Starting phenix.real_space_refine on Sat Feb 17 15:00:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7m_20266/02_2024/6p7m_20266.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7m_20266/02_2024/6p7m_20266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7m_20266/02_2024/6p7m_20266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7m_20266/02_2024/6p7m_20266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7m_20266/02_2024/6p7m_20266.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7m_20266/02_2024/6p7m_20266.pdb" } resolution = 3.0 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= 0.001 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8946 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 25 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 6417 2.51 5 N 1673 2.21 5 O 1996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A ASP 64": "OD1" <-> "OD2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A ASP 297": "OD1" <-> "OD2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A ASP 450": "OD1" <-> "OD2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 495": "OD1" <-> "OD2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A ASP 691": "OD1" <-> "OD2" Residue "A TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A ARG 737": "NH1" <-> "NH2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A ASP 824": "OD1" <-> "OD2" Residue "A ASP 832": "OD1" <-> "OD2" Residue "A TYR 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 867": "NH1" <-> "NH2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A ARG 1054": "NH1" <-> "NH2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "A PHE 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C GLU 219": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10141 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8796 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 1048} Chain breaks: 7 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 533 Classifications: {'DNA': 1, 'RNA': 25} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 9, 'rna3p': 16} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.21, per 1000 atoms: 0.61 Number of scatterers: 10141 At special positions: 0 Unit cell: (100.8, 114.3, 122.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 25 15.00 Mg 2 11.99 O 1996 8.00 N 1673 7.00 C 6417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 1.8 seconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2234 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 48.2% alpha, 12.6% beta 6 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 26 through 33 Processing helix chain 'A' and resid 38 through 66 removed outlier: 4.573A pdb=" N LYS A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.616A pdb=" N ARG A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 114 through 120 removed outlier: 4.209A pdb=" N PHE A 119 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.544A pdb=" N LEU A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.904A pdb=" N LEU A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 151 through 159 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.598A pdb=" N GLU A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 Processing helix chain 'A' and resid 201 through 211 removed outlier: 4.451A pdb=" N ILE A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 312 through 327 Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.648A pdb=" N SER A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.966A pdb=" N ILE A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 409 through 431 Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.479A pdb=" N ASP A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 718 through 728 removed outlier: 4.077A pdb=" N PHE A 728 " --> pdb=" O PHE A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 791 removed outlier: 4.101A pdb=" N GLU A 791 " --> pdb=" O ARG A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 822 Processing helix chain 'A' and resid 872 through 886 Processing helix chain 'A' and resid 890 through 919 removed outlier: 4.005A pdb=" N HIS A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 917 " --> pdb=" O GLU A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 955 Processing helix chain 'A' and resid 969 through 973 removed outlier: 4.296A pdb=" N GLY A 973 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1030 Processing helix chain 'A' and resid 1048 through 1052 Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1111 through 1116 Processing helix chain 'A' and resid 1120 through 1135 removed outlier: 4.255A pdb=" N TYR A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER A1125 " --> pdb=" O LYS A1121 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A1135 " --> pdb=" O MET A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1167 Processing helix chain 'A' and resid 1178 through 1201 removed outlier: 3.793A pdb=" N VAL A1191 " --> pdb=" O ILE A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1209 Processing helix chain 'A' and resid 1214 through 1225 Processing helix chain 'C' and resid 137 through 148 Processing helix chain 'C' and resid 151 through 155 removed outlier: 3.533A pdb=" N ARG C 155 " --> pdb=" O TYR C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 229 through 233 Processing sheet with id=AA1, first strand: chain 'A' and resid 545 through 549 removed outlier: 4.794A pdb=" N TYR A 553 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR A 794 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 545 through 549 removed outlier: 4.794A pdb=" N TYR A 553 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR A 794 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA4, first strand: chain 'A' and resid 783 through 784 removed outlier: 3.764A pdb=" N GLU C 184 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 783 through 784 removed outlier: 4.158A pdb=" N ASN C 157 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG C 222 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 765 through 766 Processing sheet with id=AA7, first strand: chain 'A' and resid 850 through 855 removed outlier: 6.410A pdb=" N VAL A 843 " --> pdb=" O VAL A 851 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN A 853 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE A 841 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU A 925 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 922 " --> pdb=" O PHE A 994 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE A 996 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU A 924 " --> pdb=" O ILE A 996 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 858 through 863 Processing sheet with id=AA9, first strand: chain 'A' and resid 1033 through 1037 removed outlier: 3.509A pdb=" N LEU A1065 " --> pdb=" O PHE A1045 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1070 through 1073 455 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2510 1.33 - 1.45: 2118 1.45 - 1.57: 5668 1.57 - 1.69: 50 1.69 - 1.81: 47 Bond restraints: 10393 Sorted by residual: bond pdb=" CB VAL A 921 " pdb=" CG1 VAL A 921 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CB ILE A 802 " pdb=" CG2 ILE A 802 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 bond pdb=" C VAL A 921 " pdb=" N ILE A 922 " ideal model delta sigma weight residual 1.332 1.311 0.021 1.73e-02 3.34e+03 1.45e+00 bond pdb=" C ILE A 829 " pdb=" N GLY A 830 " ideal model delta sigma weight residual 1.332 1.324 0.008 6.60e-03 2.30e+04 1.36e+00 bond pdb=" CB VAL A 757 " pdb=" CG2 VAL A 757 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.25e+00 ... (remaining 10388 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.93: 251 105.93 - 112.96: 5506 112.96 - 120.00: 3788 120.00 - 127.03: 4435 127.03 - 134.06: 123 Bond angle restraints: 14103 Sorted by residual: angle pdb=" C SER A 987 " pdb=" N THR A 988 " pdb=" CA THR A 988 " ideal model delta sigma weight residual 121.54 128.40 -6.86 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C2' C B 9 " pdb=" C1' C B 9 " pdb=" N1 C B 9 " ideal model delta sigma weight residual 112.00 115.88 -3.88 1.50e+00 4.44e-01 6.68e+00 angle pdb=" C LEU A 497 " pdb=" N LEU A 498 " pdb=" CA LEU A 498 " ideal model delta sigma weight residual 122.31 117.20 5.11 2.00e+00 2.50e-01 6.53e+00 angle pdb=" N THR A 988 " pdb=" CA THR A 988 " pdb=" C THR A 988 " ideal model delta sigma weight residual 110.80 115.87 -5.07 2.13e+00 2.20e-01 5.67e+00 angle pdb=" C GLU A 354 " pdb=" N TRP A 355 " pdb=" CA TRP A 355 " ideal model delta sigma weight residual 121.19 124.96 -3.77 1.59e+00 3.96e-01 5.61e+00 ... (remaining 14098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.22: 6104 31.22 - 62.44: 182 62.44 - 93.66: 19 93.66 - 124.89: 0 124.89 - 156.11: 1 Dihedral angle restraints: 6306 sinusoidal: 2845 harmonic: 3461 Sorted by residual: dihedral pdb=" O4' U B 14 " pdb=" C1' U B 14 " pdb=" N1 U B 14 " pdb=" C2 U B 14 " ideal model delta sinusoidal sigma weight residual 232.00 75.89 156.11 1 1.70e+01 3.46e-03 6.36e+01 dihedral pdb=" CA ALA A 195 " pdb=" C ALA A 195 " pdb=" N ILE A 196 " pdb=" CA ILE A 196 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLN A1170 " pdb=" C GLN A1170 " pdb=" N GLU A1171 " pdb=" CA GLU A1171 " ideal model delta harmonic sigma weight residual 180.00 158.16 21.84 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 6303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1015 0.041 - 0.082: 408 0.082 - 0.122: 97 0.122 - 0.163: 20 0.163 - 0.204: 1 Chirality restraints: 1541 Sorted by residual: chirality pdb=" C1' C B 9 " pdb=" O4' C B 9 " pdb=" C2' C B 9 " pdb=" N1 C B 9 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C1' U B 4 " pdb=" O4' U B 4 " pdb=" C2' U B 4 " pdb=" N1 U B 4 " both_signs ideal model delta sigma weight residual False 2.47 2.32 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA GLU A 257 " pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CB GLU A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 1538 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 9 " -0.023 2.00e-02 2.50e+03 1.34e-02 4.03e+00 pdb=" N1 C B 9 " 0.032 2.00e-02 2.50e+03 pdb=" C2 C B 9 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C B 9 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C B 9 " -0.000 2.00e-02 2.50e+03 pdb=" C4 C B 9 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C B 9 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C B 9 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C B 9 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 128 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 129 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 5 " -0.019 2.00e-02 2.50e+03 9.93e-03 2.22e+00 pdb=" N1 U B 5 " 0.021 2.00e-02 2.50e+03 pdb=" C2 U B 5 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U B 5 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U B 5 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U B 5 " -0.002 2.00e-02 2.50e+03 pdb=" O4 U B 5 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U B 5 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U B 5 " 0.004 2.00e-02 2.50e+03 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 116 2.61 - 3.19: 9062 3.19 - 3.76: 15101 3.76 - 4.33: 22524 4.33 - 4.90: 36716 Nonbonded interactions: 83519 Sorted by model distance: nonbonded pdb=" OP2 A B 17 " pdb="MG MG B 101 " model vdw 2.043 2.170 nonbonded pdb=" OD1 ASP A 367 " pdb=" OH TYR A 381 " model vdw 2.105 2.440 nonbonded pdb=" O TYR A1049 " pdb=" OG1 THR A1055 " model vdw 2.138 2.440 nonbonded pdb=" NZ LYS A 206 " pdb=" O LYS A 253 " model vdw 2.162 2.520 nonbonded pdb=" OD1 ASP A 297 " pdb=" OH TYR A 510 " model vdw 2.181 2.440 ... (remaining 83514 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 8.640 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 33.230 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10393 Z= 0.379 Angle : 0.627 7.037 14103 Z= 0.349 Chirality : 0.045 0.204 1541 Planarity : 0.003 0.041 1709 Dihedral : 14.905 156.108 4072 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.21), residues: 1150 helix: -1.49 (0.20), residues: 515 sheet: -2.84 (0.37), residues: 143 loop : -2.78 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 355 HIS 0.010 0.001 HIS A 720 PHE 0.017 0.002 PHE A 328 TYR 0.025 0.002 TYR A 840 ARG 0.003 0.000 ARG A1189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 GLN cc_start: 0.7868 (mt0) cc_final: 0.7261 (pt0) REVERT: A 858 GLU cc_start: 0.8357 (pt0) cc_final: 0.8153 (pt0) REVERT: A 1128 MET cc_start: 0.8630 (mmm) cc_final: 0.8187 (mmm) REVERT: C 230 ARG cc_start: 0.7849 (ttm170) cc_final: 0.7250 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 1.1893 time to fit residues: 173.4636 Evaluate side-chains 94 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 157 ASN A 268 GLN A 420 GLN A 793 GLN A 864 ASN A 963 ASN C 168 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10393 Z= 0.242 Angle : 0.543 6.982 14103 Z= 0.288 Chirality : 0.043 0.186 1541 Planarity : 0.003 0.033 1709 Dihedral : 11.402 160.456 1636 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.09 % Allowed : 10.33 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.24), residues: 1150 helix: -0.12 (0.23), residues: 515 sheet: -2.66 (0.41), residues: 125 loop : -2.09 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1193 HIS 0.006 0.001 HIS A 720 PHE 0.011 0.001 PHE A 328 TYR 0.010 0.001 TYR A 794 ARG 0.007 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7968 (p) REVERT: A 264 GLN cc_start: 0.7859 (mt0) cc_final: 0.7122 (pt0) REVERT: A 746 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7010 (tmt) REVERT: A 819 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7870 (mm) REVERT: C 222 ARG cc_start: 0.8575 (ptt90) cc_final: 0.8348 (ptt90) REVERT: C 227 GLU cc_start: 0.8505 (tp30) cc_final: 0.8133 (tp30) REVERT: C 230 ARG cc_start: 0.7687 (ttm170) cc_final: 0.7327 (mtm-85) outliers start: 22 outliers final: 7 residues processed: 126 average time/residue: 1.0107 time to fit residues: 139.4626 Evaluate side-chains 105 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 162 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 864 ASN A 909 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10393 Z= 0.247 Angle : 0.529 6.913 14103 Z= 0.279 Chirality : 0.042 0.183 1541 Planarity : 0.003 0.030 1709 Dihedral : 11.314 162.362 1636 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.03 % Allowed : 12.32 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.25), residues: 1150 helix: 0.34 (0.24), residues: 521 sheet: -2.53 (0.41), residues: 125 loop : -1.72 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 355 HIS 0.006 0.001 HIS A 720 PHE 0.010 0.001 PHE A 328 TYR 0.018 0.001 TYR A 262 ARG 0.007 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 107 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7155 (mtm110) REVERT: A 236 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8004 (p) REVERT: A 264 GLN cc_start: 0.7857 (mt0) cc_final: 0.7161 (pt0) REVERT: A 746 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.7253 (tmt) REVERT: A 819 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7882 (mm) REVERT: A 1035 MET cc_start: 0.8162 (ptm) cc_final: 0.7893 (ptm) REVERT: A 1065 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7950 (pp) REVERT: C 222 ARG cc_start: 0.8538 (ptt90) cc_final: 0.8277 (ptt180) REVERT: C 227 GLU cc_start: 0.8695 (tp30) cc_final: 0.8285 (tp30) REVERT: C 230 ARG cc_start: 0.7673 (ttm170) cc_final: 0.7465 (mtm-85) outliers start: 32 outliers final: 16 residues processed: 122 average time/residue: 1.0709 time to fit residues: 143.0572 Evaluate side-chains 115 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1178 ASN Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 ASN A 864 ASN A 975 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10393 Z= 0.248 Angle : 0.520 7.511 14103 Z= 0.275 Chirality : 0.043 0.181 1541 Planarity : 0.003 0.034 1709 Dihedral : 11.277 162.808 1636 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.13 % Allowed : 15.45 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.25), residues: 1150 helix: 0.61 (0.24), residues: 521 sheet: -2.27 (0.39), residues: 147 loop : -1.54 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 355 HIS 0.006 0.001 HIS A 720 PHE 0.010 0.001 PHE A 486 TYR 0.022 0.001 TYR A 262 ARG 0.008 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7191 (mtm110) REVERT: A 236 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8042 (p) REVERT: A 264 GLN cc_start: 0.7866 (mt0) cc_final: 0.7189 (pt0) REVERT: A 746 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7215 (tmt) REVERT: A 819 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7889 (mm) REVERT: A 1035 MET cc_start: 0.8195 (ptm) cc_final: 0.7900 (ptm) REVERT: A 1065 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7906 (pp) REVERT: C 222 ARG cc_start: 0.8528 (ptt90) cc_final: 0.8306 (ptt180) REVERT: C 227 GLU cc_start: 0.8787 (tp30) cc_final: 0.8471 (tp30) outliers start: 33 outliers final: 18 residues processed: 120 average time/residue: 0.9612 time to fit residues: 126.9769 Evaluate side-chains 117 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1178 ASN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.0040 chunk 102 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 ASN A 906 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10393 Z= 0.174 Angle : 0.484 7.684 14103 Z= 0.255 Chirality : 0.041 0.167 1541 Planarity : 0.003 0.036 1709 Dihedral : 11.216 166.355 1636 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.32 % Allowed : 15.92 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.25), residues: 1150 helix: 0.88 (0.24), residues: 522 sheet: -2.14 (0.39), residues: 147 loop : -1.30 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1193 HIS 0.004 0.001 HIS A 720 PHE 0.010 0.001 PHE A 227 TYR 0.012 0.001 TYR A 262 ARG 0.009 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 103 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7116 (mtm110) REVERT: A 264 GLN cc_start: 0.7829 (mt0) cc_final: 0.7169 (pt0) REVERT: A 722 MET cc_start: 0.8154 (mtp) cc_final: 0.7941 (mtp) REVERT: A 746 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7233 (tmt) REVERT: A 819 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7875 (mm) REVERT: A 1065 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7854 (pp) REVERT: C 202 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.7780 (tppp) REVERT: C 222 ARG cc_start: 0.8494 (ptt90) cc_final: 0.8135 (ptt180) REVERT: C 227 GLU cc_start: 0.8810 (tp30) cc_final: 0.8562 (tp30) outliers start: 35 outliers final: 18 residues processed: 121 average time/residue: 0.9600 time to fit residues: 127.8848 Evaluate side-chains 118 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1178 ASN Chi-restraints excluded: chain A residue 1207 ASP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 216 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 ASN A 864 ASN C 233 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10393 Z= 0.300 Angle : 0.539 7.296 14103 Z= 0.285 Chirality : 0.044 0.185 1541 Planarity : 0.003 0.031 1709 Dihedral : 11.235 161.716 1636 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.51 % Allowed : 16.68 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.25), residues: 1150 helix: 0.84 (0.24), residues: 522 sheet: -2.22 (0.38), residues: 152 loop : -1.31 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 355 HIS 0.010 0.001 HIS C 190 PHE 0.012 0.001 PHE A 486 TYR 0.023 0.001 TYR A 262 ARG 0.009 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 98 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6951 (mtm110) REVERT: A 264 GLN cc_start: 0.7866 (mt0) cc_final: 0.7229 (pt0) REVERT: A 434 LYS cc_start: 0.8355 (pttm) cc_final: 0.8149 (pmtt) REVERT: A 746 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7082 (tmt) REVERT: A 819 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7876 (mm) REVERT: A 1035 MET cc_start: 0.8151 (ptm) cc_final: 0.7915 (ptm) REVERT: A 1065 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7948 (pp) REVERT: C 222 ARG cc_start: 0.8498 (ptt90) cc_final: 0.8234 (ptt180) outliers start: 37 outliers final: 21 residues processed: 120 average time/residue: 0.9612 time to fit residues: 126.9462 Evaluate side-chains 119 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1178 ASN Chi-restraints excluded: chain A residue 1207 ASP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 83 optimal weight: 0.0040 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 ASN C 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10393 Z= 0.182 Angle : 0.495 8.338 14103 Z= 0.260 Chirality : 0.041 0.171 1541 Planarity : 0.003 0.034 1709 Dihedral : 11.215 165.047 1636 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.65 % Allowed : 17.73 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.25), residues: 1150 helix: 1.03 (0.24), residues: 523 sheet: -2.13 (0.39), residues: 152 loop : -1.17 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 999 HIS 0.005 0.001 HIS C 190 PHE 0.008 0.001 PHE A1045 TYR 0.020 0.001 TYR A 262 ARG 0.009 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7102 (mtm110) REVERT: A 264 GLN cc_start: 0.7818 (mt0) cc_final: 0.7213 (pt0) REVERT: A 434 LYS cc_start: 0.8325 (pttm) cc_final: 0.8078 (pmtt) REVERT: A 746 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7230 (tmt) REVERT: A 819 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7864 (mm) REVERT: A 1035 MET cc_start: 0.8133 (ptm) cc_final: 0.7919 (ptm) REVERT: A 1065 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7900 (pp) REVERT: A 1204 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: C 202 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.7836 (tppp) REVERT: C 222 ARG cc_start: 0.8467 (ptt90) cc_final: 0.8124 (ptt180) outliers start: 28 outliers final: 17 residues processed: 114 average time/residue: 0.9802 time to fit residues: 123.1364 Evaluate side-chains 117 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1178 ASN Chi-restraints excluded: chain A residue 1204 GLU Chi-restraints excluded: chain A residue 1207 ASP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 0.0270 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 864 ASN C 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10393 Z= 0.249 Angle : 0.525 8.230 14103 Z= 0.276 Chirality : 0.043 0.176 1541 Planarity : 0.003 0.034 1709 Dihedral : 11.214 163.452 1636 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.32 % Allowed : 17.44 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1150 helix: 1.01 (0.24), residues: 523 sheet: -2.08 (0.39), residues: 152 loop : -1.13 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 999 HIS 0.005 0.001 HIS C 190 PHE 0.011 0.001 PHE A 224 TYR 0.023 0.001 TYR A 262 ARG 0.009 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 92 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7068 (mtm110) REVERT: A 227 PHE cc_start: 0.7430 (t80) cc_final: 0.7128 (t80) REVERT: A 264 GLN cc_start: 0.7861 (mt0) cc_final: 0.7249 (pt0) REVERT: A 378 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8284 (m) REVERT: A 434 LYS cc_start: 0.8351 (pttm) cc_final: 0.8080 (pmtt) REVERT: A 746 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.7211 (tmt) REVERT: A 819 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7860 (mm) REVERT: A 858 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: A 1035 MET cc_start: 0.8145 (ptm) cc_final: 0.7917 (ptm) REVERT: A 1065 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7908 (pp) REVERT: C 202 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.7836 (tppp) outliers start: 35 outliers final: 19 residues processed: 113 average time/residue: 0.9601 time to fit residues: 119.6877 Evaluate side-chains 117 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1178 ASN Chi-restraints excluded: chain A residue 1207 ASP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 0.1980 chunk 69 optimal weight: 0.0980 chunk 112 optimal weight: 0.0770 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 864 ASN C 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10393 Z= 0.119 Angle : 0.474 9.042 14103 Z= 0.247 Chirality : 0.040 0.151 1541 Planarity : 0.003 0.039 1709 Dihedral : 11.191 171.764 1636 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.80 % Allowed : 19.24 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1150 helix: 1.43 (0.24), residues: 516 sheet: -1.91 (0.39), residues: 154 loop : -0.84 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 362 HIS 0.005 0.001 HIS C 233 PHE 0.009 0.001 PHE A 227 TYR 0.014 0.001 TYR A 262 ARG 0.010 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7209 (mtm110) REVERT: A 64 ASP cc_start: 0.7840 (t0) cc_final: 0.7071 (m-30) REVERT: A 227 PHE cc_start: 0.7177 (t80) cc_final: 0.6883 (t80) REVERT: A 264 GLN cc_start: 0.7748 (mt0) cc_final: 0.7211 (pt0) REVERT: A 434 LYS cc_start: 0.8318 (pttm) cc_final: 0.8092 (pmtt) REVERT: A 722 MET cc_start: 0.8162 (mtp) cc_final: 0.7952 (mtp) REVERT: A 746 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7110 (tmt) REVERT: A 819 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7878 (mm) REVERT: A 858 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: A 1065 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7786 (pp) REVERT: C 217 ARG cc_start: 0.7780 (mtp85) cc_final: 0.7162 (mtp180) outliers start: 19 outliers final: 8 residues processed: 122 average time/residue: 0.9674 time to fit residues: 129.8979 Evaluate side-chains 109 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1178 ASN Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 864 ASN C 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10393 Z= 0.192 Angle : 0.528 7.945 14103 Z= 0.278 Chirality : 0.042 0.212 1541 Planarity : 0.003 0.037 1709 Dihedral : 11.130 167.974 1636 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.42 % Allowed : 20.85 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1150 helix: 1.38 (0.24), residues: 523 sheet: -1.78 (0.39), residues: 154 loop : -0.86 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 999 HIS 0.004 0.001 HIS C 190 PHE 0.010 0.001 PHE A1045 TYR 0.014 0.001 TYR A 469 ARG 0.009 0.000 ARG C 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7905 (t0) cc_final: 0.7128 (m-30) REVERT: A 227 PHE cc_start: 0.7268 (t80) cc_final: 0.6965 (t80) REVERT: A 264 GLN cc_start: 0.7770 (mt0) cc_final: 0.7218 (pt0) REVERT: A 434 LYS cc_start: 0.8366 (pttm) cc_final: 0.8109 (pmtt) REVERT: A 746 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7091 (tmt) REVERT: A 819 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7828 (mm) REVERT: A 858 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: A 1065 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7881 (pp) REVERT: C 217 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7216 (mtp180) outliers start: 15 outliers final: 9 residues processed: 108 average time/residue: 0.9426 time to fit residues: 112.2947 Evaluate side-chains 109 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1178 ASN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 26 optimal weight: 4.9990 chunk 93 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 864 ASN C 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.127216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099275 restraints weight = 14636.729| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.33 r_work: 0.3166 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10393 Z= 0.158 Angle : 0.514 10.497 14103 Z= 0.265 Chirality : 0.041 0.228 1541 Planarity : 0.003 0.037 1709 Dihedral : 11.148 169.057 1636 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.99 % Allowed : 20.28 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1150 helix: 1.60 (0.24), residues: 509 sheet: -1.75 (0.39), residues: 154 loop : -0.66 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 999 HIS 0.010 0.001 HIS C 233 PHE 0.008 0.001 PHE A1045 TYR 0.012 0.001 TYR A 469 ARG 0.009 0.001 ARG C 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3268.99 seconds wall clock time: 59 minutes 52.53 seconds (3592.53 seconds total)