Starting phenix.real_space_refine on Tue Sep 24 16:05:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/09_2024/6jxr_9895.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/09_2024/6jxr_9895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/09_2024/6jxr_9895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/09_2024/6jxr_9895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/09_2024/6jxr_9895.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/09_2024/6jxr_9895.cif" } resolution = 3.7 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= 0.003 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 54 5.16 5 C 5379 2.51 5 N 1386 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8437 Number of models: 1 Model: "" Number of chains: 8 Chain: "a" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 286 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 260 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "d" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 840 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "f" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 118} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "g" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 904 Classifications: {'peptide': 115} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 111} Chain: "m" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1940 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 235} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2246 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Time building chain proxies: 5.37, per 1000 atoms: 0.64 Number of scatterers: 8437 At special positions: 0 Unit cell: (116.27, 90.902, 133.182, 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 54 16.00 O 1618 8.00 N 1386 7.00 C 5379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.04 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.02 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.02 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 111 " distance=2.03 Simple disulfide: pdb=" SG CYS m 155 " - pdb=" SG CYS m 205 " distance=2.03 Simple disulfide: pdb=" SG CYS m 227 " - pdb=" SG CYS n 264 " distance=2.03 Simple disulfide: pdb=" SG CYS n 42 " - pdb=" SG CYS n 110 " distance=2.03 Simple disulfide: pdb=" SG CYS n 164 " - pdb=" SG CYS n 229 " distance=2.02 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2002 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 16 sheets defined 26.6% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'a' and resid 28 through 57 removed outlier: 4.572A pdb=" N CYS a 32 " --> pdb=" O ASP a 28 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 54 removed outlier: 4.132A pdb=" N LEU b 31 " --> pdb=" O LEU b 27 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR b 42 " --> pdb=" O ILE b 38 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 128 removed outlier: 3.763A pdb=" N HIS d 128 " --> pdb=" O CYS d 124 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 Processing helix chain 'f' and resid 128 through 155 Processing helix chain 'g' and resid 111 through 137 Processing helix chain 'm' and resid 102 through 106 removed outlier: 3.518A pdb=" N ASP m 105 " --> pdb=" O GLN m 102 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER m 106 " --> pdb=" O PRO m 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 102 through 106' Processing helix chain 'm' and resid 204 through 208 removed outlier: 3.570A pdb=" N ALA m 208 " --> pdb=" O CYS m 205 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 233 removed outlier: 3.731A pdb=" N VAL m 232 " --> pdb=" O ASP m 228 " (cutoff:3.500A) Processing helix chain 'm' and resid 239 through 273 removed outlier: 3.633A pdb=" N ASN m 243 " --> pdb=" O ASP m 239 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 105 removed outlier: 4.263A pdb=" N THR n 105 " --> pdb=" O PRO n 102 " (cutoff:3.500A) Processing helix chain 'n' and resid 150 through 157 removed outlier: 3.639A pdb=" N ILE n 154 " --> pdb=" O SER n 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 269 through 308 Processing helix chain 'e' and resid 104 through 108 removed outlier: 3.783A pdb=" N ALA e 108 " --> pdb=" O PRO e 105 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 154 removed outlier: 3.529A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 27 removed outlier: 5.516A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 42 through 46 removed outlier: 6.849A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N TYR e 111 " --> pdb=" O GLU d 83 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN d 87 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ARG e 115 " --> pdb=" O GLN d 87 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS d 89 " --> pdb=" O ARG e 115 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE e 110 " --> pdb=" O CYS e 98 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N CYS e 98 " --> pdb=" O PHE e 110 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TRP e 59 " --> pdb=" O ILE e 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'f' and resid 37 through 41 Processing sheet with id=AA5, first strand: chain 'f' and resid 65 through 66 removed outlier: 4.110A pdb=" N TRP f 59 " --> pdb=" O ILE f 66 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR f 111 " --> pdb=" O GLN g 98 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N TYR g 100 " --> pdb=" O TYR f 111 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG g 102 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG f 115 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LYS g 57 " --> pdb=" O MET g 61 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N MET g 61 " --> pdb=" O LYS g 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 122 through 123 removed outlier: 3.756A pdb=" N MET f 123 " --> pdb=" O ILE g 108 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE g 108 " --> pdb=" O MET f 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.575A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'm' and resid 27 through 28 Processing sheet with id=AA9, first strand: chain 'm' and resid 33 through 36 removed outlier: 6.196A pdb=" N LEU m 33 " --> pdb=" O LEU m 129 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER m 131 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL m 35 " --> pdb=" O SER m 131 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER m 114 " --> pdb=" O TYR m 54 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR m 54 " --> pdb=" O SER m 114 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE m 55 " --> pdb=" O TYR m 71 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR m 71 " --> pdb=" O PHE m 55 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP m 57 " --> pdb=" O LEU m 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'm' and resid 33 through 36 removed outlier: 6.196A pdb=" N LEU m 33 " --> pdb=" O LEU m 129 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER m 131 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL m 35 " --> pdb=" O SER m 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 140 through 143 removed outlier: 3.947A pdb=" N SER m 153 " --> pdb=" O SER m 198 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER m 198 " --> pdb=" O SER m 153 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA m 196 " --> pdb=" O CYS m 155 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET m 184 " --> pdb=" O PHE m 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'n' and resid 23 through 26 Processing sheet with id=AB4, first strand: chain 'n' and resid 29 through 33 removed outlier: 3.509A pdb=" N LEU n 32 " --> pdb=" O THR n 131 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR n 133 " --> pdb=" O LEU n 32 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N MET n 51 " --> pdb=" O TYR n 67 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR n 67 " --> pdb=" O MET n 51 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP n 53 " --> pdb=" O ILE n 65 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP n 57 " --> pdb=" O GLY n 61 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY n 61 " --> pdb=" O ASP n 57 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'n' and resid 143 through 147 removed outlier: 5.244A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'n' and resid 183 through 184 removed outlier: 3.746A pdb=" N ALA n 256 " --> pdb=" O CYS n 229 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'e' and resid 37 through 41 401 hydrogen bonds defined for protein. 1083 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: 2.31 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2693 1.34 - 1.46: 2032 1.46 - 1.59: 3817 1.59 - 1.71: 1 1.71 - 1.83: 76 Bond restraints: 8619 Sorted by residual: bond pdb=" CE LYS m 190 " pdb=" NZ LYS m 190 " ideal model delta sigma weight residual 1.489 1.620 -0.131 3.00e-02 1.11e+03 1.90e+01 bond pdb=" CB VAL d 33 " pdb=" CG2 VAL d 33 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.78e+00 bond pdb=" C PHE n 147 " pdb=" N GLU n 148 " ideal model delta sigma weight residual 1.330 1.300 0.030 1.47e-02 4.63e+03 4.12e+00 bond pdb=" CB VAL m 154 " pdb=" CG2 VAL m 154 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" CG ARG d 57 " pdb=" CD ARG d 57 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.45e+00 ... (remaining 8614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 11382 2.59 - 5.18: 257 5.18 - 7.76: 35 7.76 - 10.35: 9 10.35 - 12.94: 4 Bond angle restraints: 11687 Sorted by residual: angle pdb=" C THR m 158 " pdb=" N ASP m 159 " pdb=" CA ASP m 159 " ideal model delta sigma weight residual 121.54 134.48 -12.94 1.91e+00 2.74e-01 4.59e+01 angle pdb=" C LEU b 27 " pdb=" N ASP b 28 " pdb=" CA ASP b 28 " ideal model delta sigma weight residual 121.62 130.41 -8.79 1.57e+00 4.06e-01 3.13e+01 angle pdb=" N PHE n 219 " pdb=" CA PHE n 219 " pdb=" C PHE n 219 " ideal model delta sigma weight residual 114.04 107.14 6.90 1.24e+00 6.50e-01 3.10e+01 angle pdb=" C THR d 76 " pdb=" N ASP d 77 " pdb=" CA ASP d 77 " ideal model delta sigma weight residual 121.54 131.46 -9.92 1.91e+00 2.74e-01 2.70e+01 angle pdb=" N PHE m 160 " pdb=" CA PHE m 160 " pdb=" C PHE m 160 " ideal model delta sigma weight residual 110.80 121.85 -11.05 2.13e+00 2.20e-01 2.69e+01 ... (remaining 11682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 4882 15.70 - 31.40: 204 31.40 - 47.10: 65 47.10 - 62.80: 15 62.80 - 78.50: 10 Dihedral angle restraints: 5176 sinusoidal: 2056 harmonic: 3120 Sorted by residual: dihedral pdb=" CA ASP m 217 " pdb=" C ASP m 217 " pdb=" N THR m 218 " pdb=" CA THR m 218 " ideal model delta harmonic sigma weight residual 180.00 129.80 50.20 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA ILE b 38 " pdb=" C ILE b 38 " pdb=" N LEU b 39 " pdb=" CA LEU b 39 " ideal model delta harmonic sigma weight residual 180.00 132.28 47.72 0 5.00e+00 4.00e-02 9.11e+01 dihedral pdb=" CA ASP m 159 " pdb=" C ASP m 159 " pdb=" N PHE m 160 " pdb=" CA PHE m 160 " ideal model delta harmonic sigma weight residual 180.00 144.29 35.71 0 5.00e+00 4.00e-02 5.10e+01 ... (remaining 5173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1040 0.068 - 0.135: 241 0.135 - 0.203: 22 0.203 - 0.270: 5 0.270 - 0.338: 1 Chirality restraints: 1309 Sorted by residual: chirality pdb=" CB ILE d 78 " pdb=" CA ILE d 78 " pdb=" CG1 ILE d 78 " pdb=" CG2 ILE d 78 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CG LEU f 90 " pdb=" CB LEU f 90 " pdb=" CD1 LEU f 90 " pdb=" CD2 LEU f 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA TYR d 79 " pdb=" N TYR d 79 " pdb=" C TYR d 79 " pdb=" CB TYR d 79 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1306 not shown) Planarity restraints: 1492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE m 157 " -0.022 2.00e-02 2.50e+03 2.51e-02 1.10e+01 pdb=" CG PHE m 157 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE m 157 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE m 157 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE m 157 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE m 157 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE m 157 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN n 222 " -0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO n 223 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO n 223 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO n 223 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE n 140 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO n 141 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO n 141 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO n 141 " 0.036 5.00e-02 4.00e+02 ... (remaining 1489 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2100 2.80 - 3.32: 7266 3.32 - 3.85: 13211 3.85 - 4.37: 14744 4.37 - 4.90: 26395 Nonbonded interactions: 63716 Sorted by model distance: nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.273 3.040 nonbonded pdb=" O THR d 47 " pdb=" OH TYR d 71 " model vdw 2.289 3.040 nonbonded pdb=" NH1 ARG d 57 " pdb=" O ARG m 185 " model vdw 2.297 3.120 nonbonded pdb=" OD1 ASP g 35 " pdb=" OH TYR g 101 " model vdw 2.303 3.040 nonbonded pdb=" O PHE m 160 " pdb=" OG1 THR m 164 " model vdw 2.313 3.040 ... (remaining 63711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and resid 24 through 55) selection = chain 'b' } ncs_group { reference = chain 'e' selection = (chain 'f' and resid 33 through 155) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.310 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 0.008 0.131 8619 Z= 0.490 Angle : 1.011 12.938 11687 Z= 0.558 Chirality : 0.057 0.338 1309 Planarity : 0.007 0.076 1492 Dihedral : 10.827 78.503 3132 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.19 % Favored : 92.62 % Rotamer: Outliers : 0.74 % Allowed : 3.72 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.45 (0.21), residues: 1057 helix: -1.00 (0.26), residues: 249 sheet: -1.78 (0.27), residues: 270 loop : -3.29 (0.21), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP n 179 HIS 0.008 0.002 HIS n 173 PHE 0.058 0.003 PHE m 157 TYR 0.039 0.003 TYR e 149 ARG 0.007 0.001 ARG n 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 350 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 111 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7800 (m-10) REVERT: m 138 ASP cc_start: 0.7993 (t0) cc_final: 0.7781 (t0) REVERT: n 69 VAL cc_start: 0.8985 (m) cc_final: 0.8726 (p) REVERT: n 208 CYS cc_start: 0.8034 (m) cc_final: 0.7003 (m) outliers start: 7 outliers final: 3 residues processed: 356 average time/residue: 0.1964 time to fit residues: 94.5884 Evaluate side-chains 211 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 207 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 93 optimal weight: 0.0370 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 94 GLN f 92 GLN g 28 ASN m 28 GLN m 199 ASN m 211 ASN n 122 GLN e 60 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8619 Z= 0.222 Angle : 0.711 12.227 11687 Z= 0.369 Chirality : 0.045 0.282 1309 Planarity : 0.005 0.048 1492 Dihedral : 6.826 58.776 1167 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.13 % Rotamer: Outliers : 3.19 % Allowed : 14.03 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.07 (0.24), residues: 1057 helix: 1.11 (0.30), residues: 261 sheet: -1.19 (0.28), residues: 285 loop : -2.93 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP m 271 HIS 0.003 0.001 HIS n 226 PHE 0.024 0.002 PHE m 157 TYR 0.026 0.002 TYR n 50 ARG 0.007 0.001 ARG m 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 50 PHE cc_start: 0.7058 (t80) cc_final: 0.6658 (t80) REVERT: f 111 TYR cc_start: 0.7649 (OUTLIER) cc_final: 0.7333 (m-80) REVERT: f 122 CYS cc_start: 0.3861 (t) cc_final: 0.3397 (t) REVERT: g 109 GLU cc_start: 0.7010 (mp0) cc_final: 0.6748 (mm-30) REVERT: m 207 ASN cc_start: 0.7575 (t0) cc_final: 0.7206 (t0) REVERT: m 233 GLU cc_start: 0.7780 (mm-30) cc_final: 0.6537 (mm-30) REVERT: n 32 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8136 (pp) REVERT: n 204 ASP cc_start: 0.7668 (p0) cc_final: 0.7408 (p0) outliers start: 30 outliers final: 23 residues processed: 255 average time/residue: 0.1876 time to fit residues: 65.9958 Evaluate side-chains 229 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 204 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 75 ASP Chi-restraints excluded: chain n residue 187 SER Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 122 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 31 optimal weight: 0.0170 chunk 75 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 211 ASN n 104 GLN n 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8619 Z= 0.197 Angle : 0.650 9.747 11687 Z= 0.338 Chirality : 0.044 0.262 1309 Planarity : 0.004 0.048 1492 Dihedral : 6.657 59.940 1167 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.36 % Allowed : 14.77 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.30 (0.25), residues: 1057 helix: 2.03 (0.31), residues: 261 sheet: -0.58 (0.30), residues: 275 loop : -2.69 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP m 271 HIS 0.004 0.001 HIS f 61 PHE 0.018 0.001 PHE m 157 TYR 0.027 0.002 TYR n 83 ARG 0.006 0.001 ARG m 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 227 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 PHE cc_start: 0.7138 (t80) cc_final: 0.6757 (t80) REVERT: f 111 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.7119 (m-80) REVERT: g 25 ILE cc_start: 0.8779 (mm) cc_final: 0.8387 (mm) REVERT: g 109 GLU cc_start: 0.7194 (mp0) cc_final: 0.6871 (mp0) REVERT: n 73 ILE cc_start: 0.8153 (mp) cc_final: 0.7590 (tp) REVERT: n 204 ASP cc_start: 0.7857 (p0) cc_final: 0.7503 (p0) outliers start: 41 outliers final: 27 residues processed: 253 average time/residue: 0.1894 time to fit residues: 66.1349 Evaluate side-chains 234 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 206 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 107 ASP Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 268 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 146 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 0.0570 chunk 89 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8619 Z= 0.186 Angle : 0.635 9.608 11687 Z= 0.329 Chirality : 0.043 0.207 1309 Planarity : 0.004 0.051 1492 Dihedral : 6.323 58.814 1167 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.25 % Allowed : 16.37 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -0.87 (0.25), residues: 1057 helix: 2.42 (0.31), residues: 263 sheet: -0.21 (0.30), residues: 274 loop : -2.53 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP m 197 HIS 0.004 0.001 HIS f 61 PHE 0.020 0.001 PHE m 157 TYR 0.016 0.001 TYR n 50 ARG 0.007 0.001 ARG m 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 217 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7802 (t80) cc_final: 0.7525 (t80) REVERT: f 90 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8392 (mm) REVERT: f 111 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.7000 (m-80) REVERT: g 103 MET cc_start: 0.6700 (mmm) cc_final: 0.6454 (mmm) REVERT: n 32 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8044 (pp) REVERT: n 73 ILE cc_start: 0.8227 (mp) cc_final: 0.7704 (tp) REVERT: n 204 ASP cc_start: 0.7942 (p0) cc_final: 0.7558 (p0) outliers start: 40 outliers final: 30 residues processed: 239 average time/residue: 0.2047 time to fit residues: 67.7992 Evaluate side-chains 237 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 204 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 107 ASP Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 103 SER Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 146 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 28 GLN m 211 ASN e 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8619 Z= 0.271 Angle : 0.656 9.500 11687 Z= 0.343 Chirality : 0.044 0.210 1309 Planarity : 0.004 0.042 1492 Dihedral : 6.027 58.953 1165 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.68 % Allowed : 17.75 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -0.70 (0.26), residues: 1057 helix: 2.56 (0.31), residues: 262 sheet: -0.06 (0.31), residues: 269 loop : -2.42 (0.24), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP m 197 HIS 0.003 0.001 HIS f 61 PHE 0.019 0.001 PHE m 157 TYR 0.019 0.002 TYR e 111 ARG 0.009 0.001 ARG m 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 209 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7809 (t80) cc_final: 0.7540 (t80) REVERT: f 90 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8479 (mm) REVERT: f 106 GLU cc_start: 0.6372 (pm20) cc_final: 0.5966 (pm20) REVERT: f 111 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.7088 (m-80) REVERT: g 38 GLU cc_start: 0.6784 (pm20) cc_final: 0.5815 (mp0) REVERT: m 269 ARG cc_start: 0.6775 (ttp80) cc_final: 0.6514 (tmt-80) REVERT: n 32 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.7955 (pp) REVERT: n 73 ILE cc_start: 0.8288 (mp) cc_final: 0.7773 (tp) REVERT: n 204 ASP cc_start: 0.7919 (p0) cc_final: 0.7521 (p0) REVERT: e 58 LEU cc_start: 0.8795 (mm) cc_final: 0.8510 (mm) REVERT: e 92 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8199 (mt0) outliers start: 44 outliers final: 30 residues processed: 235 average time/residue: 0.1829 time to fit residues: 59.8784 Evaluate side-chains 228 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 107 ASP Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 270 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 106 SER Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 146 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8619 Z= 0.197 Angle : 0.630 9.453 11687 Z= 0.327 Chirality : 0.043 0.212 1309 Planarity : 0.004 0.033 1492 Dihedral : 5.851 59.219 1165 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.25 % Allowed : 18.49 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -0.49 (0.26), residues: 1057 helix: 2.99 (0.31), residues: 258 sheet: 0.05 (0.32), residues: 263 loop : -2.37 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP m 197 HIS 0.005 0.001 HIS f 61 PHE 0.015 0.001 PHE m 157 TYR 0.018 0.001 TYR e 111 ARG 0.007 0.001 ARG m 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 206 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7805 (t80) cc_final: 0.7556 (t80) REVERT: f 90 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8381 (mm) REVERT: g 84 MET cc_start: 0.7669 (mmp) cc_final: 0.7469 (mmp) REVERT: m 63 ARG cc_start: 0.7218 (mmm160) cc_final: 0.6969 (mtm180) REVERT: n 32 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7963 (pp) REVERT: n 73 ILE cc_start: 0.8308 (mp) cc_final: 0.7839 (tp) REVERT: n 204 ASP cc_start: 0.7900 (p0) cc_final: 0.7521 (p0) REVERT: n 263 ASP cc_start: 0.7553 (p0) cc_final: 0.7297 (p0) REVERT: e 92 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.7989 (mp10) REVERT: e 101 ARG cc_start: 0.6868 (mmm160) cc_final: 0.6316 (mmt180) outliers start: 40 outliers final: 29 residues processed: 229 average time/residue: 0.1828 time to fit residues: 58.2371 Evaluate side-chains 228 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 107 ASP Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 106 SER Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 146 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8619 Z= 0.217 Angle : 0.630 9.260 11687 Z= 0.329 Chirality : 0.043 0.211 1309 Planarity : 0.004 0.033 1492 Dihedral : 5.747 56.535 1165 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.36 % Allowed : 19.77 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -0.39 (0.26), residues: 1057 helix: 2.98 (0.31), residues: 262 sheet: 0.11 (0.32), residues: 266 loop : -2.31 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP n 178 HIS 0.004 0.001 HIS f 61 PHE 0.018 0.001 PHE m 55 TYR 0.017 0.001 TYR d 71 ARG 0.009 0.001 ARG m 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 200 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7766 (t80) cc_final: 0.7535 (t80) REVERT: f 90 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8449 (mm) REVERT: g 38 GLU cc_start: 0.6747 (pm20) cc_final: 0.5797 (mp0) REVERT: m 63 ARG cc_start: 0.7203 (mmm160) cc_final: 0.6989 (mtm180) REVERT: n 32 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.7937 (pp) REVERT: n 73 ILE cc_start: 0.8326 (mp) cc_final: 0.7835 (tp) REVERT: n 204 ASP cc_start: 0.7912 (p0) cc_final: 0.7498 (p0) REVERT: e 58 LEU cc_start: 0.8827 (mm) cc_final: 0.8500 (mm) REVERT: e 92 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.7811 (mp10) outliers start: 41 outliers final: 33 residues processed: 225 average time/residue: 0.1762 time to fit residues: 56.0756 Evaluate side-chains 223 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 126 THR Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 106 SER Chi-restraints excluded: chain n residue 187 SER Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 146 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8619 Z= 0.194 Angle : 0.631 9.022 11687 Z= 0.327 Chirality : 0.043 0.222 1309 Planarity : 0.004 0.047 1492 Dihedral : 5.669 54.343 1165 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.25 % Allowed : 19.98 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -0.31 (0.26), residues: 1057 helix: 3.04 (0.31), residues: 264 sheet: 0.22 (0.32), residues: 266 loop : -2.31 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP m 197 HIS 0.005 0.001 HIS f 61 PHE 0.028 0.001 PHE m 55 TYR 0.020 0.001 TYR f 150 ARG 0.008 0.001 ARG m 269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 193 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7775 (t80) cc_final: 0.7530 (t80) REVERT: f 90 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8362 (mm) REVERT: g 38 GLU cc_start: 0.6780 (pm20) cc_final: 0.5740 (mp0) REVERT: m 94 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8990 (pt) REVERT: n 32 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7912 (pp) REVERT: n 73 ILE cc_start: 0.8344 (mp) cc_final: 0.7858 (tp) REVERT: n 204 ASP cc_start: 0.7892 (p0) cc_final: 0.7504 (p0) REVERT: e 92 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7771 (mp10) outliers start: 40 outliers final: 30 residues processed: 218 average time/residue: 0.1858 time to fit residues: 56.3305 Evaluate side-chains 227 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 126 THR Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 106 SER Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8619 Z= 0.220 Angle : 0.639 8.980 11687 Z= 0.330 Chirality : 0.043 0.216 1309 Planarity : 0.004 0.051 1492 Dihedral : 5.626 50.280 1165 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.14 % Allowed : 20.09 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1057 helix: 3.10 (0.31), residues: 263 sheet: 0.25 (0.32), residues: 268 loop : -2.31 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP m 57 HIS 0.004 0.001 HIS f 61 PHE 0.021 0.001 PHE m 55 TYR 0.022 0.001 TYR f 150 ARG 0.007 0.001 ARG f 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 197 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 90 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8433 (mm) REVERT: g 38 GLU cc_start: 0.6747 (pm20) cc_final: 0.5727 (mp0) REVERT: n 32 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7869 (pp) REVERT: n 73 ILE cc_start: 0.8366 (mp) cc_final: 0.7842 (tp) REVERT: n 204 ASP cc_start: 0.7923 (p0) cc_final: 0.7513 (p0) REVERT: e 92 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.7802 (mp10) outliers start: 39 outliers final: 33 residues processed: 220 average time/residue: 0.1915 time to fit residues: 58.1652 Evaluate side-chains 225 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 189 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 126 THR Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 106 SER Chi-restraints excluded: chain n residue 187 SER Chi-restraints excluded: chain n residue 286 LEU Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 0.0980 chunk 94 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 0.0870 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8619 Z= 0.275 Angle : 0.668 9.092 11687 Z= 0.346 Chirality : 0.044 0.225 1309 Planarity : 0.004 0.038 1492 Dihedral : 5.692 47.019 1165 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.57 % Allowed : 19.87 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -0.33 (0.26), residues: 1057 helix: 3.01 (0.31), residues: 263 sheet: 0.13 (0.32), residues: 272 loop : -2.28 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP m 57 HIS 0.003 0.001 HIS f 61 PHE 0.022 0.002 PHE m 262 TYR 0.023 0.002 TYR f 150 ARG 0.007 0.001 ARG d 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 183 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 90 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8519 (mm) REVERT: f 111 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.7201 (m-80) REVERT: g 38 GLU cc_start: 0.6798 (pm20) cc_final: 0.5789 (mp0) REVERT: g 84 MET cc_start: 0.7864 (mmp) cc_final: 0.7466 (mmp) REVERT: n 32 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7927 (pp) REVERT: n 73 ILE cc_start: 0.8389 (mp) cc_final: 0.7835 (tp) REVERT: e 92 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.7945 (mt0) outliers start: 43 outliers final: 36 residues processed: 209 average time/residue: 0.1818 time to fit residues: 53.6630 Evaluate side-chains 220 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 54 TYR Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 126 THR Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 267 THR Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 39 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 106 SER Chi-restraints excluded: chain n residue 187 SER Chi-restraints excluded: chain n residue 291 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 119 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.102691 restraints weight = 13574.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106248 restraints weight = 8087.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108657 restraints weight = 5828.990| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8619 Z= 0.229 Angle : 0.661 13.198 11687 Z= 0.339 Chirality : 0.044 0.229 1309 Planarity : 0.004 0.038 1492 Dihedral : 5.625 44.437 1165 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.25 % Allowed : 20.72 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1057 helix: 3.06 (0.30), residues: 263 sheet: 0.28 (0.33), residues: 263 loop : -2.32 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP m 57 HIS 0.004 0.001 HIS f 61 PHE 0.021 0.002 PHE m 262 TYR 0.022 0.001 TYR f 150 ARG 0.009 0.001 ARG m 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2165.23 seconds wall clock time: 39 minutes 1.83 seconds (2341.83 seconds total)