Starting phenix.real_space_refine on Tue Feb 13 17:00:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcl_29934/02_2024/8gcl_29934.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcl_29934/02_2024/8gcl_29934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcl_29934/02_2024/8gcl_29934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcl_29934/02_2024/8gcl_29934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcl_29934/02_2024/8gcl_29934.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcl_29934/02_2024/8gcl_29934.pdb" } resolution = 2.89 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= 0.053 sd= 0.213 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4588 2.51 5 N 1172 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 16": "OE1" <-> "OE2" Residue "A PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "B PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C ASP 200": "OD1" <-> "OD2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D ASP 200": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7016 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1754 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 227} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1754 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 227} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1754 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 227} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1754 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 227} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 4.40, per 1000 atoms: 0.63 Number of scatterers: 7016 At special positions: 0 Unit cell: (85.44, 85.44, 66.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1232 8.00 N 1172 7.00 C 4588 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: 2.80 Conformation dependent library (CDL) restraints added in 1.4 seconds 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.550A pdb=" N GLY A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 64 removed outlier: 3.592A pdb=" N ILE A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N HIS A 61 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 78 Processing helix chain 'A' and resid 82 through 108 Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.287A pdb=" N GLY A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 149 removed outlier: 3.684A pdb=" N THR A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.581A pdb=" N GLY A 154 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 180 removed outlier: 3.759A pdb=" N LEU A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 196 Proline residue: A 191 - end of helix removed outlier: 3.796A pdb=" N VAL A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 222 Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 229 through 238 Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.550A pdb=" N GLY B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 64 removed outlier: 3.592A pdb=" N ILE B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N HIS B 61 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 78 Processing helix chain 'B' and resid 82 through 108 Processing helix chain 'B' and resid 109 through 114 removed outlier: 4.287A pdb=" N GLY B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 149 removed outlier: 3.684A pdb=" N THR B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.581A pdb=" N GLY B 154 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 180 removed outlier: 3.759A pdb=" N LEU B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 196 Proline residue: B 191 - end of helix removed outlier: 3.796A pdb=" N VAL B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 222 Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 229 through 238 Processing helix chain 'C' and resid 6 through 31 removed outlier: 3.550A pdb=" N GLY C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 30 " --> pdb=" O PHE C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 64 removed outlier: 3.592A pdb=" N ILE C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N HIS C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 78 Processing helix chain 'C' and resid 82 through 108 Processing helix chain 'C' and resid 109 through 114 removed outlier: 4.287A pdb=" N GLY C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 149 removed outlier: 3.684A pdb=" N THR C 132 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.581A pdb=" N GLY C 154 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 180 removed outlier: 3.759A pdb=" N LEU C 174 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 196 Proline residue: C 191 - end of helix removed outlier: 3.796A pdb=" N VAL C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 222 Proline residue: C 208 - end of helix Processing helix chain 'C' and resid 229 through 238 Processing helix chain 'D' and resid 6 through 31 removed outlier: 3.550A pdb=" N GLY D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER D 30 " --> pdb=" O PHE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 64 removed outlier: 3.592A pdb=" N ILE D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N HIS D 61 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 Processing helix chain 'D' and resid 82 through 108 Processing helix chain 'D' and resid 109 through 114 removed outlier: 4.287A pdb=" N GLY D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 149 removed outlier: 3.684A pdb=" N THR D 132 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 154 removed outlier: 3.581A pdb=" N GLY D 154 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 180 removed outlier: 3.759A pdb=" N LEU D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 196 Proline residue: D 191 - end of helix removed outlier: 3.796A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 222 Proline residue: D 208 - end of helix Processing helix chain 'D' and resid 229 through 238 512 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1212 1.32 - 1.44: 1844 1.44 - 1.57: 4092 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 7180 Sorted by residual: bond pdb=" CE1 HIS D 105 " pdb=" NE2 HIS D 105 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.69e+01 bond pdb=" CE1 HIS C 105 " pdb=" NE2 HIS C 105 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.69e+01 bond pdb=" CE1 HIS A 105 " pdb=" NE2 HIS A 105 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.69e+01 bond pdb=" CE1 HIS B 105 " pdb=" NE2 HIS B 105 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.69e+01 bond pdb=" CE1 HIS A 201 " pdb=" NE2 HIS A 201 " ideal model delta sigma weight residual 1.321 1.368 -0.047 1.00e-02 1.00e+04 2.22e+01 ... (remaining 7175 not shown) Histogram of bond angle deviations from ideal: 97.35 - 104.72: 148 104.72 - 112.09: 3656 112.09 - 119.47: 2344 119.47 - 126.84: 3580 126.84 - 134.21: 92 Bond angle restraints: 9820 Sorted by residual: angle pdb=" NE ARG A 11 " pdb=" CZ ARG A 11 " pdb=" NH1 ARG A 11 " ideal model delta sigma weight residual 121.50 119.15 2.35 1.00e+00 1.00e+00 5.51e+00 angle pdb=" NE ARG B 11 " pdb=" CZ ARG B 11 " pdb=" NH1 ARG B 11 " ideal model delta sigma weight residual 121.50 119.15 2.35 1.00e+00 1.00e+00 5.51e+00 angle pdb=" NE ARG D 11 " pdb=" CZ ARG D 11 " pdb=" NH1 ARG D 11 " ideal model delta sigma weight residual 121.50 119.15 2.35 1.00e+00 1.00e+00 5.51e+00 angle pdb=" NE ARG C 11 " pdb=" CZ ARG C 11 " pdb=" NH1 ARG C 11 " ideal model delta sigma weight residual 121.50 119.15 2.35 1.00e+00 1.00e+00 5.51e+00 angle pdb=" CA VAL A 83 " pdb=" CB VAL A 83 " pdb=" CG1 VAL A 83 " ideal model delta sigma weight residual 110.40 114.23 -3.83 1.70e+00 3.46e-01 5.08e+00 ... (remaining 9815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 3800 17.90 - 35.80: 264 35.80 - 53.70: 60 53.70 - 71.60: 4 71.60 - 89.49: 4 Dihedral angle restraints: 4132 sinusoidal: 1436 harmonic: 2696 Sorted by residual: dihedral pdb=" CA GLU C 155 " pdb=" CB GLU C 155 " pdb=" CG GLU C 155 " pdb=" CD GLU C 155 " ideal model delta sinusoidal sigma weight residual -60.00 -110.21 50.21 3 1.50e+01 4.44e-03 8.87e+00 dihedral pdb=" CA GLU D 155 " pdb=" CB GLU D 155 " pdb=" CG GLU D 155 " pdb=" CD GLU D 155 " ideal model delta sinusoidal sigma weight residual -60.00 -110.21 50.21 3 1.50e+01 4.44e-03 8.87e+00 dihedral pdb=" CA GLU A 155 " pdb=" CB GLU A 155 " pdb=" CG GLU A 155 " pdb=" CD GLU A 155 " ideal model delta sinusoidal sigma weight residual -60.00 -110.21 50.21 3 1.50e+01 4.44e-03 8.87e+00 ... (remaining 4129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 676 0.048 - 0.095: 360 0.095 - 0.143: 100 0.143 - 0.191: 52 0.191 - 0.239: 12 Chirality restraints: 1200 Sorted by residual: chirality pdb=" CB VAL C 83 " pdb=" CA VAL C 83 " pdb=" CG1 VAL C 83 " pdb=" CG2 VAL C 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL D 83 " pdb=" CA VAL D 83 " pdb=" CG1 VAL D 83 " pdb=" CG2 VAL D 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL B 83 " pdb=" CA VAL B 83 " pdb=" CG1 VAL B 83 " pdb=" CG2 VAL B 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1197 not shown) Planarity restraints: 1236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 136 " 0.037 2.00e-02 2.50e+03 2.44e-02 1.04e+01 pdb=" CG PHE C 136 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 136 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 136 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE C 136 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 136 " 0.023 2.00e-02 2.50e+03 pdb=" CZ PHE C 136 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 136 " -0.037 2.00e-02 2.50e+03 2.44e-02 1.04e+01 pdb=" CG PHE B 136 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 136 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 136 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE B 136 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 136 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE B 136 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 136 " -0.037 2.00e-02 2.50e+03 2.44e-02 1.04e+01 pdb=" CG PHE A 136 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 136 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 136 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE A 136 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 136 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE A 136 " -0.013 2.00e-02 2.50e+03 ... (remaining 1233 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2684 2.89 - 3.39: 7480 3.39 - 3.90: 12704 3.90 - 4.40: 15012 4.40 - 4.90: 25248 Nonbonded interactions: 63128 Sorted by model distance: nonbonded pdb=" OG SER D 182 " pdb=" OG SER D 188 " model vdw 2.391 2.440 nonbonded pdb=" OG SER B 182 " pdb=" OG SER B 188 " model vdw 2.391 2.440 nonbonded pdb=" OG SER C 182 " pdb=" OG SER C 188 " model vdw 2.391 2.440 nonbonded pdb=" OG SER A 182 " pdb=" OG SER A 188 " model vdw 2.391 2.440 nonbonded pdb=" ND2 ASN A 123 " pdb=" O HIS A 177 " model vdw 2.410 2.520 ... (remaining 63123 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 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.040 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: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.390 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 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 : 0.010 0.052 7180 Z= 0.641 Angle : 0.872 5.095 9820 Z= 0.566 Chirality : 0.068 0.239 1200 Planarity : 0.007 0.032 1236 Dihedral : 13.225 89.494 2404 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.78 % Allowed : 5.00 % Favored : 92.22 % 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: -2.60 (0.23), residues: 948 helix: -1.67 (0.15), residues: 616 sheet: None (None), residues: 0 loop : -1.48 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.008 TRP B 34 HIS 0.006 0.002 HIS B 201 PHE 0.038 0.009 PHE C 14 TYR 0.012 0.004 TYR B 221 ARG 0.022 0.004 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 48 time to evaluate : 0.804 Fit side-chains REVERT: A 106 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7005 (mt-10) REVERT: B 106 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7004 (mt-10) REVERT: C 106 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7004 (mt-10) REVERT: D 106 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7003 (mt-10) outliers start: 20 outliers final: 12 residues processed: 68 average time/residue: 0.6538 time to fit residues: 49.3433 Evaluate side-chains 56 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 122 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN C 57 GLN D 57 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7180 Z= 0.174 Angle : 0.494 5.236 9820 Z= 0.253 Chirality : 0.037 0.118 1200 Planarity : 0.005 0.032 1236 Dihedral : 3.884 21.794 1008 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.11 % Allowed : 6.67 % Favored : 92.22 % 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: 0.37 (0.26), residues: 948 helix: 0.86 (0.18), residues: 656 sheet: None (None), residues: 0 loop : -1.05 (0.40), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 205 HIS 0.003 0.001 HIS D 172 PHE 0.009 0.001 PHE B 48 TYR 0.003 0.001 TYR B 89 ARG 0.004 0.000 ARG C 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.703 Fit side-chains REVERT: A 106 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6715 (mt-10) REVERT: B 106 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6714 (mt-10) REVERT: C 106 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6714 (mt-10) REVERT: D 106 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6713 (mt-10) outliers start: 8 outliers final: 0 residues processed: 60 average time/residue: 0.7114 time to fit residues: 47.2575 Evaluate side-chains 44 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 129 GLN B 33 ASN B 129 GLN C 33 ASN C 129 GLN D 33 ASN D 129 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7180 Z= 0.168 Angle : 0.479 5.117 9820 Z= 0.241 Chirality : 0.036 0.117 1200 Planarity : 0.004 0.033 1236 Dihedral : 3.548 15.407 996 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.67 % Allowed : 5.56 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.28), residues: 948 helix: 1.58 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.73 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 205 HIS 0.002 0.001 HIS D 105 PHE 0.007 0.001 PHE C 136 TYR 0.004 0.001 TYR B 219 ARG 0.001 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.750 Fit side-chains REVERT: A 106 GLU cc_start: 0.7534 (mm-30) cc_final: 0.6844 (mt-10) REVERT: B 106 GLU cc_start: 0.7534 (mm-30) cc_final: 0.6843 (mt-10) REVERT: C 106 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6844 (mt-10) REVERT: D 106 GLU cc_start: 0.7534 (mm-30) cc_final: 0.6843 (mt-10) outliers start: 12 outliers final: 4 residues processed: 56 average time/residue: 0.7786 time to fit residues: 48.0734 Evaluate side-chains 48 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 138 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 57 GLN B 33 ASN B 57 GLN C 33 ASN C 57 GLN D 33 ASN D 57 GLN D 220 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7180 Z= 0.252 Angle : 0.516 5.130 9820 Z= 0.259 Chirality : 0.038 0.123 1200 Planarity : 0.004 0.036 1236 Dihedral : 3.743 16.203 996 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.67 % Allowed : 6.11 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.28), residues: 948 helix: 1.60 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.50 (0.44), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 205 HIS 0.004 0.001 HIS C 172 PHE 0.011 0.002 PHE D 14 TYR 0.004 0.001 TYR D 89 ARG 0.001 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 0.793 Fit side-chains REVERT: A 106 GLU cc_start: 0.7522 (mm-30) cc_final: 0.6776 (mt-10) REVERT: B 106 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6776 (mt-10) REVERT: C 106 GLU cc_start: 0.7522 (mm-30) cc_final: 0.6776 (mt-10) REVERT: D 106 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6777 (mt-10) outliers start: 12 outliers final: 0 residues processed: 48 average time/residue: 0.8393 time to fit residues: 44.2296 Evaluate side-chains 36 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 220 ASN B 33 ASN B 220 ASN C 33 ASN C 220 ASN D 33 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 7180 Z= 0.386 Angle : 0.579 5.271 9820 Z= 0.289 Chirality : 0.041 0.131 1200 Planarity : 0.005 0.039 1236 Dihedral : 4.044 19.290 996 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.67 % Allowed : 6.67 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.28), residues: 948 helix: 1.35 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.49 (0.44), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 205 HIS 0.005 0.001 HIS C 172 PHE 0.015 0.002 PHE D 14 TYR 0.007 0.002 TYR B 89 ARG 0.002 0.001 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.792 Fit side-chains REVERT: A 106 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6726 (mt-10) REVERT: B 106 GLU cc_start: 0.7526 (mm-30) cc_final: 0.6726 (mt-10) REVERT: C 106 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6724 (mt-10) REVERT: D 106 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6724 (mt-10) outliers start: 12 outliers final: 4 residues processed: 52 average time/residue: 0.9837 time to fit residues: 55.4445 Evaluate side-chains 40 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 138 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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: 0.7090 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7180 Z= 0.211 Angle : 0.501 5.042 9820 Z= 0.253 Chirality : 0.037 0.121 1200 Planarity : 0.004 0.038 1236 Dihedral : 3.799 18.236 996 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.67 % Allowed : 7.22 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.28), residues: 948 helix: 1.70 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.42 (0.45), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 34 HIS 0.003 0.001 HIS C 172 PHE 0.009 0.001 PHE B 136 TYR 0.004 0.001 TYR B 89 ARG 0.001 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 0.797 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 48 average time/residue: 0.8509 time to fit residues: 44.8120 Evaluate side-chains 36 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 65 optimal weight: 0.0370 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- 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: 0.7056 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7180 Z= 0.151 Angle : 0.472 4.955 9820 Z= 0.237 Chirality : 0.036 0.117 1200 Planarity : 0.004 0.037 1236 Dihedral : 3.595 16.532 996 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.11 % Allowed : 7.22 % Favored : 91.67 % 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: 2.10 (0.29), residues: 948 helix: 2.12 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -0.14 (0.44), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 34 HIS 0.002 0.001 HIS C 172 PHE 0.008 0.001 PHE B 25 TYR 0.003 0.001 TYR A 219 ARG 0.001 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.698 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 48 average time/residue: 0.8024 time to fit residues: 42.3735 Evaluate side-chains 40 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7065 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7180 Z= 0.169 Angle : 0.483 5.014 9820 Z= 0.242 Chirality : 0.037 0.117 1200 Planarity : 0.004 0.036 1236 Dihedral : 3.609 15.785 996 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.11 % Allowed : 6.67 % Favored : 92.22 % 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: 2.14 (0.29), residues: 948 helix: 2.15 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -0.11 (0.45), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 34 HIS 0.002 0.001 HIS A 172 PHE 0.008 0.001 PHE A 17 TYR 0.003 0.001 TYR D 89 ARG 0.001 0.000 ARG C 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.688 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 52 average time/residue: 0.8428 time to fit residues: 47.9986 Evaluate side-chains 44 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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: 0.7111 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7180 Z= 0.314 Angle : 0.547 5.172 9820 Z= 0.273 Chirality : 0.040 0.127 1200 Planarity : 0.004 0.036 1236 Dihedral : 3.919 18.404 996 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.67 % Allowed : 6.67 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.29), residues: 948 helix: 1.78 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.35 (0.46), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 202 HIS 0.004 0.001 HIS A 172 PHE 0.014 0.002 PHE C 14 TYR 0.006 0.001 TYR D 89 ARG 0.002 0.001 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.773 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 52 average time/residue: 0.8386 time to fit residues: 48.0466 Evaluate side-chains 40 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.7084 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7180 Z= 0.211 Angle : 0.504 5.074 9820 Z= 0.253 Chirality : 0.037 0.120 1200 Planarity : 0.004 0.036 1236 Dihedral : 3.751 17.023 996 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.56 % Allowed : 7.78 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.29), residues: 948 helix: 1.96 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -0.06 (0.45), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 34 HIS 0.003 0.001 HIS D 172 PHE 0.009 0.001 PHE C 14 TYR 0.004 0.001 TYR D 89 ARG 0.001 0.000 ARG A 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.763 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 44 average time/residue: 0.9767 time to fit residues: 46.7636 Evaluate side-chains 40 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 6.9990 chunk 10 optimal weight: 0.0030 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.139683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.115363 restraints weight = 7233.784| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.75 r_work: 0.3107 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7180 Z= 0.178 Angle : 0.488 5.030 9820 Z= 0.244 Chirality : 0.037 0.118 1200 Planarity : 0.004 0.036 1236 Dihedral : 3.647 16.081 996 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.56 % Allowed : 8.33 % Favored : 91.11 % 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: 2.17 (0.29), residues: 948 helix: 2.13 (0.19), residues: 640 sheet: None (None), residues: 0 loop : 0.03 (0.46), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 34 HIS 0.002 0.001 HIS D 172 PHE 0.008 0.001 PHE C 14 TYR 0.003 0.001 TYR A 89 ARG 0.001 0.000 ARG C 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1724.45 seconds wall clock time: 32 minutes 17.71 seconds (1937.71 seconds total)