Starting phenix.real_space_refine on Tue Feb 13 12:35:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8j_15231/02_2024/8a8j_15231_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8j_15231/02_2024/8a8j_15231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8j_15231/02_2024/8a8j_15231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8j_15231/02_2024/8a8j_15231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8j_15231/02_2024/8a8j_15231_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8j_15231/02_2024/8a8j_15231_updated.pdb" } resolution = 3.1 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= 0.077 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: 6 Type Number sf(0) Gaussians P 44 5.49 5 Mg 2 5.21 5 S 6 5.16 5 C 3748 2.51 5 N 1173 2.21 5 O 1186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6159 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2656 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2660 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 341, 2652 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 341, 2652 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2692 Chain: "X" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "Y" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 388 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.93, per 1000 atoms: 0.80 Number of scatterers: 6159 At special positions: 0 Unit cell: (77.4, 89.44, 94.6, 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 6 16.00 P 44 15.00 Mg 2 11.99 O 1186 8.00 N 1173 7.00 C 3748 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: 2.51 Conformation dependent library (CDL) restraints added in 1.6 seconds 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 8 sheets defined 42.7% alpha, 15.4% beta 12 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.692A pdb=" N ARG A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 161 Processing helix chain 'A' and resid 168 through 203 removed outlier: 3.710A pdb=" N ASP A 172 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 174 " --> pdb=" O TRP A 171 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 175 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 177 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 191 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 193 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA A 194 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 229 through 235 Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 262 through 284 Processing helix chain 'A' and resid 301 through 313 removed outlier: 4.373A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 46 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.936A pdb=" N GLU B 106 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 119 Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.661A pdb=" N LEU B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 163 removed outlier: 3.851A pdb=" N ALA B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 204 removed outlier: 3.610A pdb=" N ASP B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) Proline residue: B 195 - end of helix removed outlier: 4.250A pdb=" N ALA B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 235 removed outlier: 3.867A pdb=" N ALA B 227 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 262 through 284 removed outlier: 3.925A pdb=" N THR B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 282 " --> pdb=" O ARG B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 313 removed outlier: 3.599A pdb=" N GLN B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 24 through 29 removed outlier: 3.677A pdb=" N LEU A 319 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU A 290 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ALA A 320 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 292 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.623A pdb=" N LEU A 5 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 209 through 214 Processing sheet with id= D, first strand: chain 'A' and resid 331 through 334 Processing sheet with id= E, first strand: chain 'B' and resid 24 through 29 removed outlier: 3.718A pdb=" N ALA B 317 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 319 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 290 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ALA B 320 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL B 292 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 92 through 94 removed outlier: 3.548A pdb=" N ALA B 66 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 5 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU B 73 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU B 3 " --> pdb=" O GLU B 73 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 209 through 214 Processing sheet with id= H, first strand: chain 'B' and resid 332 through 334 removed outlier: 3.655A pdb=" N SER B 332 " --> pdb=" O LEU B 339 " (cutoff:3.500A) 235 hydrogen bonds defined for protein. 599 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1694 1.33 - 1.45: 1156 1.45 - 1.57: 3409 1.57 - 1.69: 84 1.69 - 1.81: 10 Bond restraints: 6353 Sorted by residual: bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.694 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" O5' ANP B 901 " pdb=" PA ANP B 901 " ideal model delta sigma weight residual 1.655 1.573 0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 6348 not shown) Histogram of bond angle deviations from ideal: 100.80 - 107.44: 474 107.44 - 114.07: 3521 114.07 - 120.71: 2705 120.71 - 127.35: 1952 127.35 - 133.98: 121 Bond angle restraints: 8773 Sorted by residual: angle pdb=" PB ANP B 901 " pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 126.95 112.61 14.34 3.00e+00 1.11e-01 2.29e+01 angle pdb=" PB ANP A 901 " pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 126.95 112.74 14.21 3.00e+00 1.11e-01 2.24e+01 angle pdb=" O1B ANP A 901 " pdb=" PB ANP A 901 " pdb=" O2B ANP A 901 " ideal model delta sigma weight residual 120.08 109.17 10.91 3.00e+00 1.11e-01 1.32e+01 angle pdb=" O1B ANP B 901 " pdb=" PB ANP B 901 " pdb=" O2B ANP B 901 " ideal model delta sigma weight residual 120.08 109.51 10.57 3.00e+00 1.11e-01 1.24e+01 angle pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " pdb=" O2G ANP A 901 " ideal model delta sigma weight residual 101.05 110.86 -9.81 3.00e+00 1.11e-01 1.07e+01 ... (remaining 8768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 3096 17.62 - 35.24: 413 35.24 - 52.86: 204 52.86 - 70.48: 37 70.48 - 88.10: 14 Dihedral angle restraints: 3764 sinusoidal: 1830 harmonic: 1934 Sorted by residual: dihedral pdb=" CG ARG A 192 " pdb=" CD ARG A 192 " pdb=" NE ARG A 192 " pdb=" CZ ARG A 192 " ideal model delta sinusoidal sigma weight residual -180.00 -135.54 -44.46 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA GLN A 8 " pdb=" C GLN A 8 " pdb=" N ARG A 9 " pdb=" CA ARG A 9 " ideal model delta harmonic sigma weight residual 180.00 163.97 16.03 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" N ARG B 198 " pdb=" CA BARG B 198 " pdb=" CB BARG B 198 " pdb=" CG BARG B 198 " ideal model delta sinusoidal sigma weight residual -60.00 -114.43 54.43 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 3761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 868 0.056 - 0.112: 90 0.112 - 0.169: 13 0.169 - 0.225: 0 0.225 - 0.281: 2 Chirality restraints: 973 Sorted by residual: chirality pdb=" C3' ANP A 901 " pdb=" C2' ANP A 901 " pdb=" C4' ANP A 901 " pdb=" O3' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLU A 294 " pdb=" N GLU A 294 " pdb=" C GLU A 294 " pdb=" CB GLU A 294 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 970 not shown) Planarity restraints: 1011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 86 " 0.039 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO B 87 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 241 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 242 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 242 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 242 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 114 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO B 115 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " -0.018 5.00e-02 4.00e+02 ... (remaining 1008 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 25 2.59 - 3.17: 4357 3.17 - 3.74: 8496 3.74 - 4.32: 11977 4.32 - 4.90: 20277 Nonbonded interactions: 45132 Sorted by model distance: nonbonded pdb=" O2G ANP A 901 " pdb="MG MG A 902 " model vdw 2.009 2.170 nonbonded pdb=" OG1 THR B 37 " pdb="MG MG B 902 " model vdw 2.032 2.170 nonbonded pdb=" O2G ANP B 901 " pdb="MG MG B 902 " model vdw 2.048 2.170 nonbonded pdb=" O1B ANP A 901 " pdb=" O2G ANP A 901 " model vdw 2.150 3.040 nonbonded pdb=" O1B ANP B 901 " pdb=" O2G ANP B 901 " model vdw 2.155 3.040 ... (remaining 45127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 74 or (resid 75 and (name N or name CA or name C \ or name O or name CB )) or resid 76 through 197 or resid 199 through 341 or res \ id 901 through 902)) selection = (chain 'B' and (resid 1 through 197 or resid 199 through 341 or resid 901 throug \ h 902)) } 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=0.50 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: 1.860 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: 7.680 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.200 Find NCS groups from input model: 0.330 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 6353 Z= 0.283 Angle : 0.706 14.342 8773 Z= 0.316 Chirality : 0.039 0.281 973 Planarity : 0.005 0.058 1011 Dihedral : 19.597 88.099 2526 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.19 % Allowed : 0.76 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.33), residues: 679 helix: 1.46 (0.32), residues: 275 sheet: 0.34 (0.45), residues: 138 loop : -1.55 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.005 0.001 HIS A 277 PHE 0.005 0.001 PHE A 259 TYR 0.009 0.001 TYR B 150 ARG 0.009 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.568 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.3926 time to fit residues: 24.3710 Evaluate side-chains 46 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.0980 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6353 Z= 0.165 Angle : 0.522 6.003 8773 Z= 0.272 Chirality : 0.036 0.128 973 Planarity : 0.005 0.034 1011 Dihedral : 20.178 84.921 1243 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.95 % Allowed : 4.39 % Favored : 94.66 % 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: 0.24 (0.33), residues: 679 helix: 1.40 (0.32), residues: 275 sheet: 1.20 (0.47), residues: 124 loop : -1.67 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 171 HIS 0.004 0.001 HIS A 277 PHE 0.005 0.001 PHE A 139 TYR 0.007 0.001 TYR B 150 ARG 0.009 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.668 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.3304 time to fit residues: 20.0701 Evaluate side-chains 48 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 0.0030 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS B 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6353 Z= 0.164 Angle : 0.493 5.391 8773 Z= 0.255 Chirality : 0.036 0.138 973 Planarity : 0.004 0.034 1011 Dihedral : 19.770 88.345 1243 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.76 % Allowed : 6.30 % Favored : 92.94 % 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: 0.32 (0.33), residues: 679 helix: 1.35 (0.33), residues: 275 sheet: 1.11 (0.45), residues: 134 loop : -1.52 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.004 0.001 HIS A 277 PHE 0.004 0.001 PHE A 139 TYR 0.008 0.001 TYR B 150 ARG 0.007 0.000 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.648 Fit side-chains REVERT: A 308 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7909 (mt) outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.3569 time to fit residues: 19.6491 Evaluate side-chains 45 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6353 Z= 0.164 Angle : 0.481 5.305 8773 Z= 0.250 Chirality : 0.035 0.126 973 Planarity : 0.004 0.033 1011 Dihedral : 19.601 87.894 1243 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.15 % Allowed : 9.35 % Favored : 89.50 % 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: 0.41 (0.33), residues: 679 helix: 1.46 (0.33), residues: 271 sheet: 1.25 (0.45), residues: 134 loop : -1.52 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 67 HIS 0.004 0.001 HIS A 277 PHE 0.004 0.001 PHE A 139 TYR 0.008 0.001 TYR B 150 ARG 0.007 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.618 Fit side-chains REVERT: A 308 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7848 (mt) REVERT: B 339 LEU cc_start: 0.7654 (pt) cc_final: 0.7217 (tp) outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.3317 time to fit residues: 19.2264 Evaluate side-chains 44 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS B 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6353 Z= 0.359 Angle : 0.632 6.248 8773 Z= 0.317 Chirality : 0.041 0.136 973 Planarity : 0.005 0.041 1011 Dihedral : 19.731 88.012 1243 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.34 % Allowed : 11.26 % Favored : 87.40 % 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 (0.32), residues: 679 helix: 1.15 (0.33), residues: 269 sheet: 1.39 (0.47), residues: 124 loop : -1.83 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 295 HIS 0.010 0.002 HIS A 277 PHE 0.009 0.001 PHE B 193 TYR 0.013 0.002 TYR B 150 ARG 0.008 0.001 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.670 Fit side-chains REVERT: A 339 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6797 (pp) REVERT: B 122 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8464 (pp) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.3700 time to fit residues: 22.6175 Evaluate side-chains 50 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.0060 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS B 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6353 Z= 0.154 Angle : 0.475 5.682 8773 Z= 0.249 Chirality : 0.035 0.128 973 Planarity : 0.004 0.035 1011 Dihedral : 19.663 88.809 1243 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.53 % Allowed : 12.40 % Favored : 86.07 % 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: 0.29 (0.33), residues: 679 helix: 1.40 (0.33), residues: 269 sheet: 1.26 (0.45), residues: 134 loop : -1.65 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 67 HIS 0.004 0.001 HIS A 277 PHE 0.003 0.001 PHE A 139 TYR 0.008 0.001 TYR B 150 ARG 0.008 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.572 Fit side-chains REVERT: A 339 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6709 (pp) REVERT: B 122 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8358 (pp) REVERT: B 339 LEU cc_start: 0.7665 (pt) cc_final: 0.7251 (tp) outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 0.3550 time to fit residues: 20.6008 Evaluate side-chains 46 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.0000 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6353 Z= 0.231 Angle : 0.533 6.053 8773 Z= 0.274 Chirality : 0.037 0.139 973 Planarity : 0.005 0.036 1011 Dihedral : 19.672 89.316 1243 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.72 % Allowed : 12.21 % Favored : 86.07 % 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: 0.21 (0.33), residues: 679 helix: 1.34 (0.33), residues: 269 sheet: 1.22 (0.45), residues: 134 loop : -1.71 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 171 HIS 0.007 0.001 HIS A 277 PHE 0.006 0.001 PHE A 193 TYR 0.010 0.001 TYR B 150 ARG 0.008 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.671 Fit side-chains REVERT: A 339 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6725 (pp) REVERT: B 122 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8417 (pp) REVERT: B 339 LEU cc_start: 0.7726 (pt) cc_final: 0.7289 (tp) outliers start: 8 outliers final: 5 residues processed: 46 average time/residue: 0.3741 time to fit residues: 20.3329 Evaluate side-chains 48 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 0.0030 chunk 37 optimal weight: 0.5980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6353 Z= 0.168 Angle : 0.482 5.618 8773 Z= 0.252 Chirality : 0.035 0.141 973 Planarity : 0.005 0.035 1011 Dihedral : 19.627 89.446 1243 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.72 % Allowed : 12.21 % Favored : 86.07 % 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: 0.35 (0.33), residues: 679 helix: 1.45 (0.33), residues: 269 sheet: 1.35 (0.45), residues: 134 loop : -1.66 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 171 HIS 0.004 0.001 HIS A 277 PHE 0.004 0.001 PHE A 139 TYR 0.008 0.001 TYR B 150 ARG 0.008 0.000 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.641 Fit side-chains REVERT: A 308 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7890 (mt) REVERT: A 339 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6723 (pp) REVERT: B 122 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8345 (pp) REVERT: B 339 LEU cc_start: 0.7672 (pt) cc_final: 0.7254 (tp) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 0.3571 time to fit residues: 20.9912 Evaluate side-chains 50 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 62 optimal weight: 0.0870 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 0.0000 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 overall best weight: 0.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6353 Z= 0.140 Angle : 0.470 6.356 8773 Z= 0.245 Chirality : 0.035 0.152 973 Planarity : 0.004 0.034 1011 Dihedral : 19.572 88.791 1243 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.53 % Allowed : 12.60 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.33), residues: 679 helix: 1.50 (0.33), residues: 271 sheet: 1.41 (0.44), residues: 134 loop : -1.58 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 67 HIS 0.003 0.001 HIS A 69 PHE 0.010 0.001 PHE B 11 TYR 0.007 0.001 TYR B 150 ARG 0.009 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.664 Fit side-chains REVERT: A 308 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7878 (mt) REVERT: B 122 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8327 (pp) REVERT: B 339 LEU cc_start: 0.7617 (pt) cc_final: 0.7217 (tp) outliers start: 7 outliers final: 3 residues processed: 47 average time/residue: 0.3492 time to fit residues: 19.6791 Evaluate side-chains 48 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 5 optimal weight: 0.0070 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6353 Z= 0.241 Angle : 0.554 6.890 8773 Z= 0.281 Chirality : 0.038 0.189 973 Planarity : 0.005 0.036 1011 Dihedral : 19.642 88.933 1243 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.34 % Allowed : 12.79 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.33), residues: 679 helix: 1.37 (0.33), residues: 269 sheet: 1.32 (0.45), residues: 134 loop : -1.64 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 105 HIS 0.008 0.002 HIS A 277 PHE 0.006 0.001 PHE A 193 TYR 0.010 0.001 TYR B 150 ARG 0.009 0.000 ARG B 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.561 Fit side-chains REVERT: B 122 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8394 (pp) outliers start: 6 outliers final: 5 residues processed: 46 average time/residue: 0.3749 time to fit residues: 20.4046 Evaluate side-chains 49 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 0.0570 chunk 63 optimal weight: 0.0010 chunk 37 optimal weight: 2.9990 overall best weight: 1.0110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.167616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133523 restraints weight = 13113.606| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.70 r_work: 0.3328 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6353 Z= 0.221 Angle : 0.536 6.980 8773 Z= 0.273 Chirality : 0.037 0.174 973 Planarity : 0.005 0.039 1011 Dihedral : 19.647 89.121 1243 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.53 % Allowed : 12.79 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.33), residues: 679 helix: 1.34 (0.33), residues: 269 sheet: 1.31 (0.45), residues: 134 loop : -1.66 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 105 HIS 0.006 0.001 HIS A 277 PHE 0.006 0.001 PHE A 193 TYR 0.010 0.001 TYR B 150 ARG 0.009 0.000 ARG B 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1595.41 seconds wall clock time: 29 minutes 20.53 seconds (1760.53 seconds total)