Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 22:53:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8j_15231/08_2023/8a8j_15231_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8j_15231/08_2023/8a8j_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_15231/08_2023/8a8j_15231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8j_15231/08_2023/8a8j_15231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8j_15231/08_2023/8a8j_15231_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8j_15231/08_2023/8a8j_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-1.21rc1-5044/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: 4.97, per 1000 atoms: 0.81 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: 2.54 Conformation dependent library (CDL) restraints added in 1.3 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: 2.32 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: 1.86 Time building geometry restraints manager: 2.71 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: 3068 17.62 - 35.24: 384 35.24 - 52.86: 195 52.86 - 70.48: 31 70.48 - 88.10: 6 Dihedral angle restraints: 3684 sinusoidal: 1750 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 3681 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.760 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.330 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- 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 : 18.758 88.099 2446 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 % 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 *********************** 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 : 0.639 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.3919 time to fit residues: 24.4044 Evaluate side-chains 46 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.665 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8597 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.7998 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6353 Z= 0.167 Angle : 0.517 5.485 8773 Z= 0.272 Chirality : 0.036 0.129 973 Planarity : 0.005 0.034 1011 Dihedral : 19.521 59.941 1163 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.95 % 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: 1.35 (0.32), residues: 275 sheet: 1.21 (0.47), residues: 124 loop : -1.67 (0.35), residues: 280 *********************** 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 50 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.649 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 49 average time/residue: 0.3380 time to fit residues: 20.0119 Evaluate side-chains 47 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.638 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1818 time to fit residues: 1.7734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.8076 moved from start: 0.1101 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= 0.273 Angle : 0.597 6.300 8773 Z= 0.301 Chirality : 0.039 0.143 973 Planarity : 0.005 0.037 1011 Dihedral : 19.645 59.828 1163 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.32), residues: 679 helix: 1.17 (0.33), residues: 271 sheet: 1.20 (0.46), residues: 124 loop : -1.82 (0.34), residues: 284 *********************** 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 48 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.637 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.3969 time to fit residues: 22.5227 Evaluate side-chains 46 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.633 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 0.2980 chunk 60 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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: 0.8025 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 6353 Z= 0.170 Angle : 0.494 5.567 8773 Z= 0.257 Chirality : 0.036 0.139 973 Planarity : 0.005 0.035 1011 Dihedral : 19.556 59.566 1163 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.38 % 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: 1.38 (0.33), residues: 269 sheet: 1.44 (0.46), residues: 124 loop : -1.72 (0.34), residues: 286 *********************** 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 47 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.643 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.3804 time to fit residues: 21.1788 Evaluate side-chains 44 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.592 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.8069 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 6353 Z= 0.264 Angle : 0.557 5.134 8773 Z= 0.285 Chirality : 0.038 0.147 973 Planarity : 0.005 0.036 1011 Dihedral : 19.593 59.891 1163 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 0.95 % 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: 0.11 (0.32), residues: 679 helix: 1.26 (0.33), residues: 269 sheet: 1.40 (0.46), residues: 124 loop : -1.78 (0.34), residues: 286 *********************** 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 51 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.641 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.3831 time to fit residues: 21.8360 Evaluate side-chains 47 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2808 time to fit residues: 1.4988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.0170 chunk 67 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.0222 ------------------------------------------------------------------------------- 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: 0.8058 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 6353 Z= 0.225 Angle : 0.553 11.437 8773 Z= 0.278 Chirality : 0.037 0.128 973 Planarity : 0.005 0.036 1011 Dihedral : 19.586 59.832 1163 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.38 % 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: 0.15 (0.33), residues: 679 helix: 1.27 (0.33), residues: 269 sheet: 1.17 (0.45), residues: 134 loop : -1.71 (0.35), residues: 276 *********************** 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 48 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.573 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.4097 time to fit residues: 22.6431 Evaluate side-chains 43 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.642 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0604 time to fit residues: 0.9755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.0470 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.9882 ------------------------------------------------------------------------------- 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: 0.8057 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 6353 Z= 0.221 Angle : 0.542 7.960 8773 Z= 0.276 Chirality : 0.037 0.152 973 Planarity : 0.005 0.036 1011 Dihedral : 19.580 59.765 1163 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.57 % 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: 0.14 (0.33), residues: 679 helix: 1.28 (0.33), residues: 269 sheet: 1.45 (0.46), residues: 124 loop : -1.77 (0.34), residues: 286 *********************** 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 45 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.586 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 0.4031 time to fit residues: 20.8597 Evaluate side-chains 42 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.628 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0591 time to fit residues: 0.9447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 37 optimal weight: 0.0870 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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: 0.8003 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 6353 Z= 0.150 Angle : 0.478 7.536 8773 Z= 0.248 Chirality : 0.035 0.135 973 Planarity : 0.005 0.035 1011 Dihedral : 19.509 59.969 1163 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.19 % 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: 0.36 (0.33), residues: 679 helix: 1.40 (0.33), residues: 271 sheet: 1.34 (0.44), residues: 134 loop : -1.60 (0.35), residues: 274 *********************** 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 45 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.583 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.3800 time to fit residues: 20.4180 Evaluate side-chains 43 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.662 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.0170 chunk 46 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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: 0.8019 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 6353 Z= 0.172 Angle : 0.501 7.126 8773 Z= 0.256 Chirality : 0.036 0.148 973 Planarity : 0.005 0.038 1011 Dihedral : 19.486 59.463 1163 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 0.19 % 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: 0.36 (0.33), residues: 679 helix: 1.39 (0.33), residues: 271 sheet: 1.33 (0.44), residues: 134 loop : -1.59 (0.35), residues: 274 *********************** 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 44 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.617 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.4128 time to fit residues: 21.3852 Evaluate side-chains 43 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- 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: 0.8048 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6353 Z= 0.215 Angle : 0.540 7.097 8773 Z= 0.274 Chirality : 0.037 0.157 973 Planarity : 0.005 0.039 1011 Dihedral : 19.541 59.840 1163 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 0.57 % 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: 1.32 (0.33), residues: 269 sheet: 1.34 (0.45), residues: 134 loop : -1.64 (0.35), residues: 276 ********************** 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 46 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.644 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 44 average time/residue: 0.4020 time to fit residues: 20.8890 Evaluate side-chains 46 residues out of total 525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.642 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0593 time to fit residues: 1.0876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 0.0670 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 0.9720 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.166991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.132128 restraints weight = 12988.679| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.90 r_work: 0.3302 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6353 Z= 0.219 Angle : 0.546 7.000 8773 Z= 0.278 Chirality : 0.037 0.165 973 Planarity : 0.005 0.040 1011 Dihedral : 19.539 59.962 1163 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.19 % 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: 0.20 (0.33), residues: 679 helix: 1.24 (0.33), residues: 269 sheet: 1.32 (0.45), residues: 134 loop : -1.67 (0.35), residues: 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1570.49 seconds wall clock time: 28 minutes 42.53 seconds (1722.53 seconds total)