Starting phenix.real_space_refine (version: dev) on Tue Apr 5 10:27:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn4_4282/04_2022/6fn4_4282_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn4_4282/04_2022/6fn4_4282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn4_4282/04_2022/6fn4_4282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn4_4282/04_2022/6fn4_4282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn4_4282/04_2022/6fn4_4282_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn4_4282/04_2022/6fn4_4282_updated.pdb" } resolution = 4.14 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= 0.015 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 PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 542": "NH1" <-> "NH2" Residue "A ARG 831": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 82": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 222": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 12702 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9182 Classifications: {'peptide': 1181} Link IDs: {'CIS': 5, 'PTRANS': 27, 'TRANS': 1148} Chain breaks: 1 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 207, 'PCIS': 4} Chain: "C" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1717 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 211, 'PCIS': 3} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'NAG': 3, '3PE': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.72, per 1000 atoms: 0.77 Number of scatterers: 12702 At special positions: 0 Unit cell: (97.09, 98.477, 208.05, 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 48 16.00 P 1 15.00 O 2386 8.00 N 2122 7.00 C 8145 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A1203 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.05 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 204 " distance=2.03 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 Atom "HETATM12649 O5 NAG A1303 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1303 " - " ASN A 98 " Time building additional restraints: 6.70 Conformation dependent library (CDL) restraints added in 2.6 seconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2998 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 14 sheets defined 45.4% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.11 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 46 through 63 removed outlier: 4.612A pdb=" N ALA A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 87 Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 113 through 155 removed outlier: 4.200A pdb=" N LYS A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 185 removed outlier: 3.685A pdb=" N THR A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 207 Processing helix chain 'A' and resid 212 through 236 removed outlier: 3.540A pdb=" N VAL A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Proline residue: A 222 - end of helix Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 260 through 266 removed outlier: 3.773A pdb=" N ALA A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 322 removed outlier: 4.511A pdb=" N SER A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 345 Processing helix chain 'A' and resid 348 through 368 Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 462 through 467 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 496 through 505 Processing helix chain 'A' and resid 509 through 514 removed outlier: 3.516A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 520 No H-bonds generated for 'chain 'A' and resid 518 through 520' Processing helix chain 'A' and resid 532 through 545 Processing helix chain 'A' and resid 564 through 576 removed outlier: 3.524A pdb=" N VAL A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 593 Processing helix chain 'A' and resid 611 through 617 Processing helix chain 'A' and resid 620 through 628 Processing helix chain 'A' and resid 696 through 703 removed outlier: 4.603A pdb=" N ASN A 703 " --> pdb=" O ILE A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 725 through 737 Processing helix chain 'A' and resid 744 through 797 Processing helix chain 'A' and resid 801 through 803 No H-bonds generated for 'chain 'A' and resid 801 through 803' Processing helix chain 'A' and resid 810 through 829 removed outlier: 4.508A pdb=" N GLY A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR A 828 " --> pdb=" O VAL A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 852 removed outlier: 3.932A pdb=" N TYR A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 862 removed outlier: 4.240A pdb=" N ALA A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 879 removed outlier: 3.526A pdb=" N VAL A 872 " --> pdb=" O ALA A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 900 removed outlier: 4.033A pdb=" N LYS A 894 " --> pdb=" O GLU A 890 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE A 895 " --> pdb=" O GLY A 891 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 908 Processing helix chain 'A' and resid 913 through 965 removed outlier: 3.999A pdb=" N GLN A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER A 922 " --> pdb=" O MET A 918 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 923 " --> pdb=" O TYR A 919 " (cutoff:3.500A) Proline residue: A 926 - end of helix removed outlier: 3.815A pdb=" N ALA A 953 " --> pdb=" O TYR A 949 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS A 965 " --> pdb=" O TYR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 990 Processing helix chain 'A' and resid 998 through 1012 Processing helix chain 'A' and resid 1044 through 1046 No H-bonds generated for 'chain 'A' and resid 1044 through 1046' Processing helix chain 'A' and resid 1075 through 1082 removed outlier: 4.231A pdb=" N VAL A1079 " --> pdb=" O LYS A1075 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A1080 " --> pdb=" O SER A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1102 No H-bonds generated for 'chain 'A' and resid 1100 through 1102' Processing helix chain 'A' and resid 1105 through 1110 Processing helix chain 'A' and resid 1126 through 1131 Processing helix chain 'A' and resid 1141 through 1150 removed outlier: 3.992A pdb=" N VAL A1145 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG A1146 " --> pdb=" O GLU A1142 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A1147 " --> pdb=" O GLU A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1159 removed outlier: 3.797A pdb=" N SER A1159 " --> pdb=" O GLN A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1209 through 1220 Processing helix chain 'A' and resid 1233 through 1238 removed outlier: 3.886A pdb=" N GLN A1237 " --> pdb=" O LEU A1233 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN A1238 " --> pdb=" O SER A1234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1233 through 1238' Processing helix chain 'A' and resid 1256 through 1262 Processing helix chain 'A' and resid 1265 through 1272 removed outlier: 3.664A pdb=" N VAL A1272 " --> pdb=" O SER A1268 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 189 through 193 removed outlier: 4.029A pdb=" N GLU B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 189 through 193' Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 449 through 452 removed outlier: 4.982A pdb=" N LEU A 412 " --> pdb=" O ASN A 395 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 605 through 609 removed outlier: 6.925A pdb=" N GLY A 599 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN A 608 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A 597 " --> pdb=" O GLN A 608 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR A 581 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU A 424 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A 583 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLY A 426 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1057 through 1059 Processing sheet with id= D, first strand: chain 'A' and resid 1249 through 1254 removed outlier: 7.069A pdb=" N VAL A1244 " --> pdb=" O LYS A1251 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HIS A1253 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A1242 " --> pdb=" O HIS A1253 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR A1226 " --> pdb=" O LEU A1065 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU A1067 " --> pdb=" O THR A1226 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A1228 " --> pdb=" O LEU A1067 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N GLY A1069 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY A1113 " --> pdb=" O LEU A1197 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1039 through 1041 removed outlier: 7.543A pdb=" N PHE A1041 " --> pdb=" O GLN A1053 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLN A1053 " --> pdb=" O PHE A1041 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 5 through 7 Processing sheet with id= G, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.330A pdb=" N LYS B 109 " --> pdb=" O LEU B 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.808A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 120 through 124 removed outlier: 5.665A pdb=" N TYR B 179 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 151 through 156 Processing sheet with id= K, first strand: chain 'C' and resid 3 through 6 Processing sheet with id= L, first strand: chain 'C' and resid 10 through 13 Processing sheet with id= M, first strand: chain 'C' and resid 129 through 133 Processing sheet with id= N, first strand: chain 'C' and resid 160 through 163 650 hydrogen bonds defined for protein. 1851 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: 12.73 Time building geometry restraints manager: 6.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2062 1.29 - 1.43: 3355 1.43 - 1.57: 7460 1.57 - 1.71: 2 1.71 - 1.84: 83 Bond restraints: 12962 Sorted by residual: bond pdb=" C7 NAG A1303 " pdb=" N2 NAG A1303 " ideal model delta sigma weight residual 1.337 1.491 -0.154 1.10e-02 8.26e+03 1.95e+02 bond pdb=" C7 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.337 1.470 -0.133 1.10e-02 8.26e+03 1.46e+02 bond pdb=" C7 NAG A1302 " pdb=" N2 NAG A1302 " ideal model delta sigma weight residual 1.337 1.469 -0.132 1.10e-02 8.26e+03 1.45e+02 bond pdb=" C2 NAG A1303 " pdb=" N2 NAG A1303 " ideal model delta sigma weight residual 1.454 1.511 -0.057 1.00e-02 1.00e+04 3.24e+01 bond pdb=" C3 NAG A1302 " pdb=" C4 NAG A1302 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.00e-02 1.00e+04 2.43e+01 ... (remaining 12957 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.40: 214 105.40 - 112.57: 6857 112.57 - 119.74: 4223 119.74 - 126.90: 6128 126.90 - 134.07: 125 Bond angle restraints: 17547 Sorted by residual: angle pdb=" C3 NAG A1302 " pdb=" C2 NAG A1302 " pdb=" N2 NAG A1302 " ideal model delta sigma weight residual 110.58 98.23 12.35 9.20e-01 1.18e+00 1.80e+02 angle pdb=" C3 NAG A1301 " pdb=" C2 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 110.58 98.27 12.31 9.20e-01 1.18e+00 1.79e+02 angle pdb=" O12 3PE A1304 " pdb=" P 3PE A1304 " pdb=" O14 3PE A1304 " ideal model delta sigma weight residual 123.79 101.27 22.52 3.00e+00 1.11e-01 5.64e+01 angle pdb=" C8 NAG A1303 " pdb=" C7 NAG A1303 " pdb=" O7 NAG A1303 " ideal model delta sigma weight residual 122.09 116.64 5.45 9.70e-01 1.06e+00 3.15e+01 angle pdb=" C8 NAG A1303 " pdb=" C7 NAG A1303 " pdb=" N2 NAG A1303 " ideal model delta sigma weight residual 116.06 121.31 -5.25 9.90e-01 1.02e+00 2.81e+01 ... (remaining 17542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 7329 16.25 - 32.50: 307 32.50 - 48.75: 62 48.75 - 65.00: 4 65.00 - 81.25: 7 Dihedral angle restraints: 7709 sinusoidal: 3032 harmonic: 4677 Sorted by residual: dihedral pdb=" CB CYS A 558 " pdb=" SG CYS A 558 " pdb=" SG CYS A1203 " pdb=" CB CYS A1203 " ideal model delta sinusoidal sigma weight residual -86.00 -159.27 73.27 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" CA ARG A 488 " pdb=" C ARG A 488 " pdb=" N TYR A 489 " pdb=" CA TYR A 489 " ideal model delta harmonic sigma weight residual 180.00 149.08 30.92 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA GLY C 153 " pdb=" C GLY C 153 " pdb=" N TYR C 154 " pdb=" CA TYR C 154 " ideal model delta harmonic sigma weight residual -180.00 -152.69 -27.31 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 7706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1364 0.041 - 0.083: 476 0.083 - 0.124: 140 0.124 - 0.166: 27 0.166 - 0.207: 1 Chirality restraints: 2008 Sorted by residual: chirality pdb=" CB ILE A 97 " pdb=" CA ILE A 97 " pdb=" CG1 ILE A 97 " pdb=" CG2 ILE A 97 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE A 839 " pdb=" CA ILE A 839 " pdb=" CG1 ILE A 839 " pdb=" CG2 ILE A 839 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA ILE B 80 " pdb=" N ILE B 80 " pdb=" C ILE B 80 " pdb=" CB ILE B 80 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 2005 not shown) Planarity restraints: 2219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " 0.062 2.00e-02 2.50e+03 9.79e-02 1.20e+02 pdb=" CG ASN A 98 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " 0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " -0.170 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 100 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO B 101 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO B 101 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 101 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 99 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO B 100 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " -0.037 5.00e-02 4.00e+02 ... (remaining 2216 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 156 2.66 - 3.22: 12327 3.22 - 3.78: 18567 3.78 - 4.34: 25286 4.34 - 4.90: 40216 Nonbonded interactions: 96552 Sorted by model distance: nonbonded pdb=" ND2 ASN A 90 " pdb=" C1 NAG A1302 " model vdw 2.096 3.550 nonbonded pdb=" OG1 THR A 198 " pdb=" OG SER A 343 " model vdw 2.140 2.440 nonbonded pdb=" OD1 ASP A 742 " pdb=" NZ LYS A 747 " model vdw 2.172 2.520 nonbonded pdb=" NH1 ARG A 546 " pdb=" O LEU A 909 " model vdw 2.190 2.520 nonbonded pdb=" OG1 THR C 14 " pdb=" OG SER C 122 " model vdw 2.205 2.440 ... (remaining 96547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 48 5.16 5 C 8145 2.51 5 N 2122 2.21 5 O 2386 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 group one per residue 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: 1.010 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: 5.720 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.260 Process input model: 52.720 Find NCS groups from input model: 0.420 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:5.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 0.005 0.154 12962 Z= 0.320 Angle : 0.801 22.520 17547 Z= 0.452 Chirality : 0.046 0.207 2008 Planarity : 0.006 0.113 2218 Dihedral : 9.958 81.253 4693 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 1.17 % Allowed : 7.54 % Favored : 91.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.18), residues: 1618 helix: -1.47 (0.16), residues: 739 sheet: -1.26 (0.30), residues: 265 loop : -2.74 (0.21), residues: 614 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.649 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.3106 time to fit residues: 107.5751 Evaluate side-chains 121 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 8.9990 chunk 122 optimal weight: 0.0870 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 126 optimal weight: 0.0770 chunk 49 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 171 ASN A 356 ASN ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS A 611 HIS A 628 GLN A 924 GLN A1063 GLN A1106 GLN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 12962 Z= 0.178 Angle : 0.669 17.642 17547 Z= 0.340 Chirality : 0.043 0.302 2008 Planarity : 0.005 0.098 2218 Dihedral : 6.357 58.722 1797 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.26 % Favored : 95.61 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.50 (0.20), residues: 1618 helix: 0.01 (0.18), residues: 743 sheet: -0.88 (0.30), residues: 271 loop : -2.27 (0.23), residues: 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 193 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 195 average time/residue: 0.2336 time to fit residues: 69.2654 Evaluate side-chains 121 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.516 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1437 time to fit residues: 2.3455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 40 optimal weight: 0.1980 chunk 147 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS A 628 GLN ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN B 195 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 12962 Z= 0.168 Angle : 0.622 18.019 17547 Z= 0.316 Chirality : 0.042 0.167 2008 Planarity : 0.005 0.096 2218 Dihedral : 5.913 58.652 1797 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.68 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % 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: -0.84 (0.20), residues: 1618 helix: 0.57 (0.19), residues: 747 sheet: -0.51 (0.30), residues: 276 loop : -2.01 (0.23), residues: 595 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 191 average time/residue: 0.2205 time to fit residues: 63.7872 Evaluate side-chains 133 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.415 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1305 time to fit residues: 2.2965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.0270 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 143 ASN B 144 ASN B 195 HIS C 114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 12962 Z= 0.153 Angle : 0.610 17.903 17547 Z= 0.304 Chirality : 0.042 0.159 2008 Planarity : 0.004 0.086 2218 Dihedral : 5.690 55.794 1797 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.08 % Favored : 95.86 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % 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: -0.45 (0.21), residues: 1618 helix: 0.86 (0.19), residues: 745 sheet: -0.19 (0.31), residues: 267 loop : -1.82 (0.24), residues: 606 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 188 average time/residue: 0.2265 time to fit residues: 64.9759 Evaluate side-chains 137 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1239 time to fit residues: 2.6196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.7980 chunk 88 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 133 optimal weight: 0.0870 chunk 108 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 79 optimal weight: 0.0270 chunk 140 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 12962 Z= 0.140 Angle : 0.586 18.357 17547 Z= 0.294 Chirality : 0.041 0.196 2008 Planarity : 0.004 0.082 2218 Dihedral : 5.506 53.420 1797 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.14 % Favored : 95.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % 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: -0.15 (0.21), residues: 1618 helix: 1.08 (0.19), residues: 745 sheet: 0.02 (0.31), residues: 272 loop : -1.67 (0.24), residues: 601 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2413 time to fit residues: 70.7632 Evaluate side-chains 131 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12962 Z= 0.184 Angle : 0.623 18.237 17547 Z= 0.315 Chirality : 0.042 0.177 2008 Planarity : 0.004 0.088 2218 Dihedral : 5.498 49.087 1797 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.51 % Favored : 95.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % 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 (0.21), residues: 1618 helix: 1.10 (0.19), residues: 745 sheet: 0.02 (0.31), residues: 273 loop : -1.65 (0.24), residues: 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2223 time to fit residues: 66.3344 Evaluate side-chains 130 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.450 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 156 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12962 Z= 0.211 Angle : 0.641 18.766 17547 Z= 0.326 Chirality : 0.044 0.180 2008 Planarity : 0.004 0.092 2218 Dihedral : 5.545 48.263 1797 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % 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: -0.22 (0.21), residues: 1618 helix: 1.00 (0.19), residues: 747 sheet: 0.09 (0.31), residues: 272 loop : -1.75 (0.24), residues: 599 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2243 time to fit residues: 63.4732 Evaluate side-chains 130 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.502 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 12962 Z= 0.172 Angle : 0.623 19.316 17547 Z= 0.312 Chirality : 0.043 0.176 2008 Planarity : 0.005 0.086 2218 Dihedral : 5.454 49.504 1797 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % 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: -0.05 (0.21), residues: 1618 helix: 1.16 (0.19), residues: 747 sheet: 0.10 (0.31), residues: 287 loop : -1.68 (0.24), residues: 584 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2204 time to fit residues: 59.8064 Evaluate side-chains 124 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.555 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 0.0980 chunk 114 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN A1063 GLN A1155 GLN B 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 12962 Z= 0.157 Angle : 0.611 19.695 17547 Z= 0.306 Chirality : 0.042 0.171 2008 Planarity : 0.004 0.081 2218 Dihedral : 5.390 50.833 1797 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % 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: 0.15 (0.21), residues: 1618 helix: 1.30 (0.19), residues: 739 sheet: 0.24 (0.31), residues: 286 loop : -1.52 (0.24), residues: 593 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2187 time to fit residues: 58.6591 Evaluate side-chains 129 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.466 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 106 optimal weight: 0.0070 chunk 161 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 99 optimal weight: 0.0980 chunk 78 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 12962 Z= 0.151 Angle : 0.617 19.445 17547 Z= 0.307 Chirality : 0.042 0.200 2008 Planarity : 0.004 0.084 2218 Dihedral : 5.350 52.468 1797 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.20 % Favored : 95.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % 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: 0.24 (0.21), residues: 1618 helix: 1.37 (0.19), residues: 738 sheet: 0.35 (0.31), residues: 286 loop : -1.49 (0.24), residues: 594 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2234 time to fit residues: 62.5256 Evaluate side-chains 134 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.594 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 128 optimal weight: 0.0470 chunk 53 optimal weight: 0.2980 chunk 132 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.170058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156597 restraints weight = 19469.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.154707 restraints weight = 30715.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155021 restraints weight = 29897.223| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.092 12962 Z= 0.502 Angle : 0.764 43.480 17547 Z= 0.416 Chirality : 0.042 0.179 2008 Planarity : 0.006 0.155 2218 Dihedral : 5.297 56.458 1797 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.14 % Favored : 95.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.32 % 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: 0.34 (0.21), residues: 1618 helix: 1.44 (0.19), residues: 742 sheet: 0.38 (0.31), residues: 286 loop : -1.44 (0.25), residues: 590 =============================================================================== Job complete usr+sys time: 2394.86 seconds wall clock time: 45 minutes 6.88 seconds (2706.88 seconds total)