Starting phenix.real_space_refine on Thu Feb 15 15:43:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn4_4282/02_2024/6fn4_4282_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn4_4282/02_2024/6fn4_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_4282/02_2024/6fn4_4282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn4_4282/02_2024/6fn4_4282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn4_4282/02_2024/6fn4_4282_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fn4_4282/02_2024/6fn4_4282_updated.pdb" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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-5238/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: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 207} Chain: "C" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1717 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'3PE': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.52, per 1000 atoms: 0.59 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: 5.08 Conformation dependent library (CDL) restraints added in 2.4 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: 3.47 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: 4.80 Time building geometry restraints manager: 5.50 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 1.346 1.491 -0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" C7 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.346 1.470 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C7 NAG A1302 " pdb=" N2 NAG A1302 " ideal model delta sigma weight residual 1.346 1.469 -0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.521 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.521 -0.115 2.00e-02 2.50e+03 3.31e+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=" 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=" C ASP A 375 " pdb=" N SER A 376 " pdb=" CA SER A 376 " ideal model delta sigma weight residual 121.70 133.19 -11.49 1.80e+00 3.09e-01 4.07e+01 angle pdb=" C SER A 237 " pdb=" N PHE A 238 " pdb=" CA PHE A 238 " ideal model delta sigma weight residual 121.70 131.52 -9.82 1.80e+00 3.09e-01 2.98e+01 angle pdb=" C VAL A 33 " pdb=" N SER A 34 " pdb=" CA SER A 34 " ideal model delta sigma weight residual 121.70 129.70 -8.00 1.80e+00 3.09e-01 1.98e+01 angle pdb=" C3 NAG A1302 " pdb=" C2 NAG A1302 " pdb=" N2 NAG A1302 " ideal model delta sigma weight residual 110.74 98.23 12.51 3.00e+00 1.11e-01 1.74e+01 ... (remaining 17542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 7365 16.25 - 32.50: 318 32.50 - 48.75: 69 48.75 - 65.00: 7 65.00 - 81.25: 7 Dihedral angle restraints: 7766 sinusoidal: 3089 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 7763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1362 0.041 - 0.083: 476 0.083 - 0.124: 142 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 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.600 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 38.820 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 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 0.145 12962 Z= 0.334 Angle : 0.808 22.520 17547 Z= 0.423 Chirality : 0.046 0.207 2008 Planarity : 0.006 0.113 2218 Dihedral : 10.230 81.253 4750 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 % Allowed : 2.64 % Favored : 97.36 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 112 HIS 0.009 0.001 HIS B 98 PHE 0.027 0.002 PHE B 92 TYR 0.025 0.002 TYR C 33 ARG 0.010 0.001 ARG A1191 *********************** 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 : 1.756 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.8666 (mmt) cc_final: 0.8079 (mmt) REVERT: A 104 MET cc_start: 0.7078 (tmm) cc_final: 0.6833 (tmm) REVERT: A 742 ASP cc_start: 0.8908 (p0) cc_final: 0.8561 (p0) REVERT: A 802 TRP cc_start: 0.8825 (t60) cc_final: 0.8243 (t60) REVERT: A 947 MET cc_start: 0.7873 (tpp) cc_final: 0.7620 (tpp) REVERT: B 1 GLN cc_start: 0.8217 (mp10) cc_final: 0.7991 (mp10) REVERT: B 27 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8062 (tt0) REVERT: B 84 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8005 (mt-10) REVERT: B 140 CYS cc_start: 0.6700 (m) cc_final: 0.6266 (m) REVERT: B 154 TRP cc_start: 0.7618 (m100) cc_final: 0.7354 (m100) REVERT: B 201 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6762 (mt-10) REVERT: C 197 TRP cc_start: 0.7632 (t60) cc_final: 0.7349 (t60) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.3046 time to fit residues: 103.1177 Evaluate side-chains 126 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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: 7.9990 chunk 122 optimal weight: 0.0870 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 126 optimal weight: 0.6980 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: 0.5158 ------------------------------------------------------------------------------- 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** ** A1237 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: 0.7258 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12962 Z= 0.175 Angle : 0.642 11.086 17547 Z= 0.334 Chirality : 0.043 0.198 2008 Planarity : 0.005 0.085 2218 Dihedral : 7.006 63.778 1854 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.77 % Favored : 96.11 % Rotamer: Outliers : 0.15 % Allowed : 3.95 % Favored : 95.90 % 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: -1.44 (0.20), residues: 1618 helix: 0.06 (0.18), residues: 741 sheet: -0.85 (0.30), residues: 277 loop : -2.24 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 112 HIS 0.007 0.001 HIS B 98 PHE 0.025 0.002 PHE A 758 TYR 0.024 0.002 TYR A 489 ARG 0.013 0.001 ARG A1187 *********************** 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 199 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8769 (mmt) cc_final: 0.8202 (mmt) REVERT: A 104 MET cc_start: 0.7111 (tmm) cc_final: 0.6769 (tmm) REVERT: A 203 PHE cc_start: 0.7848 (t80) cc_final: 0.7347 (t80) REVERT: A 234 ILE cc_start: 0.7074 (mt) cc_final: 0.6788 (mt) REVERT: A 449 MET cc_start: 0.6554 (ptm) cc_final: 0.6280 (ptt) REVERT: A 500 GLU cc_start: 0.6244 (mt-10) cc_final: 0.6032 (tt0) REVERT: A 742 ASP cc_start: 0.8639 (p0) cc_final: 0.8370 (p0) REVERT: A 802 TRP cc_start: 0.8796 (t60) cc_final: 0.8310 (t60) REVERT: A 1083 GLU cc_start: 0.8263 (mp0) cc_final: 0.7694 (mp0) REVERT: B 1 GLN cc_start: 0.8221 (mp10) cc_final: 0.8013 (mp10) REVERT: B 27 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7778 (tt0) REVERT: B 140 CYS cc_start: 0.7109 (m) cc_final: 0.6674 (m) REVERT: B 201 GLU cc_start: 0.6659 (mt-10) cc_final: 0.6405 (mt-10) REVERT: C 85 SER cc_start: 0.8655 (m) cc_final: 0.8328 (t) outliers start: 2 outliers final: 0 residues processed: 199 average time/residue: 0.2410 time to fit residues: 72.5444 Evaluate side-chains 133 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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: 2.9990 chunk 45 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 GLN 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 6 GLN B 144 ASN B 162 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12962 Z= 0.200 Angle : 0.626 11.013 17547 Z= 0.329 Chirality : 0.043 0.160 2008 Planarity : 0.005 0.083 2218 Dihedral : 6.455 55.139 1854 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.19 % Rotamer: Outliers : 0.15 % Allowed : 3.88 % Favored : 95.97 % 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: -0.88 (0.20), residues: 1618 helix: 0.54 (0.19), residues: 746 sheet: -0.63 (0.30), residues: 280 loop : -1.98 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 154 HIS 0.007 0.001 HIS B 98 PHE 0.022 0.002 PHE B 92 TYR 0.017 0.002 TYR C 33 ARG 0.008 0.001 ARG A1221 *********************** 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 188 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7115 (tmm) cc_final: 0.6516 (tmm) REVERT: A 166 ASP cc_start: 0.7247 (t0) cc_final: 0.6960 (t0) REVERT: A 203 PHE cc_start: 0.7469 (t80) cc_final: 0.7213 (t80) REVERT: A 485 GLU cc_start: 0.6720 (mp0) cc_final: 0.6465 (mm-30) REVERT: A 489 TYR cc_start: 0.8178 (m-10) cc_final: 0.7874 (m-10) REVERT: A 586 HIS cc_start: 0.6928 (t70) cc_final: 0.6592 (t70) REVERT: A 802 TRP cc_start: 0.8893 (t60) cc_final: 0.8262 (t60) REVERT: A 947 MET cc_start: 0.7980 (tmm) cc_final: 0.7500 (tpp) REVERT: B 27 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7889 (tt0) REVERT: B 140 CYS cc_start: 0.6961 (m) cc_final: 0.6154 (m) REVERT: B 154 TRP cc_start: 0.8299 (m100) cc_final: 0.7188 (m100) REVERT: B 201 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6637 (mt-10) REVERT: C 78 THR cc_start: 0.9207 (m) cc_final: 0.8896 (p) REVERT: C 85 SER cc_start: 0.8526 (m) cc_final: 0.8221 (t) outliers start: 2 outliers final: 1 residues processed: 188 average time/residue: 0.2254 time to fit residues: 63.6370 Evaluate side-chains 135 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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: 0.5980 chunk 110 optimal weight: 7.9990 chunk 76 optimal weight: 0.0270 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 98 optimal weight: 0.4980 chunk 147 optimal weight: 0.5980 chunk 156 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 42 optimal weight: 0.0770 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 143 ASN B 195 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12962 Z= 0.144 Angle : 0.580 11.091 17547 Z= 0.300 Chirality : 0.041 0.183 2008 Planarity : 0.004 0.080 2218 Dihedral : 6.105 53.468 1854 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -0.38 (0.21), residues: 1618 helix: 0.92 (0.19), residues: 745 sheet: -0.17 (0.31), residues: 273 loop : -1.79 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 154 HIS 0.015 0.001 HIS B 98 PHE 0.023 0.001 PHE A 758 TYR 0.017 0.001 TYR A 952 ARG 0.005 0.000 ARG A 911 *********************** 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 193 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7498 (m) cc_final: 0.7067 (t) REVERT: A 104 MET cc_start: 0.7028 (tmm) cc_final: 0.6487 (tmm) REVERT: A 166 ASP cc_start: 0.7387 (t0) cc_final: 0.7087 (t0) REVERT: A 203 PHE cc_start: 0.7544 (t80) cc_final: 0.6893 (t80) REVERT: A 311 LEU cc_start: 0.4701 (mp) cc_final: 0.4394 (tt) REVERT: A 403 ARG cc_start: 0.4487 (mpp80) cc_final: 0.3758 (ttp80) REVERT: A 581 THR cc_start: 0.4441 (t) cc_final: 0.4097 (t) REVERT: A 769 PHE cc_start: 0.7391 (t80) cc_final: 0.6633 (t80) REVERT: A 939 ILE cc_start: 0.8600 (tp) cc_final: 0.8130 (tp) REVERT: A 947 MET cc_start: 0.8158 (tmm) cc_final: 0.7485 (tpp) REVERT: A 1083 GLU cc_start: 0.8116 (mp0) cc_final: 0.7496 (pm20) REVERT: B 140 CYS cc_start: 0.6918 (m) cc_final: 0.6137 (m) REVERT: B 154 TRP cc_start: 0.8142 (m100) cc_final: 0.6981 (m100) REVERT: B 201 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6641 (mt-10) REVERT: C 60 TYR cc_start: 0.8447 (m-80) cc_final: 0.8159 (m-80) REVERT: C 85 SER cc_start: 0.8418 (m) cc_final: 0.8089 (t) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2393 time to fit residues: 68.4893 Evaluate side-chains 131 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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: 7.9990 chunk 88 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 108 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 79 optimal weight: 0.0030 chunk 140 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3886 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= 0.161 Angle : 0.577 10.782 17547 Z= 0.302 Chirality : 0.042 0.175 2008 Planarity : 0.004 0.074 2218 Dihedral : 5.939 52.849 1854 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.64 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: 1.07 (0.19), residues: 746 sheet: 0.04 (0.32), residues: 273 loop : -1.67 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 154 HIS 0.007 0.001 HIS B 98 PHE 0.021 0.001 PHE A 758 TYR 0.017 0.001 TYR A 952 ARG 0.004 0.000 ARG A1221 *********************** 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 188 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7054 (tmm) cc_final: 0.6493 (tmm) REVERT: A 166 ASP cc_start: 0.7312 (t0) cc_final: 0.6951 (t0) REVERT: A 439 MET cc_start: 0.8937 (tpt) cc_final: 0.8506 (tpp) REVERT: A 802 TRP cc_start: 0.8838 (t60) cc_final: 0.8188 (t60) REVERT: A 939 ILE cc_start: 0.8655 (tp) cc_final: 0.8223 (tp) REVERT: A 947 MET cc_start: 0.7812 (tmm) cc_final: 0.7077 (tpp) REVERT: A 1083 GLU cc_start: 0.8469 (mp0) cc_final: 0.7850 (pm20) REVERT: B 140 CYS cc_start: 0.7153 (m) cc_final: 0.6755 (m) REVERT: B 154 TRP cc_start: 0.8182 (m100) cc_final: 0.6923 (m100) REVERT: B 201 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6674 (mt-10) REVERT: C 78 THR cc_start: 0.9205 (m) cc_final: 0.8944 (p) REVERT: C 85 SER cc_start: 0.8448 (m) cc_final: 0.8086 (t) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2305 time to fit residues: 65.4971 Evaluate side-chains 141 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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: 7.9990 chunk 141 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 156 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 51 optimal weight: 0.0670 chunk 82 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 130 GLN B 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12962 Z= 0.145 Angle : 0.569 11.007 17547 Z= 0.296 Chirality : 0.042 0.193 2008 Planarity : 0.004 0.066 2218 Dihedral : 5.811 50.952 1854 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.08 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 0.04 (0.21), residues: 1618 helix: 1.26 (0.19), residues: 742 sheet: 0.21 (0.32), residues: 273 loop : -1.65 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 112 HIS 0.003 0.001 HIS A 586 PHE 0.025 0.001 PHE A 203 TYR 0.018 0.001 TYR A 952 ARG 0.003 0.000 ARG A 542 *********************** 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 189 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7554 (m) cc_final: 0.7104 (t) REVERT: A 104 MET cc_start: 0.6854 (tmm) cc_final: 0.6318 (tmm) REVERT: A 166 ASP cc_start: 0.7228 (t0) cc_final: 0.6864 (t0) REVERT: A 439 MET cc_start: 0.8979 (tpt) cc_final: 0.8578 (tpp) REVERT: A 449 MET cc_start: 0.7389 (ptt) cc_final: 0.7118 (ptt) REVERT: A 769 PHE cc_start: 0.7288 (t80) cc_final: 0.6811 (t80) REVERT: A 939 ILE cc_start: 0.8603 (tp) cc_final: 0.8134 (tp) REVERT: A 947 MET cc_start: 0.7780 (tmm) cc_final: 0.7029 (tpp) REVERT: B 86 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8689 (tm-30) REVERT: B 140 CYS cc_start: 0.7163 (m) cc_final: 0.6358 (m) REVERT: B 154 TRP cc_start: 0.8127 (m100) cc_final: 0.6927 (m100) REVERT: C 85 SER cc_start: 0.8465 (m) cc_final: 0.8118 (t) REVERT: C 205 ASN cc_start: 0.6963 (m110) cc_final: 0.6682 (t0) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2320 time to fit residues: 66.0324 Evaluate side-chains 135 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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: 2.9990 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN B 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12962 Z= 0.250 Angle : 0.664 11.034 17547 Z= 0.349 Chirality : 0.045 0.187 2008 Planarity : 0.005 0.090 2218 Dihedral : 6.058 50.246 1854 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: -0.26 (0.21), residues: 1618 helix: 0.94 (0.19), residues: 746 sheet: 0.11 (0.31), residues: 285 loop : -1.77 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 112 HIS 0.005 0.001 HIS A 586 PHE 0.029 0.002 PHE B 92 TYR 0.039 0.002 TYR A 306 ARG 0.004 0.000 ARG A 537 *********************** 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 187 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7541 (m) cc_final: 0.7140 (t) REVERT: A 74 MET cc_start: 0.8172 (tmm) cc_final: 0.7654 (tmm) REVERT: A 104 MET cc_start: 0.7011 (tmm) cc_final: 0.6464 (tmm) REVERT: A 166 ASP cc_start: 0.7369 (t0) cc_final: 0.7117 (t0) REVERT: A 434 THR cc_start: 0.7787 (m) cc_final: 0.7343 (t) REVERT: A 439 MET cc_start: 0.9260 (tpt) cc_final: 0.8968 (tpp) REVERT: A 449 MET cc_start: 0.7799 (ptt) cc_final: 0.7463 (ptt) REVERT: A 450 VAL cc_start: 0.8080 (t) cc_final: 0.7630 (m) REVERT: A 939 ILE cc_start: 0.8678 (tp) cc_final: 0.8227 (tp) REVERT: A 947 MET cc_start: 0.7507 (tmm) cc_final: 0.6899 (tpp) REVERT: A 1083 GLU cc_start: 0.8701 (mp0) cc_final: 0.8101 (pm20) REVERT: B 86 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8808 (tm-30) REVERT: B 140 CYS cc_start: 0.7150 (m) cc_final: 0.6792 (m) REVERT: B 154 TRP cc_start: 0.8208 (m100) cc_final: 0.7042 (m100) REVERT: C 85 SER cc_start: 0.8548 (m) cc_final: 0.8202 (t) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2423 time to fit residues: 67.8800 Evaluate side-chains 128 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.532 ------------------------------------------------------------------------------- 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: 3.9990 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12962 Z= 0.215 Angle : 0.633 11.142 17547 Z= 0.332 Chirality : 0.044 0.197 2008 Planarity : 0.004 0.082 2218 Dihedral : 6.041 48.120 1854 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -0.17 (0.21), residues: 1618 helix: 0.97 (0.19), residues: 739 sheet: 0.17 (0.31), residues: 283 loop : -1.63 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 102 HIS 0.004 0.001 HIS C 35 PHE 0.024 0.002 PHE B 92 TYR 0.016 0.001 TYR A 952 ARG 0.003 0.000 ARG A 542 *********************** 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 173 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.433 Fit side-chains revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7672 (m) cc_final: 0.7206 (t) REVERT: A 104 MET cc_start: 0.7091 (tmm) cc_final: 0.6565 (tmm) REVERT: A 166 ASP cc_start: 0.7187 (t0) cc_final: 0.6901 (t0) REVERT: A 434 THR cc_start: 0.7830 (m) cc_final: 0.7394 (t) REVERT: A 439 MET cc_start: 0.9341 (tpt) cc_final: 0.8896 (tpp) REVERT: A 939 ILE cc_start: 0.8661 (tp) cc_final: 0.8179 (tp) REVERT: A 947 MET cc_start: 0.7487 (tmm) cc_final: 0.6893 (tpp) REVERT: A 1083 GLU cc_start: 0.8668 (mp0) cc_final: 0.8052 (pm20) REVERT: B 86 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8791 (tm-30) REVERT: B 140 CYS cc_start: 0.7086 (m) cc_final: 0.6532 (m) REVERT: B 154 TRP cc_start: 0.8158 (m100) cc_final: 0.7040 (m100) REVERT: C 78 THR cc_start: 0.9220 (m) cc_final: 0.8994 (p) REVERT: C 85 SER cc_start: 0.8591 (m) cc_final: 0.8242 (t) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2194 time to fit residues: 58.0157 Evaluate side-chains 134 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.477 ------------------------------------------------------------------------------- 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: 1.9990 chunk 136 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN B 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12962 Z= 0.179 Angle : 0.606 10.555 17547 Z= 0.315 Chirality : 0.043 0.186 2008 Planarity : 0.004 0.087 2218 Dihedral : 5.912 48.295 1854 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -0.01 (0.21), residues: 1618 helix: 1.11 (0.19), residues: 738 sheet: 0.24 (0.31), residues: 283 loop : -1.55 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 707 HIS 0.004 0.001 HIS A 586 PHE 0.020 0.001 PHE B 92 TYR 0.023 0.001 TYR A 952 ARG 0.006 0.000 ARG A1232 *********************** 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 172 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7450 (m) cc_final: 0.7049 (t) REVERT: A 104 MET cc_start: 0.7036 (tmm) cc_final: 0.6509 (tmm) REVERT: A 166 ASP cc_start: 0.7310 (t0) cc_final: 0.7090 (t0) REVERT: A 434 THR cc_start: 0.7835 (m) cc_final: 0.7445 (t) REVERT: A 439 MET cc_start: 0.9288 (tpt) cc_final: 0.8890 (tpp) REVERT: A 450 VAL cc_start: 0.8314 (t) cc_final: 0.7920 (m) REVERT: A 482 THR cc_start: 0.4924 (p) cc_final: 0.4425 (p) REVERT: A 485 GLU cc_start: 0.7326 (mp0) cc_final: 0.6778 (mm-30) REVERT: A 513 MET cc_start: 0.4032 (tmm) cc_final: 0.3809 (tmm) REVERT: A 939 ILE cc_start: 0.8698 (tp) cc_final: 0.8246 (tp) REVERT: A 947 MET cc_start: 0.7436 (tmm) cc_final: 0.6822 (tpp) REVERT: A 1083 GLU cc_start: 0.8629 (mp0) cc_final: 0.8055 (pm20) REVERT: B 86 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8790 (tm-30) REVERT: B 140 CYS cc_start: 0.7078 (m) cc_final: 0.6349 (m) REVERT: B 154 TRP cc_start: 0.8022 (m100) cc_final: 0.6812 (m100) REVERT: C 78 THR cc_start: 0.9214 (m) cc_final: 0.9009 (p) REVERT: C 85 SER cc_start: 0.8644 (m) cc_final: 0.8244 (t) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2201 time to fit residues: 58.3487 Evaluate side-chains 134 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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: 0.7980 chunk 93 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12962 Z= 0.165 Angle : 0.595 10.996 17547 Z= 0.309 Chirality : 0.042 0.187 2008 Planarity : 0.004 0.085 2218 Dihedral : 5.844 49.140 1854 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.57 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 0.08 (0.21), residues: 1618 helix: 1.18 (0.19), residues: 744 sheet: 0.24 (0.31), residues: 286 loop : -1.50 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 154 HIS 0.004 0.001 HIS A 586 PHE 0.020 0.001 PHE B 92 TYR 0.020 0.001 TYR A 927 ARG 0.002 0.000 ARG A1232 ********************** 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 175 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7515 (m) cc_final: 0.7176 (t) REVERT: A 104 MET cc_start: 0.6912 (tmm) cc_final: 0.6341 (tmm) REVERT: A 166 ASP cc_start: 0.7238 (t0) cc_final: 0.7021 (t0) REVERT: A 434 THR cc_start: 0.7921 (m) cc_final: 0.7523 (t) REVERT: A 439 MET cc_start: 0.9309 (tpt) cc_final: 0.8946 (tpp) REVERT: A 450 VAL cc_start: 0.8458 (t) cc_final: 0.8198 (m) REVERT: A 482 THR cc_start: 0.4877 (p) cc_final: 0.4463 (p) REVERT: A 485 GLU cc_start: 0.7417 (mp0) cc_final: 0.6870 (mm-30) REVERT: A 513 MET cc_start: 0.4213 (tmm) cc_final: 0.3953 (tmm) REVERT: A 518 GLN cc_start: 0.7227 (mt0) cc_final: 0.6374 (mp10) REVERT: A 939 ILE cc_start: 0.8664 (tp) cc_final: 0.8178 (tp) REVERT: A 947 MET cc_start: 0.7496 (tmm) cc_final: 0.6899 (tpp) REVERT: A 1083 GLU cc_start: 0.8573 (mp0) cc_final: 0.7981 (pm20) REVERT: A 1128 GLU cc_start: 0.6362 (mm-30) cc_final: 0.5848 (tm-30) REVERT: B 86 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8777 (tm-30) REVERT: C 78 THR cc_start: 0.9215 (m) cc_final: 0.9013 (p) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2225 time to fit residues: 59.8082 Evaluate side-chains 141 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.481 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 6.9990 chunk 118 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.0270 chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 0.0030 chunk 132 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 overall best weight: 0.3848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN A1155 GLN B 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.176392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.160672 restraints weight = 21033.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.157820 restraints weight = 36280.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.158574 restraints weight = 36469.839| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.5697 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= 0.142 Angle : 0.586 10.238 17547 Z= 0.300 Chirality : 0.042 0.169 2008 Planarity : 0.004 0.081 2218 Dihedral : 5.720 50.564 1854 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: 1.34 (0.19), residues: 740 sheet: 0.31 (0.31), residues: 289 loop : -1.47 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 154 HIS 0.004 0.000 HIS A 586 PHE 0.018 0.001 PHE B 92 TYR 0.021 0.001 TYR A 927 ARG 0.007 0.000 ARG A1191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2546.52 seconds wall clock time: 47 minutes 18.91 seconds (2838.91 seconds total)