Starting phenix.real_space_refine on Fri Jul 19 21:34:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0f_35901/07_2024/8j0f_35901_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0f_35901/07_2024/8j0f_35901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0f_35901/07_2024/8j0f_35901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0f_35901/07_2024/8j0f_35901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0f_35901/07_2024/8j0f_35901_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0f_35901/07_2024/8j0f_35901_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 5588 2.51 5 N 1572 2.21 5 O 1720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 220": "OE1" <-> "OE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D GLU 220": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8932 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "F" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "A" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "B" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "G" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "D" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "H" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 5.28, per 1000 atoms: 0.59 Number of scatterers: 8932 At special positions: 0 Unit cell: (102.82, 92.22, 94.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 12 15.00 Mg 4 11.99 O 1720 8.00 N 1572 7.00 C 5588 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: 3.76 Conformation dependent library (CDL) restraints added in 1.6 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB RGP C 802 " pdb=" CB RGP A 802 " pdb=" CB RGP B 802 " pdb=" CB RGP D 802 " Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 58.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'C' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE C 10 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 27 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY C 31 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 51 Processing helix chain 'C' and resid 61 through 78 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER C 101 " --> pdb=" O GLY C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG C 129 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 147 Processing helix chain 'C' and resid 175 through 187 Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS C 285 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 77 Processing helix chain 'F' and resid 79 through 85 Processing helix chain 'A' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE A 10 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY A 31 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 51 Processing helix chain 'A' and resid 61 through 78 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER A 101 " --> pdb=" O GLY A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG A 129 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 Processing helix chain 'A' and resid 175 through 187 Processing helix chain 'A' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS A 285 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 Processing helix chain 'E' and resid 79 through 85 Processing helix chain 'B' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE B 10 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY B 31 " --> pdb=" O GLY B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 51 Processing helix chain 'B' and resid 61 through 78 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER B 101 " --> pdb=" O GLY B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG B 129 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 175 through 187 Processing helix chain 'B' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS B 285 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 Processing helix chain 'G' and resid 79 through 85 Processing helix chain 'D' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE D 10 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY D 31 " --> pdb=" O GLY D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 51 Processing helix chain 'D' and resid 61 through 78 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG D 129 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 147 Processing helix chain 'D' and resid 175 through 187 Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS D 285 " --> pdb=" O GLN D 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 Processing helix chain 'H' and resid 79 through 85 Processing sheet with id=AA1, first strand: chain 'C' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR C 117 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL C 152 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA C 119 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN C 154 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET C 121 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL C 55 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG C 16 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE C 193 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL C 18 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU C 195 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS C 20 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 192 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR C 259 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU C 194 " --> pdb=" O THR C 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR A 117 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL A 152 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA A 119 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN A 154 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A 121 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL A 55 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG A 16 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE A 193 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 18 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU A 195 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS A 20 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 192 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR A 259 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU A 194 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR B 117 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL B 152 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA B 119 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN B 154 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET B 121 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL B 55 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG B 16 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE B 193 " --> pdb=" O ARG B 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 18 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU B 195 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS B 20 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU B 192 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR B 259 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU B 194 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR D 117 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL D 152 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA D 119 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN D 154 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET D 121 " --> pdb=" O ASN D 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL D 55 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG D 16 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE D 193 " --> pdb=" O ARG D 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL D 18 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU D 195 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS D 20 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU D 192 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR D 259 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU D 194 " --> pdb=" O THR D 259 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1212 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: 2.34 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1788 1.32 - 1.44: 2040 1.44 - 1.56: 5136 1.56 - 1.68: 20 1.68 - 1.80: 64 Bond restraints: 9048 Sorted by residual: bond pdb=" OE2 RGP D 802 " pdb=" PA RGP D 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" OE2 RGP C 802 " pdb=" PA RGP C 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" OE2 RGP A 802 " pdb=" PA RGP A 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" OE2 RGP B 802 " pdb=" PA RGP B 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" CD RGP A 802 " pdb=" OE2 RGP A 802 " ideal model delta sigma weight residual 1.302 1.455 -0.153 2.00e-02 2.50e+03 5.86e+01 ... (remaining 9043 not shown) Histogram of bond angle deviations from ideal: 95.13 - 103.27: 72 103.27 - 111.40: 4128 111.40 - 119.54: 3588 119.54 - 127.67: 4364 127.67 - 135.81: 60 Bond angle restraints: 12212 Sorted by residual: angle pdb=" N ILE C 150 " pdb=" CA ILE C 150 " pdb=" C ILE C 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N ILE B 150 " pdb=" CA ILE B 150 " pdb=" C ILE B 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N ILE D 150 " pdb=" CA ILE D 150 " pdb=" C ILE D 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N ILE A 150 " pdb=" CA ILE A 150 " pdb=" C ILE A 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N VAL B 254 " pdb=" CA VAL B 254 " pdb=" C VAL B 254 " ideal model delta sigma weight residual 107.55 112.76 -5.21 9.90e-01 1.02e+00 2.77e+01 ... (remaining 12207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 5260 34.62 - 69.24: 178 69.24 - 103.86: 16 103.86 - 138.48: 8 138.48 - 173.11: 2 Dihedral angle restraints: 5464 sinusoidal: 2216 harmonic: 3248 Sorted by residual: dihedral pdb=" O1B ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 113.10 -173.11 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP C 801 " pdb=" O3A ADP C 801 " pdb=" PB ADP C 801 " pdb=" PA ADP C 801 " ideal model delta sinusoidal sigma weight residual -60.00 113.10 -173.11 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP D 801 " pdb=" O5' ADP D 801 " pdb=" PA ADP D 801 " pdb=" O2A ADP D 801 " ideal model delta sinusoidal sigma weight residual 300.00 170.94 129.07 1 2.00e+01 2.50e-03 3.91e+01 ... (remaining 5461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 972 0.043 - 0.085: 320 0.085 - 0.128: 96 0.128 - 0.170: 8 0.170 - 0.213: 12 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA MET D 110 " pdb=" N MET D 110 " pdb=" C MET D 110 " pdb=" CB MET D 110 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA MET C 110 " pdb=" N MET C 110 " pdb=" C MET C 110 " pdb=" CB MET C 110 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA MET B 110 " pdb=" N MET B 110 " pdb=" C MET B 110 " pdb=" CB MET B 110 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1405 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 115 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CG ASP A 115 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP A 115 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A 115 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 115 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CG ASP C 115 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP C 115 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP C 115 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 115 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CG ASP D 115 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP D 115 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP D 115 " 0.013 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2014 2.77 - 3.31: 9110 3.31 - 3.84: 14972 3.84 - 4.37: 17476 4.37 - 4.90: 28944 Nonbonded interactions: 72516 Sorted by model distance: nonbonded pdb=" N GLU D 265 " pdb=" OE1 GLU D 265 " model vdw 2.242 2.520 nonbonded pdb=" N GLU B 265 " pdb=" OE1 GLU B 265 " model vdw 2.242 2.520 nonbonded pdb=" N GLU A 265 " pdb=" OE1 GLU A 265 " model vdw 2.242 2.520 nonbonded pdb=" N GLU C 265 " pdb=" OE1 GLU C 265 " model vdw 2.242 2.520 nonbonded pdb=" OD2 ASP B 208 " pdb=" OG1 THR B 210 " model vdw 2.246 2.440 ... (remaining 72511 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' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.960 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.009 0.190 9048 Z= 0.639 Angle : 1.064 8.344 12212 Z= 0.653 Chirality : 0.047 0.213 1408 Planarity : 0.005 0.047 1544 Dihedral : 18.094 173.106 3368 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.13 % Allowed : 20.43 % Favored : 77.45 % 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 (0.27), residues: 1108 helix: 0.35 (0.22), residues: 580 sheet: -0.20 (0.41), residues: 188 loop : 0.56 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 174 HIS 0.006 0.001 HIS B 222 PHE 0.019 0.001 PHE B 153 TYR 0.024 0.002 TYR D 106 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.040 Fit side-chains REVERT: C 68 GLN cc_start: 0.8657 (tm-30) cc_final: 0.7830 (tm-30) REVERT: A 68 GLN cc_start: 0.8651 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 68 GLN cc_start: 0.8641 (tm-30) cc_final: 0.7797 (tm-30) REVERT: D 68 GLN cc_start: 0.8648 (tm-30) cc_final: 0.7791 (tm-30) outliers start: 20 outliers final: 0 residues processed: 194 average time/residue: 0.2411 time to fit residues: 62.2269 Evaluate side-chains 179 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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: 0.6980 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9048 Z= 0.194 Angle : 0.657 9.444 12212 Z= 0.314 Chirality : 0.041 0.134 1408 Planarity : 0.003 0.021 1544 Dihedral : 13.407 178.151 1300 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.28 % Allowed : 20.21 % Favored : 78.51 % 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: 1.15 (0.26), residues: 1108 helix: 1.14 (0.21), residues: 596 sheet: 0.02 (0.41), residues: 188 loop : 0.83 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 287 HIS 0.003 0.001 HIS C 222 PHE 0.023 0.002 PHE G 80 TYR 0.023 0.002 TYR D 106 ARG 0.003 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 195 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: C 80 PHE cc_start: 0.9338 (t80) cc_final: 0.9112 (t80) REVERT: C 89 GLU cc_start: 0.8444 (tp30) cc_final: 0.8243 (tp30) REVERT: C 115 ASP cc_start: 0.8805 (t0) cc_final: 0.8596 (t0) REVERT: C 186 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 89 GLU cc_start: 0.8496 (tp30) cc_final: 0.8259 (tp30) REVERT: A 115 ASP cc_start: 0.8808 (t0) cc_final: 0.8589 (t0) REVERT: A 131 LYS cc_start: 0.9195 (pttm) cc_final: 0.8940 (mmmt) REVERT: B 54 GLU cc_start: 0.8367 (mp0) cc_final: 0.7921 (pm20) REVERT: B 115 ASP cc_start: 0.8850 (t0) cc_final: 0.8619 (t0) REVERT: B 132 ASP cc_start: 0.8824 (t0) cc_final: 0.8537 (t0) REVERT: B 186 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8087 (tm-30) REVERT: B 220 GLU cc_start: 0.9307 (tp30) cc_final: 0.9029 (tm-30) REVERT: D 115 ASP cc_start: 0.8794 (t0) cc_final: 0.8575 (t0) REVERT: D 132 ASP cc_start: 0.8854 (t0) cc_final: 0.8587 (t0) REVERT: D 186 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8127 (tm-30) REVERT: D 248 ASN cc_start: 0.9105 (t0) cc_final: 0.8883 (t0) outliers start: 12 outliers final: 4 residues processed: 199 average time/residue: 0.2267 time to fit residues: 61.0842 Evaluate side-chains 186 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 182 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain D residue 23 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9048 Z= 0.172 Angle : 0.620 11.533 12212 Z= 0.290 Chirality : 0.040 0.141 1408 Planarity : 0.003 0.020 1544 Dihedral : 12.156 155.045 1300 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 3.62 % Allowed : 18.83 % Favored : 77.55 % 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: 1.59 (0.26), residues: 1108 helix: 1.54 (0.22), residues: 596 sheet: 0.18 (0.41), residues: 188 loop : 0.96 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 287 HIS 0.003 0.001 HIS C 222 PHE 0.019 0.001 PHE E 80 TYR 0.023 0.002 TYR D 106 ARG 0.001 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 ASP cc_start: 0.8826 (t0) cc_final: 0.8569 (t0) REVERT: C 121 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.7945 (mmm) REVERT: C 251 TYR cc_start: 0.8377 (m-80) cc_final: 0.8025 (m-80) REVERT: A 115 ASP cc_start: 0.8870 (t0) cc_final: 0.8591 (t0) REVERT: A 121 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.7955 (mmm) REVERT: A 131 LYS cc_start: 0.9163 (pttm) cc_final: 0.8942 (ptpp) REVERT: A 186 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8192 (tm-30) REVERT: A 251 TYR cc_start: 0.8366 (m-80) cc_final: 0.7998 (m-80) REVERT: B 115 ASP cc_start: 0.8844 (t0) cc_final: 0.8595 (t0) REVERT: B 121 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.7870 (mmm) REVERT: B 251 TYR cc_start: 0.8370 (m-80) cc_final: 0.8014 (m-80) REVERT: D 115 ASP cc_start: 0.8860 (t0) cc_final: 0.8580 (t0) REVERT: D 121 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.7908 (mmm) REVERT: D 186 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8239 (tm-30) REVERT: D 248 ASN cc_start: 0.9150 (t0) cc_final: 0.8899 (t0) REVERT: D 251 TYR cc_start: 0.8397 (m-80) cc_final: 0.8062 (m-80) outliers start: 34 outliers final: 11 residues processed: 208 average time/residue: 0.2225 time to fit residues: 62.4380 Evaluate side-chains 206 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 157 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0010 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9048 Z= 0.168 Angle : 0.606 6.653 12212 Z= 0.287 Chirality : 0.040 0.144 1408 Planarity : 0.003 0.021 1544 Dihedral : 11.102 141.804 1300 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 3.40 % Allowed : 20.96 % Favored : 75.64 % 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: 2.08 (0.26), residues: 1108 helix: 2.02 (0.22), residues: 572 sheet: 0.57 (0.41), residues: 180 loop : 0.96 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 287 HIS 0.002 0.001 HIS B 222 PHE 0.035 0.002 PHE H 80 TYR 0.026 0.002 TYR D 106 ARG 0.002 0.000 ARG B 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 187 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8236 (mp0) cc_final: 0.7841 (pm20) REVERT: C 115 ASP cc_start: 0.8783 (t0) cc_final: 0.8549 (t0) REVERT: C 121 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8009 (mmm) REVERT: A 83 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9140 (mp) REVERT: A 115 ASP cc_start: 0.8855 (t0) cc_final: 0.8596 (t0) REVERT: A 121 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8009 (mmm) REVERT: A 131 LYS cc_start: 0.9186 (pttm) cc_final: 0.8853 (mmmt) REVERT: A 132 ASP cc_start: 0.8907 (t0) cc_final: 0.8666 (t0) REVERT: A 186 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 54 GLU cc_start: 0.8277 (mp0) cc_final: 0.7825 (pm20) REVERT: B 72 TYR cc_start: 0.9094 (t80) cc_final: 0.8867 (t80) REVERT: B 115 ASP cc_start: 0.8772 (t0) cc_final: 0.8554 (t0) REVERT: B 121 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.7921 (mmm) REVERT: B 136 GLN cc_start: 0.9175 (tt0) cc_final: 0.8953 (tt0) REVERT: B 248 ASN cc_start: 0.9075 (t0) cc_final: 0.8835 (t0) REVERT: B 251 TYR cc_start: 0.8393 (m-80) cc_final: 0.8066 (m-80) REVERT: D 115 ASP cc_start: 0.8827 (t0) cc_final: 0.8574 (t0) REVERT: D 121 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.7950 (mmm) REVERT: D 186 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8243 (tm-30) REVERT: D 251 TYR cc_start: 0.8404 (m-80) cc_final: 0.8084 (m-80) outliers start: 32 outliers final: 15 residues processed: 208 average time/residue: 0.2209 time to fit residues: 62.2747 Evaluate side-chains 190 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 285 HIS 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: 6.9990 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9048 Z= 0.387 Angle : 0.704 6.417 12212 Z= 0.337 Chirality : 0.043 0.174 1408 Planarity : 0.003 0.020 1544 Dihedral : 11.007 139.884 1300 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.04 % Allowed : 19.57 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.26), residues: 1108 helix: 1.73 (0.21), residues: 596 sheet: 0.01 (0.38), residues: 188 loop : 1.09 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 287 HIS 0.003 0.001 HIS C 222 PHE 0.025 0.002 PHE H 80 TYR 0.034 0.002 TYR A 106 ARG 0.002 0.000 ARG D 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 181 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 115 ASP cc_start: 0.8899 (t0) cc_final: 0.8638 (t0) REVERT: C 121 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.7943 (mmm) REVERT: C 239 MET cc_start: 0.7057 (mtp) cc_final: 0.6761 (ttm) REVERT: F 80 PHE cc_start: 0.8702 (t80) cc_final: 0.8483 (t80) REVERT: A 68 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8525 (tm-30) REVERT: A 104 MET cc_start: 0.9574 (tpt) cc_final: 0.9368 (mmm) REVERT: A 115 ASP cc_start: 0.8975 (t0) cc_final: 0.8669 (t0) REVERT: A 121 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.7970 (mmm) REVERT: A 186 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8407 (tm-30) REVERT: A 239 MET cc_start: 0.7012 (mtp) cc_final: 0.6687 (ttm) REVERT: B 68 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8510 (tm-30) REVERT: B 115 ASP cc_start: 0.8859 (t0) cc_final: 0.8612 (t0) REVERT: B 121 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.7827 (mmm) REVERT: B 136 GLN cc_start: 0.9228 (tt0) cc_final: 0.9011 (tt0) REVERT: B 248 ASN cc_start: 0.9223 (t0) cc_final: 0.9004 (t0) REVERT: B 287 TRP cc_start: 0.7867 (m-10) cc_final: 0.7665 (m-10) REVERT: D 115 ASP cc_start: 0.8983 (t0) cc_final: 0.8659 (t0) REVERT: D 121 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.7865 (mmm) REVERT: D 186 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8336 (tm-30) REVERT: D 223 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8746 (tm-30) REVERT: D 239 MET cc_start: 0.7319 (mtp) cc_final: 0.7089 (ttm) REVERT: D 287 TRP cc_start: 0.7788 (m-10) cc_final: 0.7567 (m-10) outliers start: 38 outliers final: 20 residues processed: 197 average time/residue: 0.2092 time to fit residues: 56.8157 Evaluate side-chains 192 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain H residue 82 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9048 Z= 0.209 Angle : 0.649 10.160 12212 Z= 0.307 Chirality : 0.040 0.130 1408 Planarity : 0.003 0.021 1544 Dihedral : 10.688 141.551 1300 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.98 % Allowed : 23.19 % Favored : 73.83 % 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: 1.85 (0.27), residues: 1108 helix: 1.77 (0.21), residues: 596 sheet: 0.02 (0.39), residues: 188 loop : 1.23 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 287 HIS 0.002 0.000 HIS C 222 PHE 0.023 0.002 PHE H 80 TYR 0.019 0.002 TYR A 106 ARG 0.001 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8795 (tm-30) REVERT: C 115 ASP cc_start: 0.8888 (t0) cc_final: 0.8618 (t0) REVERT: C 121 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.7960 (mmm) REVERT: C 239 MET cc_start: 0.6880 (mtp) cc_final: 0.6554 (ttm) REVERT: C 251 TYR cc_start: 0.8421 (m-80) cc_final: 0.8155 (m-80) REVERT: A 115 ASP cc_start: 0.8922 (t0) cc_final: 0.8636 (t0) REVERT: A 121 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.7991 (mmm) REVERT: A 239 MET cc_start: 0.6914 (mtp) cc_final: 0.6617 (ttm) REVERT: A 251 TYR cc_start: 0.8416 (m-80) cc_final: 0.8136 (m-80) REVERT: B 115 ASP cc_start: 0.8779 (t0) cc_final: 0.8536 (t0) REVERT: B 121 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.7867 (mmm) REVERT: B 136 GLN cc_start: 0.9179 (tt0) cc_final: 0.8941 (tt0) REVERT: B 251 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: D 115 ASP cc_start: 0.8893 (t0) cc_final: 0.8593 (t0) REVERT: D 121 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.7944 (mmm) REVERT: D 186 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8308 (tm-30) REVERT: D 251 TYR cc_start: 0.8393 (m-80) cc_final: 0.8062 (m-80) REVERT: D 287 TRP cc_start: 0.7778 (m-10) cc_final: 0.7476 (m-10) outliers start: 28 outliers final: 18 residues processed: 184 average time/residue: 0.2172 time to fit residues: 54.5931 Evaluate side-chains 185 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain H residue 82 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.0770 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9048 Z= 0.172 Angle : 0.644 11.357 12212 Z= 0.304 Chirality : 0.040 0.170 1408 Planarity : 0.002 0.020 1544 Dihedral : 9.978 143.689 1300 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.87 % Allowed : 23.30 % Favored : 73.83 % 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: 2.02 (0.27), residues: 1108 helix: 1.85 (0.22), residues: 596 sheet: 0.22 (0.41), residues: 188 loop : 1.36 (0.40), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 287 HIS 0.001 0.000 HIS C 222 PHE 0.019 0.001 PHE H 80 TYR 0.027 0.002 TYR A 106 ARG 0.002 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 ASP cc_start: 0.8828 (t0) cc_final: 0.8601 (t0) REVERT: C 121 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8095 (mmm) REVERT: C 251 TYR cc_start: 0.8421 (m-80) cc_final: 0.8176 (m-80) REVERT: A 115 ASP cc_start: 0.8801 (t0) cc_final: 0.8585 (t0) REVERT: A 121 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8117 (mmm) REVERT: A 251 TYR cc_start: 0.8399 (m-80) cc_final: 0.8084 (m-80) REVERT: B 68 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8792 (tm-30) REVERT: B 115 ASP cc_start: 0.8738 (t0) cc_final: 0.8526 (t0) REVERT: B 121 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8000 (mmm) REVERT: B 136 GLN cc_start: 0.9166 (tt0) cc_final: 0.8894 (tt0) REVERT: D 115 ASP cc_start: 0.8818 (t0) cc_final: 0.8580 (t0) REVERT: D 121 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8053 (mmm) REVERT: D 186 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8342 (tm-30) REVERT: D 251 TYR cc_start: 0.8360 (m-80) cc_final: 0.8039 (m-80) REVERT: D 287 TRP cc_start: 0.7822 (m-10) cc_final: 0.7474 (m-10) outliers start: 27 outliers final: 12 residues processed: 195 average time/residue: 0.2273 time to fit residues: 60.1459 Evaluate side-chains 180 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 223 GLN Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain H residue 82 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9048 Z= 0.260 Angle : 0.686 10.816 12212 Z= 0.326 Chirality : 0.040 0.210 1408 Planarity : 0.003 0.022 1544 Dihedral : 9.885 144.746 1300 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.19 % Allowed : 22.77 % Favored : 74.04 % 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: 2.00 (0.27), residues: 1108 helix: 1.86 (0.22), residues: 596 sheet: 0.19 (0.40), residues: 188 loop : 1.29 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP B 287 HIS 0.002 0.001 HIS A 222 PHE 0.018 0.001 PHE H 80 TYR 0.045 0.002 TYR A 106 ARG 0.001 0.000 ARG B 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 165 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 ASP cc_start: 0.8870 (t0) cc_final: 0.8611 (t0) REVERT: C 121 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8148 (mmm) REVERT: C 251 TYR cc_start: 0.8436 (m-80) cc_final: 0.8173 (m-80) REVERT: A 121 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8161 (mmm) REVERT: A 251 TYR cc_start: 0.8413 (m-80) cc_final: 0.8120 (m-80) REVERT: B 115 ASP cc_start: 0.8779 (t0) cc_final: 0.8555 (t0) REVERT: B 121 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8008 (mmm) REVERT: D 110 MET cc_start: 0.8472 (mpp) cc_final: 0.8110 (mtt) REVERT: D 115 ASP cc_start: 0.8836 (t0) cc_final: 0.8586 (t0) REVERT: D 121 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8042 (mmm) REVERT: D 186 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8368 (tm-30) REVERT: D 251 TYR cc_start: 0.8379 (m-80) cc_final: 0.8038 (m-80) REVERT: D 287 TRP cc_start: 0.8063 (m-10) cc_final: 0.7738 (m-10) outliers start: 30 outliers final: 16 residues processed: 182 average time/residue: 0.2198 time to fit residues: 54.3013 Evaluate side-chains 180 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain H residue 82 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9048 Z= 0.202 Angle : 0.674 8.093 12212 Z= 0.319 Chirality : 0.040 0.166 1408 Planarity : 0.003 0.022 1544 Dihedral : 9.740 143.692 1300 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.23 % Allowed : 23.19 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.27), residues: 1108 helix: 1.85 (0.22), residues: 596 sheet: 0.29 (0.40), residues: 188 loop : 1.38 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 287 HIS 0.002 0.000 HIS C 222 PHE 0.021 0.001 PHE E 80 TYR 0.037 0.002 TYR B 106 ARG 0.003 0.000 ARG D 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 110 MET cc_start: 0.8457 (mpp) cc_final: 0.8034 (mtt) REVERT: C 115 ASP cc_start: 0.8822 (t0) cc_final: 0.8594 (t0) REVERT: C 121 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8156 (mmm) REVERT: C 251 TYR cc_start: 0.8461 (m-80) cc_final: 0.8200 (m-80) REVERT: A 104 MET cc_start: 0.9546 (mmm) cc_final: 0.9340 (tpp) REVERT: A 251 TYR cc_start: 0.8396 (m-80) cc_final: 0.8047 (m-80) REVERT: B 115 ASP cc_start: 0.8751 (t0) cc_final: 0.8539 (t0) REVERT: B 121 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8011 (mmm) REVERT: B 219 LYS cc_start: 0.8482 (mttt) cc_final: 0.8205 (ptpt) REVERT: D 115 ASP cc_start: 0.8797 (t0) cc_final: 0.8568 (t0) REVERT: D 186 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8345 (tm-30) REVERT: D 251 TYR cc_start: 0.8388 (m-80) cc_final: 0.8053 (m-80) REVERT: D 287 TRP cc_start: 0.8055 (m-10) cc_final: 0.7801 (m-10) outliers start: 21 outliers final: 17 residues processed: 177 average time/residue: 0.2092 time to fit residues: 50.6946 Evaluate side-chains 181 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain H residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.0170 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9048 Z= 0.189 Angle : 0.677 9.636 12212 Z= 0.323 Chirality : 0.039 0.150 1408 Planarity : 0.003 0.022 1544 Dihedral : 9.354 143.998 1300 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.13 % Allowed : 23.72 % Favored : 74.15 % 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: 2.09 (0.26), residues: 1108 helix: 1.82 (0.22), residues: 596 sheet: 0.39 (0.39), residues: 188 loop : 1.46 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 287 HIS 0.003 0.000 HIS C 285 PHE 0.017 0.001 PHE H 80 TYR 0.023 0.002 TYR A 106 ARG 0.002 0.000 ARG B 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 110 MET cc_start: 0.8359 (mpp) cc_final: 0.8031 (mtt) REVERT: C 251 TYR cc_start: 0.8427 (m-80) cc_final: 0.8151 (m-80) REVERT: A 104 MET cc_start: 0.9511 (mmm) cc_final: 0.9310 (tpp) REVERT: A 251 TYR cc_start: 0.8464 (m-80) cc_final: 0.8166 (m-80) REVERT: B 121 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8080 (mmm) REVERT: D 110 MET cc_start: 0.8519 (mpp) cc_final: 0.8055 (mtt) REVERT: D 186 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8339 (tm-30) REVERT: D 251 TYR cc_start: 0.8422 (m-80) cc_final: 0.8115 (m-80) outliers start: 20 outliers final: 18 residues processed: 176 average time/residue: 0.2222 time to fit residues: 53.2278 Evaluate side-chains 178 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain H residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.090237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.069616 restraints weight = 22873.155| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 4.27 r_work: 0.2930 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9048 Z= 0.194 Angle : 0.702 11.424 12212 Z= 0.337 Chirality : 0.039 0.168 1408 Planarity : 0.003 0.021 1544 Dihedral : 9.198 144.302 1300 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.23 % Allowed : 23.94 % Favored : 73.83 % 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: 2.35 (0.26), residues: 1108 helix: 2.08 (0.22), residues: 572 sheet: 0.86 (0.38), residues: 180 loop : 1.29 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 287 HIS 0.005 0.001 HIS C 285 PHE 0.020 0.001 PHE E 80 TYR 0.018 0.002 TYR C 106 ARG 0.002 0.000 ARG D 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2071.22 seconds wall clock time: 37 minutes 35.29 seconds (2255.29 seconds total)