0.033 1818 Dihedral : 14.549 82.328 2673 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.00 % 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: -0.71 (0.23), residues: 1164 helix: 1.20 (0.23), residues: 513 sheet: -0.82 (0.40), residues: 141 loop : -2.20 (0.23), residues: 510 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.320 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2686 time to fit residues: 52.4343 Evaluate side-chains 151 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 111 optimal weight: 0.0370 chunk 31 optimal weight: 6.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN C 403 GLN ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1093 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.038 12697 Angle : 0.444 6.782 17626 Chirality : 0.035 0.192 1969 Planarity : 0.003 0.052 1818 Dihedral : 14.082 81.353 2673 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 0.00 % 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: -0.27 (0.24), residues: 1164 helix: 1.61 (0.23), residues: 511 sheet: -0.53 (0.41), residues: 140 loop : -2.03 (0.24), residues: 513 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.430 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2752 time to fit residues: 51.3871 Evaluate side-chains 146 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.421 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 0.0770 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 0.0870 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN C 87 ASN C 403 GLN ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 HIS C1093 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.037 12697 Angle : 0.422 6.408 17626 Chirality : 0.034 0.179 1969 Planarity : 0.003 0.036 1818 Dihedral : 13.737 79.102 2673 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.10 % 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: 0.04 (0.24), residues: 1164 helix: 1.85 (0.23), residues: 514 sheet: -0.25 (0.41), residues: 143 loop : -1.92 (0.24), residues: 507 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 195 time to evaluate : 1.401 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.2798 time to fit residues: 57.0626 Evaluate side-chains 157 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 77 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN C 87 ASN C 403 GLN ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 HIS C1093 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.033 12697 Angle : 0.511 8.026 17626 Chirality : 0.037 0.164 1969 Planarity : 0.003 0.050 1818 Dihedral : 14.198 81.094 2673 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 0.00 % 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: -0.08 (0.24), residues: 1164 helix: 1.70 (0.23), residues: 512 sheet: -0.42 (0.41), residues: 145 loop : -1.87 (0.24), residues: 507 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.459 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2846 time to fit residues: 52.6242 Evaluate side-chains 144 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.2980 chunk 73 optimal weight: 8.9990 chunk 37 optimal weight: 0.2980 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.0060 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 60 optimal weight: 0.2980 chunk 11 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN C 403 GLN ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1093 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.031 12697 Angle : 0.441 6.398 17626 Chirality : 0.034 0.165 1969 Planarity : 0.003 0.037 1818 Dihedral : 13.858 79.251 2673 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 0.00 % 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: 0.16 (0.24), residues: 1164 helix: 1.88 (0.23), residues: 511 sheet: -0.25 (0.42), residues: 143 loop : -1.72 (0.24), residues: 510 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.182 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2961 time to fit residues: 56.5757 Evaluate side-chains 152 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN C 403 GLN ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1093 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.047 12697 Angle : 0.468 8.664 17626 Chirality : 0.035 0.159 1969 Planarity : 0.003 0.036 1818 Dihedral : 13.900 79.202 2673 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.00 % 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: 0.13 (0.24), residues: 1164 helix: 1.85 (0.23), residues: 515 sheet: -0.28 (0.41), residues: 143 loop : -1.75 (0.25), residues: 506 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.328 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2633 time to fit residues: 47.1817 Evaluate side-chains 146 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.343 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 0.0050 chunk 108 optimal weight: 6.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN C 403 GLN ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1093 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.046 12697 Angle : 0.444 6.487 17626 Chirality : 0.034 0.160 1969 Planarity : 0.003 0.034 1818 Dihedral : 13.778 78.183 2673 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 0.00 % 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: 0.30 (0.24), residues: 1164 helix: 2.02 (0.23), residues: 512 sheet: -0.17 (0.42), residues: 143 loop : -1.68 (0.25), residues: 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield and 0 Emsley and 1164 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.294 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2689 time to fit residues: 48.5898 Evaluate side-chains 143 residues out of total 1046 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 0.0010 chunk 42 optimal weight: 6.9990 chunk 104 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1093 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.171037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.139824 restraints weight = 17485.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140811 restraints weight = 13520.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142862 restraints weight = 10483.892| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.002 0.046 12697 ANGLE : 0.439 9.377 17626 CHIRALITY : 0.034 0.157 1969 PLANARITY : 0.002 0.039 1818 DIHEDRAL : 13.614 76.786 2673 MIN NONBONDED DISTANCE : 2.153 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 5.21 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 4.64 % FAVORED : 95.36 % ROTAMER OUTLIERS : 0.00 % 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: 0.46 (0.25), RESIDUES: 1164 HELIX: 2.17 (0.23), RESIDUES: 510 SHEET: -0.03 (0.42), RESIDUES: 143 LOOP : -1.63 (0.25), RESIDUES: 511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.046 12697 Angle : 0.439 9.377 17626 Chirality : 0.034 0.157 1969 Planarity : 0.002 0.039 1818 Dihedral : 13.614 76.786 2673 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.00 % 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: 0.46 (0.25), residues: 1164 helix: 2.17 (0.23), residues: 510 sheet: -0.03 (0.42), residues: 143 loop : -1.63 (0.25), residues: 511 =============================================================================== Job complete usr+sys time: 2308.53 seconds wall clock time: 43 minutes 5.61 seconds (2585.61 seconds total)