Starting phenix.real_space_refine on Thu Jan 18 15:25:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f04_31396/01_2024/7f04_31396_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f04_31396/01_2024/7f04_31396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f04_31396/01_2024/7f04_31396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f04_31396/01_2024/7f04_31396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f04_31396/01_2024/7f04_31396_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f04_31396/01_2024/7f04_31396_updated.pdb" } resolution = 2.86 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= 0.002 sd= 0.042 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 7 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 5832 2.51 5 N 1519 2.21 5 O 1527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 121": "OD1" <-> "OD2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8934 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "B" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1848 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "F" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.34, per 1000 atoms: 0.60 Number of scatterers: 8934 At special positions: 0 Unit cell: (98.176, 96.512, 118.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 46 16.00 P 7 15.00 Mg 2 11.99 O 1527 8.00 N 1519 7.00 C 5832 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 2.0 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 6 sheets defined 61.0% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 40 through 48 Processing helix chain 'A' and resid 65 through 68 No H-bonds generated for 'chain 'A' and resid 65 through 68' Processing helix chain 'A' and resid 71 through 74 No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 91 through 98 removed outlier: 3.871A pdb=" N TYR A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 131 through 141 removed outlier: 3.900A pdb=" N ALA A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TRP A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'B' and resid 3 through 14 removed outlier: 3.573A pdb=" N ALA B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 39 removed outlier: 3.734A pdb=" N ALA B 22 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Proline residue: B 24 - end of helix Proline residue: B 36 - end of helix removed outlier: 3.957A pdb=" N ILE B 39 " --> pdb=" O PRO B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 75 Proline residue: B 51 - end of helix removed outlier: 3.617A pdb=" N GLU B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 118 removed outlier: 4.140A pdb=" N LEU B 106 " --> pdb=" O MET B 102 " (cutoff:3.500A) Proline residue: B 107 - end of helix Proline residue: B 113 - end of helix removed outlier: 3.968A pdb=" N MET B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 142 Proline residue: B 138 - end of helix removed outlier: 3.790A pdb=" N GLY B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 167 through 184 removed outlier: 3.541A pdb=" N ILE B 170 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Proline residue: B 171 - end of helix removed outlier: 3.543A pdb=" N THR B 177 " --> pdb=" O ILE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 219 removed outlier: 3.629A pdb=" N THR B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Proline residue: B 208 - end of helix Processing helix chain 'C' and resid 12 through 39 removed outlier: 3.629A pdb=" N ILE C 22 " --> pdb=" O GLY C 19 " (cutoff:3.500A) Proline residue: C 23 - end of helix removed outlier: 3.507A pdb=" N ILE C 38 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP C 39 " --> pdb=" O GLY C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 83 removed outlier: 3.642A pdb=" N ILE C 56 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR C 58 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL C 61 " --> pdb=" O TYR C 58 " (cutoff:3.500A) Proline residue: C 62 - end of helix removed outlier: 3.689A pdb=" N SER C 67 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C 83 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 119 removed outlier: 3.559A pdb=" N VAL C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Proline residue: C 98 - end of helix Proline residue: C 117 - end of helix Processing helix chain 'C' and resid 127 through 147 Processing helix chain 'C' and resid 157 through 184 Proline residue: C 171 - end of helix removed outlier: 3.570A pdb=" N HIS C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 228 Processing helix chain 'C' and resid 233 through 236 Processing helix chain 'D' and resid 18 through 52 Proline residue: D 31 - end of helix Processing helix chain 'E' and resid 40 through 47 Processing helix chain 'E' and resid 69 through 72 No H-bonds generated for 'chain 'E' and resid 69 through 72' Processing helix chain 'E' and resid 91 through 98 removed outlier: 3.971A pdb=" N TYR E 98 " --> pdb=" O ASN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 114 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 129 through 141 removed outlier: 4.077A pdb=" N ALA E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG E 139 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TRP E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 175 removed outlier: 3.540A pdb=" N GLN E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR E 173 " --> pdb=" O MET E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 193 No H-bonds generated for 'chain 'E' and resid 191 through 193' Processing helix chain 'F' and resid 3 through 16 Processing helix chain 'F' and resid 22 through 38 removed outlier: 3.944A pdb=" N PHE F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) Proline residue: F 36 - end of helix Processing helix chain 'F' and resid 43 through 68 Proline residue: F 51 - end of helix removed outlier: 4.086A pdb=" N GLU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ARG F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 74 No H-bonds generated for 'chain 'F' and resid 71 through 74' Processing helix chain 'F' and resid 89 through 110 removed outlier: 3.612A pdb=" N VAL F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU F 106 " --> pdb=" O MET F 102 " (cutoff:3.500A) Proline residue: F 107 - end of helix Processing helix chain 'F' and resid 112 through 118 Processing helix chain 'F' and resid 123 through 151 Proline residue: F 138 - end of helix Proline residue: F 146 - end of helix Processing helix chain 'F' and resid 161 through 164 No H-bonds generated for 'chain 'F' and resid 161 through 164' Processing helix chain 'F' and resid 167 through 184 Proline residue: F 171 - end of helix Processing helix chain 'F' and resid 190 through 219 removed outlier: 3.564A pdb=" N LEU F 206 " --> pdb=" O GLY F 202 " (cutoff:3.500A) Proline residue: F 208 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'A' and resid 195 through 197 removed outlier: 6.383A pdb=" N LEU A 77 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASP A 151 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 79 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 9 through 11 removed outlier: 6.693A pdb=" N ARG A 11 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 2 through 5 Processing sheet with id= E, first strand: chain 'E' and resid 195 through 198 removed outlier: 6.086A pdb=" N VAL E 179 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE E 32 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU E 181 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU E 77 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP E 151 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE E 79 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.615A pdb=" N PHE E 17 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG E 11 " --> pdb=" O THR E 15 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THR E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 2856 1.36 - 1.53: 5918 1.53 - 1.71: 287 1.71 - 1.88: 87 1.88 - 2.06: 4 Bond restraints: 9152 Sorted by residual: bond pdb=" C4 ATP A 301 " pdb=" C5 ATP A 301 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.01e+01 bond pdb=" C4 ATP E 301 " pdb=" C5 ATP E 301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.96e+01 bond pdb=" C5 ATP E 301 " pdb=" C6 ATP E 301 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C5 ATP A 301 " pdb=" C6 ATP A 301 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.19e+01 bond pdb=" C8 ATP E 301 " pdb=" N7 ATP E 301 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.16e+01 ... (remaining 9147 not shown) Histogram of bond angle deviations from ideal: 89.09 - 107.05: 361 107.05 - 125.02: 11856 125.02 - 142.98: 287 142.98 - 160.94: 0 160.94 - 178.91: 2 Bond angle restraints: 12506 Sorted by residual: angle pdb=" PB ATP A 301 " pdb=" O3B ATP A 301 " pdb=" PG ATP A 301 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP E 301 " pdb=" O3B ATP E 301 " pdb=" PG ATP E 301 " ideal model delta sigma weight residual 139.87 121.32 18.55 1.00e+00 1.00e+00 3.44e+02 angle pdb=" PA ATP E 301 " pdb=" O3A ATP E 301 " pdb=" PB ATP E 301 " ideal model delta sigma weight residual 136.83 123.70 13.13 1.00e+00 1.00e+00 1.72e+02 angle pdb=" PA ATP A 301 " pdb=" O3A ATP A 301 " pdb=" PB ATP A 301 " ideal model delta sigma weight residual 136.83 124.75 12.08 1.00e+00 1.00e+00 1.46e+02 angle pdb=" C5 ATP A 301 " pdb=" C4 ATP A 301 " pdb=" N3 ATP A 301 " ideal model delta sigma weight residual 126.80 118.24 8.56 1.00e+00 1.00e+00 7.32e+01 ... (remaining 12501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 4754 15.97 - 31.94: 490 31.94 - 47.91: 112 47.91 - 63.87: 23 63.87 - 79.84: 8 Dihedral angle restraints: 5387 sinusoidal: 2163 harmonic: 3224 Sorted by residual: dihedral pdb=" CA LEU A 127 " pdb=" C LEU A 127 " pdb=" N SER A 128 " pdb=" CA SER A 128 " ideal model delta harmonic sigma weight residual 180.00 -158.04 -21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ILE C 10 " pdb=" C ILE C 10 " pdb=" N PRO C 11 " pdb=" CA PRO C 11 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA LEU C 154 " pdb=" C LEU C 154 " pdb=" N ALA C 155 " pdb=" CA ALA C 155 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 902 0.032 - 0.064: 372 0.064 - 0.096: 122 0.096 - 0.128: 57 0.128 - 0.160: 10 Chirality restraints: 1463 Sorted by residual: chirality pdb=" CB ILE C 10 " pdb=" CA ILE C 10 " pdb=" CG1 ILE C 10 " pdb=" CG2 ILE C 10 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CB THR E 15 " pdb=" CA THR E 15 " pdb=" OG1 THR E 15 " pdb=" CG2 THR E 15 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE A 149 " pdb=" N ILE A 149 " pdb=" C ILE A 149 " pdb=" CB ILE A 149 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 1460 not shown) Planarity restraints: 1529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 112 " -0.075 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO B 113 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 82 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO E 83 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 83 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 83 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 11 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO C 12 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 12 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 12 " 0.023 5.00e-02 4.00e+02 ... (remaining 1526 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.34: 25 2.34 - 2.98: 4378 2.98 - 3.62: 13717 3.62 - 4.26: 21442 4.26 - 4.90: 36215 Nonbonded interactions: 75777 Sorted by model distance: nonbonded pdb="MG MG A 300 " pdb=" O3G ATP A 301 " model vdw 1.706 2.170 nonbonded pdb="MG MG A 300 " pdb=" O2B ATP A 301 " model vdw 1.780 2.170 nonbonded pdb="MG MG E 300 " pdb=" O2B ATP E 301 " model vdw 1.795 2.170 nonbonded pdb=" OG1 THR A 41 " pdb="MG MG A 300 " model vdw 1.985 2.170 nonbonded pdb=" OG1 THR E 41 " pdb="MG MG E 300 " model vdw 2.014 2.170 ... (remaining 75772 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 7.070 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 27.940 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 0.085 9152 Z= 0.331 Angle : 0.801 19.408 12506 Z= 0.492 Chirality : 0.043 0.160 1463 Planarity : 0.006 0.109 1529 Dihedral : 13.871 79.843 3303 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.44 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -0.04 (0.26), residues: 1118 helix: 0.64 (0.20), residues: 693 sheet: -1.34 (0.69), residues: 54 loop : -0.97 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 78 HIS 0.005 0.001 HIS A 73 PHE 0.022 0.001 PHE B 3 TYR 0.016 0.001 TYR C 15 ARG 0.009 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.897 Fit side-chains REVERT: B 2 MET cc_start: 0.5527 (mtm) cc_final: 0.5307 (tpt) REVERT: E 28 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7507 (mm-30) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 1.3348 time to fit residues: 202.8442 Evaluate side-chains 121 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 101 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 HIS A 185 GLN B 17 HIS E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9152 Z= 0.215 Angle : 0.646 7.651 12506 Z= 0.321 Chirality : 0.042 0.180 1463 Planarity : 0.006 0.054 1529 Dihedral : 9.211 81.797 1323 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 1.74 % Allowed : 11.23 % Favored : 87.02 % 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: 0.08 (0.26), residues: 1118 helix: 0.79 (0.20), residues: 694 sheet: -1.20 (0.72), residues: 54 loop : -1.07 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 55 HIS 0.004 0.001 HIS B 100 PHE 0.021 0.001 PHE B 142 TYR 0.013 0.001 TYR C 15 ARG 0.006 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 0.892 Fit side-chains REVERT: A 197 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.8007 (mt) REVERT: B 2 MET cc_start: 0.5546 (mtm) cc_final: 0.5260 (tpt) REVERT: B 199 LEU cc_start: 0.7299 (mp) cc_final: 0.7096 (mp) REVERT: C 8 LEU cc_start: 0.5390 (OUTLIER) cc_final: 0.5118 (mp) REVERT: E 28 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7444 (mm-30) REVERT: E 57 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7031 (pt0) outliers start: 16 outliers final: 6 residues processed: 129 average time/residue: 1.2289 time to fit residues: 169.2750 Evaluate side-chains 130 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain E residue 57 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9152 Z= 0.211 Angle : 0.617 8.422 12506 Z= 0.303 Chirality : 0.041 0.205 1463 Planarity : 0.005 0.041 1529 Dihedral : 9.095 82.300 1323 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 3.27 % Allowed : 12.54 % Favored : 84.19 % 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: 0.29 (0.26), residues: 1118 helix: 1.00 (0.21), residues: 690 sheet: -0.86 (0.75), residues: 50 loop : -1.11 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 55 HIS 0.004 0.001 HIS A 73 PHE 0.019 0.001 PHE B 3 TYR 0.008 0.001 TYR F 192 ARG 0.009 0.000 ARG E 196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 0.993 Fit side-chains REVERT: A 197 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8059 (mt) REVERT: B 2 MET cc_start: 0.5757 (mtm) cc_final: 0.5277 (tpt) REVERT: C 8 LEU cc_start: 0.5431 (OUTLIER) cc_final: 0.5230 (mp) REVERT: E -1 MET cc_start: 0.5017 (OUTLIER) cc_final: 0.4189 (mpp) REVERT: E 28 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7431 (mm-30) REVERT: E 57 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7090 (pt0) REVERT: F 1 MET cc_start: 0.6448 (tmm) cc_final: 0.6196 (ttp) REVERT: F 10 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6870 (mm-30) REVERT: F 16 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.6272 (mtm180) outliers start: 30 outliers final: 10 residues processed: 135 average time/residue: 1.1530 time to fit residues: 166.9261 Evaluate side-chains 135 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain E residue -1 MET Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 165 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 0.0040 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.4770 ------------------------------------------------------------------------------- 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: 0.7935 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9152 Z= 0.170 Angle : 0.600 9.082 12506 Z= 0.291 Chirality : 0.040 0.206 1463 Planarity : 0.005 0.038 1529 Dihedral : 9.029 83.498 1323 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 2.62 % Allowed : 14.94 % Favored : 82.44 % 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: 0.54 (0.26), residues: 1118 helix: 1.20 (0.21), residues: 689 sheet: -0.72 (0.77), residues: 50 loop : -1.00 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 55 HIS 0.003 0.001 HIS B 100 PHE 0.017 0.001 PHE B 3 TYR 0.006 0.001 TYR C 15 ARG 0.007 0.000 ARG E 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 0.904 Fit side-chains REVERT: B 2 MET cc_start: 0.5789 (mtm) cc_final: 0.5216 (tpt) REVERT: C 8 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.5204 (mp) REVERT: C 190 MET cc_start: 0.1899 (pmt) cc_final: 0.1068 (ptp) REVERT: E 28 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7495 (mm-30) REVERT: E 57 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7029 (pt0) REVERT: F 10 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6896 (mm-30) REVERT: F 16 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.6079 (mtm180) REVERT: F 117 MET cc_start: 0.6969 (mtp) cc_final: 0.6707 (tpp) outliers start: 24 outliers final: 7 residues processed: 132 average time/residue: 1.1155 time to fit residues: 158.3805 Evaluate side-chains 126 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9152 Z= 0.262 Angle : 0.637 8.861 12506 Z= 0.310 Chirality : 0.043 0.240 1463 Planarity : 0.005 0.048 1529 Dihedral : 9.226 81.775 1323 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.44 % Favored : 93.38 % Rotamer: Outliers : 4.14 % Allowed : 14.72 % Favored : 81.13 % 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: 0.45 (0.26), residues: 1118 helix: 1.10 (0.21), residues: 701 sheet: -0.76 (0.75), residues: 50 loop : -1.04 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 55 HIS 0.005 0.001 HIS A 73 PHE 0.016 0.001 PHE B 3 TYR 0.011 0.001 TYR F 192 ARG 0.007 0.000 ARG E 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 0.999 Fit side-chains REVERT: B 2 MET cc_start: 0.5828 (mtm) cc_final: 0.5211 (tpt) REVERT: E -1 MET cc_start: 0.5087 (OUTLIER) cc_final: 0.4233 (mpp) REVERT: E 28 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7488 (mm-30) REVERT: E 57 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7008 (pt0) REVERT: F 16 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.6262 (mtm180) REVERT: F 117 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6686 (tpp) outliers start: 38 outliers final: 18 residues processed: 144 average time/residue: 1.1130 time to fit residues: 172.2369 Evaluate side-chains 141 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain E residue -1 MET Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 205 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9152 Z= 0.307 Angle : 0.665 8.509 12506 Z= 0.325 Chirality : 0.044 0.234 1463 Planarity : 0.006 0.053 1529 Dihedral : 9.350 83.282 1323 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.07 % Favored : 92.75 % Rotamer: Outliers : 3.93 % Allowed : 15.70 % Favored : 80.37 % 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 (0.26), residues: 1118 helix: 0.98 (0.20), residues: 698 sheet: -0.69 (0.75), residues: 50 loop : -1.11 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 101 HIS 0.004 0.001 HIS A 73 PHE 0.013 0.002 PHE B 3 TYR 0.013 0.001 TYR F 192 ARG 0.006 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 121 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7789 (tp30) cc_final: 0.7563 (tp30) REVERT: B 2 MET cc_start: 0.6011 (mtm) cc_final: 0.5281 (tpt) REVERT: D 9 ASN cc_start: 0.5000 (OUTLIER) cc_final: 0.4647 (p0) REVERT: E -1 MET cc_start: 0.5201 (OUTLIER) cc_final: 0.4327 (mpp) REVERT: E 28 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7523 (mm-30) REVERT: E 57 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6621 (pm20) REVERT: F 117 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6739 (tpp) outliers start: 36 outliers final: 18 residues processed: 137 average time/residue: 1.2301 time to fit residues: 180.0555 Evaluate side-chains 140 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain E residue -1 MET Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 165 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.0070 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 17 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9152 Z= 0.194 Angle : 0.613 8.515 12506 Z= 0.298 Chirality : 0.041 0.246 1463 Planarity : 0.005 0.057 1529 Dihedral : 9.183 84.612 1323 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 2.62 % Allowed : 17.67 % Favored : 79.72 % 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: 0.53 (0.26), residues: 1118 helix: 1.16 (0.21), residues: 700 sheet: -0.74 (0.76), residues: 50 loop : -1.00 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 55 HIS 0.003 0.001 HIS A 73 PHE 0.015 0.001 PHE B 3 TYR 0.008 0.001 TYR F 192 ARG 0.006 0.000 ARG E 196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.979 Fit side-chains REVERT: B 2 MET cc_start: 0.5840 (mtm) cc_final: 0.5130 (tpt) REVERT: C 190 MET cc_start: 0.1811 (pmt) cc_final: 0.1189 (ptp) REVERT: E 28 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7522 (mm-30) REVERT: E 57 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6570 (pm20) REVERT: E 175 GLN cc_start: 0.6775 (pt0) cc_final: 0.6540 (mp10) REVERT: F 16 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.6257 (mtm180) REVERT: F 117 MET cc_start: 0.6948 (mtp) cc_final: 0.6702 (tpp) outliers start: 24 outliers final: 15 residues processed: 130 average time/residue: 1.1998 time to fit residues: 166.9107 Evaluate side-chains 130 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 165 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 0.0770 chunk 10 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 17 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9152 Z= 0.159 Angle : 0.588 8.364 12506 Z= 0.286 Chirality : 0.040 0.245 1463 Planarity : 0.005 0.057 1529 Dihedral : 9.023 85.902 1323 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.37 % Favored : 94.54 % Rotamer: Outliers : 2.07 % Allowed : 19.08 % Favored : 78.84 % 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: 0.67 (0.26), residues: 1118 helix: 1.29 (0.21), residues: 689 sheet: -0.66 (0.77), residues: 50 loop : -0.92 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 179 HIS 0.003 0.001 HIS E 73 PHE 0.014 0.001 PHE B 3 TYR 0.007 0.001 TYR F 192 ARG 0.007 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 1.007 Fit side-chains REVERT: B 2 MET cc_start: 0.5528 (mtm) cc_final: 0.4892 (tpt) REVERT: C 190 MET cc_start: 0.1917 (pmt) cc_final: 0.1455 (ptp) REVERT: E 28 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7516 (mm-30) REVERT: E 57 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7001 (pt0) REVERT: E 175 GLN cc_start: 0.6678 (pt0) cc_final: 0.6431 (mp10) REVERT: F 10 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6887 (mm-30) REVERT: F 16 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.6259 (mtm180) REVERT: F 117 MET cc_start: 0.6976 (mtp) cc_final: 0.6736 (tpp) outliers start: 19 outliers final: 14 residues processed: 134 average time/residue: 1.1996 time to fit residues: 172.3530 Evaluate side-chains 131 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 165 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 17 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9152 Z= 0.207 Angle : 0.607 8.612 12506 Z= 0.296 Chirality : 0.042 0.239 1463 Planarity : 0.005 0.058 1529 Dihedral : 9.037 86.056 1323 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 2.29 % Allowed : 18.97 % Favored : 78.74 % 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: 0.64 (0.26), residues: 1118 helix: 1.25 (0.21), residues: 690 sheet: -0.61 (0.77), residues: 50 loop : -0.91 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 55 HIS 0.003 0.001 HIS E 96 PHE 0.015 0.001 PHE B 3 TYR 0.011 0.001 TYR F 192 ARG 0.004 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 1.020 Fit side-chains REVERT: B 1 MET cc_start: 0.4662 (mtt) cc_final: 0.4374 (mtt) REVERT: B 2 MET cc_start: 0.5622 (mtm) cc_final: 0.4944 (tpt) REVERT: C 190 MET cc_start: 0.1989 (pmt) cc_final: 0.1472 (ptp) REVERT: E -1 MET cc_start: 0.5000 (OUTLIER) cc_final: 0.4141 (mpp) REVERT: E 28 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7471 (mm-30) REVERT: E 57 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7007 (pt0) REVERT: E 175 GLN cc_start: 0.6681 (pt0) cc_final: 0.6426 (mp10) REVERT: F 10 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6922 (mm-30) REVERT: F 16 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.6218 (mtm180) REVERT: F 117 MET cc_start: 0.6966 (mtp) cc_final: 0.6713 (tpp) outliers start: 21 outliers final: 16 residues processed: 128 average time/residue: 1.1944 time to fit residues: 163.8472 Evaluate side-chains 134 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain E residue -1 MET Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 0.0000 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 17 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9152 Z= 0.225 Angle : 0.622 8.989 12506 Z= 0.304 Chirality : 0.042 0.240 1463 Planarity : 0.005 0.058 1529 Dihedral : 9.088 87.398 1323 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 2.18 % Allowed : 19.19 % Favored : 78.63 % 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: 0.61 (0.26), residues: 1118 helix: 1.20 (0.21), residues: 702 sheet: -0.53 (0.78), residues: 50 loop : -0.94 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 55 HIS 0.003 0.001 HIS E 96 PHE 0.015 0.001 PHE B 3 TYR 0.012 0.001 TYR F 192 ARG 0.009 0.000 ARG E 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.003 Fit side-chains REVERT: B 1 MET cc_start: 0.4716 (mtt) cc_final: 0.4515 (mtt) REVERT: B 2 MET cc_start: 0.5580 (mtm) cc_final: 0.4864 (tpt) REVERT: C 190 MET cc_start: 0.2015 (pmt) cc_final: 0.1477 (ptp) REVERT: E -1 MET cc_start: 0.5023 (OUTLIER) cc_final: 0.4162 (mpp) REVERT: E 28 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7479 (mm-30) REVERT: E 57 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6567 (pm20) REVERT: E 175 GLN cc_start: 0.6699 (pt0) cc_final: 0.6458 (mp10) REVERT: F 10 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6866 (mm-30) REVERT: F 16 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.6216 (mtm180) REVERT: F 117 MET cc_start: 0.6971 (mtp) cc_final: 0.6714 (tpp) outliers start: 20 outliers final: 15 residues processed: 129 average time/residue: 1.2139 time to fit residues: 167.6833 Evaluate side-chains 132 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain E residue -1 MET Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 17 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.152728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138195 restraints weight = 9500.800| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.32 r_work: 0.3466 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9152 Z= 0.195 Angle : 0.610 8.964 12506 Z= 0.296 Chirality : 0.041 0.241 1463 Planarity : 0.005 0.057 1529 Dihedral : 9.036 88.674 1323 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.72 % Favored : 94.19 % Rotamer: Outliers : 2.29 % Allowed : 19.52 % Favored : 78.19 % 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: 0.64 (0.26), residues: 1118 helix: 1.24 (0.21), residues: 690 sheet: -0.46 (0.80), residues: 50 loop : -0.90 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 55 HIS 0.003 0.001 HIS B 100 PHE 0.020 0.001 PHE B 3 TYR 0.013 0.001 TYR F 192 ARG 0.004 0.000 ARG D 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3321.39 seconds wall clock time: 59 minutes 53.13 seconds (3593.13 seconds total)