Starting phenix.real_space_refine on Tue Jan 14 12:40:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vjm_43289/01_2025/8vjm_43289.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vjm_43289/01_2025/8vjm_43289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vjm_43289/01_2025/8vjm_43289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vjm_43289/01_2025/8vjm_43289.map" model { file = "/net/cci-nas-00/data/ceres_data/8vjm_43289/01_2025/8vjm_43289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vjm_43289/01_2025/8vjm_43289.cif" } resolution = 4.0 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= -0.000 sd= 0.021 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 28 5.16 5 C 4423 2.51 5 N 1083 2.21 5 O 1132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6667 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2353 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 276} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 888 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2353 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 276} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 888 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 185 Unusual residues: {'LMN': 2, 'PEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.06, per 1000 atoms: 0.76 Number of scatterers: 6667 At special positions: 0 Unit cell: (88.2648, 78.9291, 129.002, 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 28 16.00 P 1 15.00 O 1132 8.00 N 1083 7.00 C 4423 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 - 3.00 Amino acid : True - 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: 1.87 Conformation dependent library (CDL) restraints added in 951.5 milliseconds 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1536 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 67.2% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 removed outlier: 4.143A pdb=" N LEU A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 26 removed outlier: 3.954A pdb=" N TRP A 18 " --> pdb=" O HIS A 14 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 19 " --> pdb=" O PRO A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 54 removed outlier: 3.943A pdb=" N PHE A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 removed outlier: 3.871A pdb=" N GLU A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.772A pdb=" N LEU A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 129 removed outlier: 3.646A pdb=" N PHE A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 147 removed outlier: 4.865A pdb=" N LEU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 178 Processing helix chain 'A' and resid 181 through 201 removed outlier: 4.007A pdb=" N TRP A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.801A pdb=" N VAL A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'B' and resid 33 through 47 Processing helix chain 'B' and resid 48 through 59 removed outlier: 3.682A pdb=" N ARG B 52 " --> pdb=" O ASP B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.670A pdb=" N ALA B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 94 Processing helix chain 'B' and resid 102 through 126 Processing helix chain 'C' and resid 2 through 9 removed outlier: 4.393A pdb=" N ASP C 6 " --> pdb=" O ASN C 2 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU C 7 " --> pdb=" O LYS C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 27 Processing helix chain 'C' and resid 30 through 54 removed outlier: 3.729A pdb=" N LEU C 34 " --> pdb=" O MET C 30 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N CYS C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C 51 " --> pdb=" O HIS C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.631A pdb=" N VAL C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 92 removed outlier: 3.945A pdb=" N LEU C 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 93 through 105 removed outlier: 3.511A pdb=" N MET C 103 " --> pdb=" O PHE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 removed outlier: 4.027A pdb=" N PHE C 115 " --> pdb=" O HIS C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 150 removed outlier: 4.213A pdb=" N GLN C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 177 removed outlier: 3.692A pdb=" N LEU C 160 " --> pdb=" O HIS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 201 removed outlier: 3.511A pdb=" N TRP C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 removed outlier: 3.660A pdb=" N VAL C 207 " --> pdb=" O HIS C 203 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 removed outlier: 4.062A pdb=" N GLU C 241 " --> pdb=" O HIS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 273 Processing helix chain 'C' and resid 280 through 286 removed outlier: 3.595A pdb=" N LEU C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 48 removed outlier: 3.919A pdb=" N LYS D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP D 48 " --> pdb=" O MET D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 59 removed outlier: 3.924A pdb=" N ASN D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.666A pdb=" N ALA D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 94 removed outlier: 3.656A pdb=" N LEU D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 126 removed outlier: 3.585A pdb=" N TYR D 106 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 7.252A pdb=" N HIS A 12 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR B 22 " --> pdb=" O GLY A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 230 removed outlier: 5.707A pdb=" N LEU A 227 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU A 253 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 229 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 250 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN A 261 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 252 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 64 removed outlier: 6.818A pdb=" N GLU C 71 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL C 61 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR C 69 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU C 63 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR D 22 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL C 70 " --> pdb=" O TYR D 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 227 through 230 372 hydrogen bonds defined for protein. 1101 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: 1.83 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1004 1.31 - 1.44: 1844 1.44 - 1.56: 3922 1.56 - 1.69: 26 1.69 - 1.82: 44 Bond restraints: 6840 Sorted by residual: bond pdb=" C1 LMN A 401 " pdb=" O5 LMN A 401 " ideal model delta sigma weight residual 1.403 1.538 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C1 LMN A 403 " pdb=" O5 LMN A 403 " ideal model delta sigma weight residual 1.403 1.535 -0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" CBS LMN A 401 " pdb=" CCM LMN A 401 " ideal model delta sigma weight residual 1.529 1.631 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C4 LMN A 403 " pdb=" O4 LMN A 403 " ideal model delta sigma weight residual 1.409 1.510 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" CBS LMN A 403 " pdb=" CCM LMN A 403 " ideal model delta sigma weight residual 1.529 1.629 -0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 6835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 9096 3.10 - 6.21: 146 6.21 - 9.31: 13 9.31 - 12.42: 3 12.42 - 15.52: 1 Bond angle restraints: 9259 Sorted by residual: angle pdb=" O3P PEF A 402 " pdb=" P PEF A 402 " pdb=" O4P PEF A 402 " ideal model delta sigma weight residual 93.96 109.48 -15.52 3.00e+00 1.11e-01 2.68e+01 angle pdb=" N VAL C 107 " pdb=" CA VAL C 107 " pdb=" C VAL C 107 " ideal model delta sigma weight residual 112.98 108.06 4.92 1.25e+00 6.40e-01 1.55e+01 angle pdb=" C4 LMN A 401 " pdb=" O4 LMN A 401 " pdb=" CCR LMN A 401 " ideal model delta sigma weight residual 120.22 109.38 10.84 3.00e+00 1.11e-01 1.31e+01 angle pdb=" O1P PEF A 402 " pdb=" P PEF A 402 " pdb=" O2P PEF A 402 " ideal model delta sigma weight residual 119.53 109.50 10.03 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CCQ LMN A 401 " pdb=" OCB LMN A 401 " pdb=" CCS LMN A 401 " ideal model delta sigma weight residual 119.65 109.82 9.83 3.00e+00 1.11e-01 1.07e+01 ... (remaining 9254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.63: 3781 24.63 - 49.25: 307 49.25 - 73.88: 60 73.88 - 98.50: 22 98.50 - 123.13: 35 Dihedral angle restraints: 4205 sinusoidal: 1841 harmonic: 2364 Sorted by residual: dihedral pdb=" CCD LMN A 403 " pdb=" CCS LMN A 403 " pdb=" OBZ LMN A 403 " pdb=" OCB LMN A 403 " ideal model delta sinusoidal sigma weight residual 60.96 -175.91 -123.13 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" O2 LMN A 403 " pdb=" C2 LMN A 403 " pdb=" C3 LMN A 403 " pdb=" O3 LMN A 403 " ideal model delta sinusoidal sigma weight residual 295.11 172.74 122.37 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" CCD LMN A 403 " pdb=" CCS LMN A 403 " pdb=" OBZ LMN A 403 " pdb=" CCW LMN A 403 " ideal model delta sinusoidal sigma weight residual -59.55 61.55 -121.10 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 4202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 806 0.041 - 0.082: 201 0.082 - 0.123: 53 0.123 - 0.164: 6 0.164 - 0.205: 5 Chirality restraints: 1071 Sorted by residual: chirality pdb=" C1 LMN A 403 " pdb=" C2 LMN A 403 " pdb=" O1 LMN A 403 " pdb=" O5 LMN A 403 " both_signs ideal model delta sigma weight residual False -2.29 -2.49 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C1 LMN A 401 " pdb=" C2 LMN A 401 " pdb=" O1 LMN A 401 " pdb=" O5 LMN A 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.48 0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CCV LMN A 401 " pdb=" CCR LMN A 401 " pdb=" CCT LMN A 401 " pdb=" OAU LMN A 401 " both_signs ideal model delta sigma weight residual False 2.28 2.46 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1068 not shown) Planarity restraints: 1110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 225 " -0.076 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO C 226 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO C 226 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 226 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 90 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.16e+00 pdb=" N PRO A 91 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 178 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO C 179 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " 0.023 5.00e-02 4.00e+02 ... (remaining 1107 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1182 2.77 - 3.30: 6438 3.30 - 3.83: 10474 3.83 - 4.37: 11155 4.37 - 4.90: 19505 Nonbonded interactions: 48754 Sorted by model distance: nonbonded pdb=" OG SER A 280 " pdb=" OE1 GLU A 283 " model vdw 2.235 3.040 nonbonded pdb=" ND2 ASN A 129 " pdb=" OG SER B 21 " model vdw 2.299 3.120 nonbonded pdb=" O PRO D 29 " pdb=" NH1 ARG D 61 " model vdw 2.309 3.120 nonbonded pdb=" O ARG C 78 " pdb=" NH2 ARG C 244 " model vdw 2.325 3.120 nonbonded pdb=" N SER B 33 " pdb=" OE2 GLU B 36 " model vdw 2.327 3.120 ... (remaining 48749 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 288) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.470 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 : 0.008 0.135 6840 Z= 0.524 Angle : 0.819 15.522 9259 Z= 0.358 Chirality : 0.041 0.205 1071 Planarity : 0.005 0.113 1110 Dihedral : 22.667 123.128 2669 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.00 % Favored : 93.75 % Rotamer: Outliers : 0.29 % Allowed : 0.29 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.48 (0.31), residues: 800 helix: 1.45 (0.24), residues: 536 sheet: 0.08 (1.12), residues: 28 loop : -2.39 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 4 HIS 0.007 0.001 HIS C 203 PHE 0.009 0.001 PHE C 272 TYR 0.015 0.001 TYR C 271 ARG 0.009 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8565 (t80) cc_final: 0.8120 (t80) REVERT: B 62 LEU cc_start: 0.9024 (mt) cc_final: 0.8777 (tt) REVERT: B 79 ASP cc_start: 0.7558 (m-30) cc_final: 0.7189 (m-30) REVERT: B 96 SER cc_start: 0.9055 (t) cc_final: 0.8796 (p) REVERT: D 43 LEU cc_start: 0.8833 (tp) cc_final: 0.8456 (tp) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.1899 time to fit residues: 45.5521 Evaluate side-chains 140 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.147071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.114731 restraints weight = 11649.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.117810 restraints weight = 6729.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.119733 restraints weight = 4771.564| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 6840 Z= 0.428 Angle : 0.839 11.213 9259 Z= 0.393 Chirality : 0.050 0.327 1071 Planarity : 0.006 0.076 1110 Dihedral : 18.497 97.539 1153 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.38 % Favored : 92.50 % Rotamer: Outliers : 2.65 % Allowed : 16.22 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.30), residues: 800 helix: 0.98 (0.23), residues: 546 sheet: -0.07 (0.92), residues: 38 loop : -2.58 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 96 HIS 0.006 0.001 HIS A 206 PHE 0.028 0.002 PHE C 118 TYR 0.022 0.002 TYR A 271 ARG 0.004 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.878 Fit side-chains REVERT: A 44 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8566 (mm-40) REVERT: A 84 PHE cc_start: 0.8641 (t80) cc_final: 0.8247 (t80) REVERT: B 79 ASP cc_start: 0.7561 (m-30) cc_final: 0.7353 (m-30) REVERT: B 96 SER cc_start: 0.9004 (t) cc_final: 0.8734 (p) REVERT: C 282 GLU cc_start: 0.8066 (mp0) cc_final: 0.7646 (mp0) REVERT: D 66 ILE cc_start: 0.8781 (mp) cc_final: 0.8562 (mp) outliers start: 18 outliers final: 13 residues processed: 149 average time/residue: 0.2125 time to fit residues: 42.0887 Evaluate side-chains 149 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 56 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 237 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.147668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.115529 restraints weight = 11639.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118718 restraints weight = 6660.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120578 restraints weight = 4686.934| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6840 Z= 0.190 Angle : 0.654 8.428 9259 Z= 0.304 Chirality : 0.043 0.386 1071 Planarity : 0.005 0.062 1110 Dihedral : 14.216 86.655 1153 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.38 % Favored : 94.50 % Rotamer: Outliers : 2.21 % Allowed : 19.32 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.37 (0.31), residues: 800 helix: 1.28 (0.23), residues: 530 sheet: -0.11 (0.88), residues: 38 loop : -2.15 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 96 HIS 0.006 0.001 HIS B 118 PHE 0.011 0.001 PHE C 118 TYR 0.023 0.001 TYR A 199 ARG 0.003 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8634 (t80) cc_final: 0.8188 (t80) REVERT: A 281 MET cc_start: 0.6961 (ptt) cc_final: 0.6749 (ptt) REVERT: B 62 LEU cc_start: 0.9107 (mp) cc_final: 0.8723 (tt) REVERT: B 79 ASP cc_start: 0.7464 (m-30) cc_final: 0.7261 (m-30) REVERT: B 96 SER cc_start: 0.9032 (t) cc_final: 0.8765 (p) REVERT: C 282 GLU cc_start: 0.8146 (mp0) cc_final: 0.7715 (mp0) REVERT: D 43 LEU cc_start: 0.8904 (tp) cc_final: 0.8529 (tp) REVERT: D 66 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8531 (mp) outliers start: 15 outliers final: 8 residues processed: 157 average time/residue: 0.1779 time to fit residues: 37.1528 Evaluate side-chains 149 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 52 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 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 237 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.143909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111660 restraints weight = 11831.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.114619 restraints weight = 6854.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.116420 restraints weight = 4883.900| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6840 Z= 0.203 Angle : 0.656 14.300 9259 Z= 0.305 Chirality : 0.042 0.308 1071 Planarity : 0.005 0.058 1110 Dihedral : 10.691 87.170 1153 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.75 % Favored : 93.12 % Rotamer: Outliers : 3.24 % Allowed : 20.65 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.48 (0.31), residues: 800 helix: 1.36 (0.23), residues: 530 sheet: -0.04 (0.88), residues: 38 loop : -2.10 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 96 HIS 0.007 0.001 HIS A 206 PHE 0.013 0.001 PHE C 118 TYR 0.010 0.001 TYR A 271 ARG 0.005 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8668 (t80) cc_final: 0.8172 (t80) REVERT: A 236 TYR cc_start: 0.9086 (t80) cc_final: 0.8869 (t80) REVERT: A 281 MET cc_start: 0.7244 (ptt) cc_final: 0.6844 (ptt) REVERT: B 37 GLU cc_start: 0.8021 (pp20) cc_final: 0.7641 (tt0) REVERT: B 62 LEU cc_start: 0.9110 (mp) cc_final: 0.8696 (tt) REVERT: B 79 ASP cc_start: 0.7565 (m-30) cc_final: 0.7361 (m-30) REVERT: B 96 SER cc_start: 0.9022 (t) cc_final: 0.8774 (p) REVERT: C 282 GLU cc_start: 0.8217 (mp0) cc_final: 0.7810 (mp0) REVERT: D 43 LEU cc_start: 0.8811 (tp) cc_final: 0.8514 (tp) REVERT: D 66 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8412 (mp) outliers start: 22 outliers final: 14 residues processed: 165 average time/residue: 0.1818 time to fit residues: 39.9081 Evaluate side-chains 160 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 9 optimal weight: 0.0030 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.0980 chunk 39 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 0.3980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 237 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114874 restraints weight = 11558.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117935 restraints weight = 6653.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119920 restraints weight = 4692.454| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6840 Z= 0.158 Angle : 0.600 12.801 9259 Z= 0.288 Chirality : 0.039 0.248 1071 Planarity : 0.004 0.052 1110 Dihedral : 9.932 88.124 1153 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.38 % Rotamer: Outliers : 3.39 % Allowed : 22.42 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.31), residues: 800 helix: 1.50 (0.24), residues: 530 sheet: 0.05 (0.89), residues: 38 loop : -2.06 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 96 HIS 0.005 0.001 HIS C 237 PHE 0.013 0.001 PHE A 66 TYR 0.019 0.001 TYR A 271 ARG 0.006 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8636 (t80) cc_final: 0.8105 (t80) REVERT: A 236 TYR cc_start: 0.9033 (t80) cc_final: 0.8733 (t80) REVERT: A 281 MET cc_start: 0.7097 (ptt) cc_final: 0.6690 (ptt) REVERT: B 62 LEU cc_start: 0.9067 (mp) cc_final: 0.8664 (tt) REVERT: B 79 ASP cc_start: 0.7570 (m-30) cc_final: 0.7359 (m-30) REVERT: B 96 SER cc_start: 0.8987 (t) cc_final: 0.8710 (p) REVERT: C 282 GLU cc_start: 0.8183 (mp0) cc_final: 0.7771 (mp0) REVERT: D 43 LEU cc_start: 0.8812 (tp) cc_final: 0.8489 (tp) REVERT: D 50 HIS cc_start: 0.7749 (t-90) cc_final: 0.7508 (t70) REVERT: D 66 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8396 (mp) outliers start: 23 outliers final: 13 residues processed: 173 average time/residue: 0.1983 time to fit residues: 45.6276 Evaluate side-chains 163 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 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 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 237 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.116540 restraints weight = 11537.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119700 restraints weight = 6556.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121739 restraints weight = 4602.050| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6840 Z= 0.186 Angle : 0.644 16.049 9259 Z= 0.302 Chirality : 0.039 0.210 1071 Planarity : 0.005 0.051 1110 Dihedral : 9.572 86.996 1153 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.62 % Favored : 93.25 % Rotamer: Outliers : 3.69 % Allowed : 24.48 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.62 (0.31), residues: 800 helix: 1.48 (0.23), residues: 530 sheet: 0.25 (1.07), residues: 28 loop : -2.04 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 96 HIS 0.005 0.001 HIS C 237 PHE 0.012 0.001 PHE A 146 TYR 0.025 0.001 TYR A 199 ARG 0.005 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8643 (t80) cc_final: 0.8191 (t80) REVERT: A 211 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8646 (tt) REVERT: A 236 TYR cc_start: 0.9018 (t80) cc_final: 0.8702 (t80) REVERT: A 281 MET cc_start: 0.7094 (ptt) cc_final: 0.6361 (ptt) REVERT: B 62 LEU cc_start: 0.9064 (mp) cc_final: 0.8693 (tt) REVERT: B 96 SER cc_start: 0.8935 (t) cc_final: 0.8667 (p) REVERT: C 282 GLU cc_start: 0.8009 (mp0) cc_final: 0.7607 (mp0) REVERT: D 43 LEU cc_start: 0.8750 (tp) cc_final: 0.8415 (tp) REVERT: D 50 HIS cc_start: 0.7652 (t-90) cc_final: 0.7438 (t70) REVERT: D 66 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8476 (mp) outliers start: 25 outliers final: 17 residues processed: 170 average time/residue: 0.1836 time to fit residues: 41.4890 Evaluate side-chains 168 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 237 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.113678 restraints weight = 11501.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116638 restraints weight = 6603.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118334 restraints weight = 4677.190| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6840 Z= 0.189 Angle : 0.639 12.215 9259 Z= 0.305 Chirality : 0.039 0.191 1071 Planarity : 0.004 0.050 1110 Dihedral : 9.421 86.854 1153 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.75 % Favored : 93.12 % Rotamer: Outliers : 3.83 % Allowed : 25.81 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.61 (0.31), residues: 800 helix: 1.46 (0.23), residues: 530 sheet: 0.43 (1.09), residues: 28 loop : -2.05 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 4 HIS 0.006 0.001 HIS C 237 PHE 0.010 0.001 PHE A 146 TYR 0.006 0.001 TYR C 204 ARG 0.002 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8629 (t80) cc_final: 0.8195 (t80) REVERT: A 236 TYR cc_start: 0.9040 (t80) cc_final: 0.8752 (t80) REVERT: A 281 MET cc_start: 0.7163 (ptt) cc_final: 0.6574 (ptt) REVERT: B 37 GLU cc_start: 0.8118 (pp20) cc_final: 0.7720 (tt0) REVERT: B 62 LEU cc_start: 0.9074 (mp) cc_final: 0.8685 (tt) REVERT: B 96 SER cc_start: 0.8933 (t) cc_final: 0.8663 (p) REVERT: C 282 GLU cc_start: 0.7979 (mp0) cc_final: 0.7477 (mp0) REVERT: D 43 LEU cc_start: 0.8759 (tp) cc_final: 0.8474 (tp) REVERT: D 50 HIS cc_start: 0.7671 (t-90) cc_final: 0.7453 (t70) REVERT: D 66 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8427 (mp) outliers start: 26 outliers final: 19 residues processed: 170 average time/residue: 0.1841 time to fit residues: 41.8663 Evaluate side-chains 174 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.0040 chunk 74 optimal weight: 0.0470 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.5490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 237 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.147163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115272 restraints weight = 11588.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118323 restraints weight = 6622.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.120230 restraints weight = 4662.895| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6840 Z= 0.171 Angle : 0.650 16.853 9259 Z= 0.304 Chirality : 0.038 0.173 1071 Planarity : 0.004 0.049 1110 Dihedral : 9.180 87.988 1153 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.88 % Favored : 93.00 % Rotamer: Outliers : 3.24 % Allowed : 26.70 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.32), residues: 800 helix: 1.55 (0.24), residues: 530 sheet: 0.54 (1.09), residues: 28 loop : -2.04 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 4 HIS 0.005 0.001 HIS C 237 PHE 0.012 0.001 PHE A 66 TYR 0.006 0.001 TYR C 204 ARG 0.002 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8603 (t80) cc_final: 0.8195 (t80) REVERT: A 236 TYR cc_start: 0.9020 (t80) cc_final: 0.8743 (t80) REVERT: A 281 MET cc_start: 0.7222 (ptt) cc_final: 0.6443 (ptt) REVERT: B 37 GLU cc_start: 0.7995 (pp20) cc_final: 0.7715 (tt0) REVERT: B 62 LEU cc_start: 0.9046 (mp) cc_final: 0.8672 (tt) REVERT: B 96 SER cc_start: 0.8899 (t) cc_final: 0.8641 (p) REVERT: C 282 GLU cc_start: 0.7889 (mp0) cc_final: 0.7312 (mp0) REVERT: D 43 LEU cc_start: 0.8739 (tp) cc_final: 0.8472 (tp) REVERT: D 50 HIS cc_start: 0.7625 (t-90) cc_final: 0.7374 (t70) REVERT: D 66 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8404 (mp) outliers start: 22 outliers final: 16 residues processed: 170 average time/residue: 0.1878 time to fit residues: 42.5780 Evaluate side-chains 170 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 237 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111852 restraints weight = 11646.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114822 restraints weight = 6714.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116800 restraints weight = 4739.906| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6840 Z= 0.241 Angle : 0.684 13.596 9259 Z= 0.326 Chirality : 0.040 0.190 1071 Planarity : 0.005 0.049 1110 Dihedral : 9.341 86.514 1153 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.50 % Favored : 93.38 % Rotamer: Outliers : 3.10 % Allowed : 26.55 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.62 (0.31), residues: 800 helix: 1.47 (0.23), residues: 530 sheet: 0.20 (0.88), residues: 38 loop : -2.10 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 96 HIS 0.007 0.001 HIS C 113 PHE 0.014 0.001 PHE C 118 TYR 0.009 0.001 TYR C 214 ARG 0.004 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8630 (t80) cc_final: 0.8228 (t80) REVERT: A 236 TYR cc_start: 0.9007 (t80) cc_final: 0.8706 (t80) REVERT: A 281 MET cc_start: 0.7337 (ptt) cc_final: 0.6664 (ptt) REVERT: B 62 LEU cc_start: 0.9099 (mp) cc_final: 0.8684 (tt) REVERT: B 96 SER cc_start: 0.8895 (t) cc_final: 0.8629 (p) REVERT: C 282 GLU cc_start: 0.7996 (mp0) cc_final: 0.7441 (mp0) REVERT: D 43 LEU cc_start: 0.8739 (tp) cc_final: 0.8444 (tp) REVERT: D 66 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8457 (mp) outliers start: 21 outliers final: 17 residues processed: 168 average time/residue: 0.1836 time to fit residues: 40.7044 Evaluate side-chains 169 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 237 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.144050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.111693 restraints weight = 11792.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114636 restraints weight = 6823.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.116570 restraints weight = 4847.166| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6840 Z= 0.240 Angle : 0.701 12.861 9259 Z= 0.335 Chirality : 0.040 0.189 1071 Planarity : 0.005 0.049 1110 Dihedral : 9.411 86.108 1153 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.50 % Favored : 93.38 % Rotamer: Outliers : 2.80 % Allowed : 26.70 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.53 (0.31), residues: 800 helix: 1.40 (0.23), residues: 530 sheet: 0.14 (0.87), residues: 38 loop : -2.15 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 4 HIS 0.005 0.001 HIS C 237 PHE 0.014 0.001 PHE C 118 TYR 0.020 0.001 TYR C 199 ARG 0.004 0.000 ARG B 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8631 (t80) cc_final: 0.8230 (t80) REVERT: A 236 TYR cc_start: 0.9012 (t80) cc_final: 0.8705 (t80) REVERT: A 281 MET cc_start: 0.7298 (ptt) cc_final: 0.6662 (ptt) REVERT: B 96 SER cc_start: 0.8918 (t) cc_final: 0.8665 (p) REVERT: C 282 GLU cc_start: 0.8004 (mp0) cc_final: 0.7440 (mp0) REVERT: D 43 LEU cc_start: 0.8754 (tp) cc_final: 0.8532 (tp) REVERT: D 66 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8457 (mp) outliers start: 19 outliers final: 16 residues processed: 167 average time/residue: 0.1815 time to fit residues: 40.5528 Evaluate side-chains 168 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN D 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.144318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112346 restraints weight = 11592.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115258 restraints weight = 6734.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117240 restraints weight = 4783.851| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6840 Z= 0.222 Angle : 0.690 12.781 9259 Z= 0.330 Chirality : 0.039 0.158 1071 Planarity : 0.004 0.048 1110 Dihedral : 9.390 86.369 1153 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.75 % Favored : 93.12 % Rotamer: Outliers : 3.24 % Allowed : 27.29 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.55 (0.31), residues: 800 helix: 1.43 (0.23), residues: 530 sheet: 0.08 (0.85), residues: 38 loop : -2.15 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 4 HIS 0.004 0.001 HIS C 237 PHE 0.013 0.001 PHE C 118 TYR 0.023 0.001 TYR C 199 ARG 0.005 0.000 ARG B 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2206.00 seconds wall clock time: 41 minutes 19.75 seconds (2479.75 seconds total)