Starting phenix.real_space_refine on Wed Feb 14 02:38:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/02_2024/6jxr_9895.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/02_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_9895/02_2024/6jxr_9895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/02_2024/6jxr_9895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/02_2024/6jxr_9895.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/02_2024/6jxr_9895.pdb" } 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 Residue "g ARG 102": "NH1" <-> "NH2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m ARG 185": "NH1" <-> "NH2" Residue "m ARG 253": "NH1" <-> "NH2" Residue "m ARG 269": "NH1" <-> "NH2" Residue "n PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 228": "NH1" <-> "NH2" Residue "n ARG 246": "NH1" <-> "NH2" Residue "e ARG 115": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 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: 4.93, per 1000 atoms: 0.58 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 - 3.50 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: 3.06 Conformation dependent library (CDL) restraints added in 1.5 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: 0.97 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: 3.36 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: 96.82 - 104.35: 130 104.35 - 111.88: 3958 111.88 - 119.42: 3098 119.42 - 126.95: 4392 126.95 - 134.48: 109 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 2.440 nonbonded pdb=" O THR d 47 " pdb=" OH TYR d 71 " model vdw 2.289 2.440 nonbonded pdb=" NH1 ARG d 57 " pdb=" O ARG m 185 " model vdw 2.297 2.520 nonbonded pdb=" OD1 ASP g 35 " pdb=" OH TYR g 101 " model vdw 2.303 2.440 nonbonded pdb=" O PHE m 160 " pdb=" OG1 THR m 164 " model vdw 2.313 2.440 ... (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 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: 1.870 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: 5.170 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.090 Find NCS groups from input model: 0.330 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.380 ------------------------------------------------------------------------------- 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 : 1.066 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: 0.1961 time to fit residues: 95.0643 Evaluate side-chains 211 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 207 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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: 0.7980 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 93 optimal weight: 0.0010 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 92 GLN g 28 ASN m 28 GLN m 199 ASN m 211 ASN n 104 GLN n 122 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3179 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= 0.212 Angle : 0.687 12.379 11687 Z= 0.354 Chirality : 0.045 0.259 1309 Planarity : 0.005 0.048 1492 Dihedral : 6.767 58.657 1167 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.87 % Favored : 93.95 % Rotamer: Outliers : 3.72 % Allowed : 13.28 % Favored : 83.00 % 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: -2.03 (0.24), residues: 1057 helix: 1.25 (0.31), residues: 261 sheet: -1.13 (0.29), residues: 272 loop : -2.96 (0.22), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP m 271 HIS 0.002 0.001 HIS f 81 PHE 0.023 0.002 PHE m 157 TYR 0.027 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 270 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 235 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: a 50 PHE cc_start: 0.7038 (t80) cc_final: 0.6556 (t80) REVERT: f 111 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: g 109 GLU cc_start: 0.7123 (mp0) cc_final: 0.6728 (mp0) REVERT: m 207 ASN cc_start: 0.7571 (t0) cc_final: 0.7180 (t0) REVERT: m 233 GLU cc_start: 0.7764 (mm-30) cc_final: 0.6607 (mm-30) REVERT: n 32 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8132 (pp) REVERT: n 204 ASP cc_start: 0.7650 (p0) cc_final: 0.7399 (p0) REVERT: n 266 PHE cc_start: 0.6959 (t80) cc_final: 0.6727 (t80) outliers start: 35 outliers final: 25 residues processed: 254 average time/residue: 0.1896 time to fit residues: 67.1163 Evaluate side-chains 227 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 g residue 80 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 162 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 190 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: 1.9990 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 75 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN n 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8619 Z= 0.198 Angle : 0.634 9.579 11687 Z= 0.327 Chirality : 0.043 0.255 1309 Planarity : 0.004 0.039 1492 Dihedral : 6.657 59.618 1167 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.24 % Favored : 93.66 % Rotamer: Outliers : 4.89 % Allowed : 14.56 % Favored : 80.55 % 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: 2.05 (0.31), residues: 267 sheet: -0.65 (0.29), residues: 275 loop : -2.71 (0.24), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP m 271 HIS 0.003 0.001 HIS f 61 PHE 0.018 0.001 PHE m 157 TYR 0.023 0.002 TYR n 50 ARG 0.005 0.001 ARG d 57 *********************** 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 269 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 223 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 PHE cc_start: 0.7135 (t80) cc_final: 0.6752 (t80) REVERT: f 56 GLU cc_start: 0.4962 (tt0) cc_final: 0.4519 (tt0) REVERT: f 111 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.7104 (m-80) REVERT: n 73 ILE cc_start: 0.8176 (mp) cc_final: 0.7594 (tp) REVERT: n 204 ASP cc_start: 0.7816 (p0) cc_final: 0.7496 (p0) outliers start: 46 outliers final: 33 residues processed: 252 average time/residue: 0.1804 time to fit residues: 63.8233 Evaluate side-chains 235 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 201 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 45 ILE 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 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 80 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 106 SER Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 162 SER 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: 1.9990 chunk 70 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 10 optimal weight: 0.0060 chunk 44 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 chunk 89 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5154 ------------------------------------------------------------------------------- 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** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN ** n 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8619 Z= 0.163 Angle : 0.593 9.177 11687 Z= 0.308 Chirality : 0.042 0.194 1309 Planarity : 0.004 0.049 1492 Dihedral : 6.109 58.823 1167 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.87 % Favored : 94.04 % Rotamer: Outliers : 4.68 % Allowed : 16.79 % Favored : 78.53 % 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: -0.78 (0.26), residues: 1057 helix: 2.60 (0.31), residues: 267 sheet: -0.27 (0.31), residues: 263 loop : -2.47 (0.24), residues: 527 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 0.018 0.001 PHE m 157 TYR 0.018 0.001 TYR b 33 ARG 0.014 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 253 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 209 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: a 27 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8511 (mt) REVERT: a 50 PHE cc_start: 0.7132 (t80) cc_final: 0.6784 (t80) REVERT: b 40 PHE cc_start: 0.7820 (t80) cc_final: 0.7526 (t80) REVERT: f 111 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: g 84 MET cc_start: 0.7915 (mmp) cc_final: 0.7445 (mmp) REVERT: n 32 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8028 (pp) REVERT: n 73 ILE cc_start: 0.8303 (mp) cc_final: 0.7727 (tp) REVERT: n 204 ASP cc_start: 0.7903 (p0) cc_final: 0.7528 (p0) outliers start: 44 outliers final: 30 residues processed: 234 average time/residue: 0.1744 time to fit residues: 57.7909 Evaluate side-chains 227 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 194 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 30 GLU 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 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 80 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 m residue 106 SER Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain m residue 255 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 0 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN ** n 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8619 Z= 0.292 Angle : 0.647 9.188 11687 Z= 0.336 Chirality : 0.043 0.212 1309 Planarity : 0.004 0.041 1492 Dihedral : 5.949 53.361 1167 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.91 % Favored : 93.00 % Rotamer: Outliers : 5.21 % Allowed : 17.11 % Favored : 77.68 % 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: -0.68 (0.26), residues: 1057 helix: 2.55 (0.31), residues: 268 sheet: -0.18 (0.31), residues: 262 loop : -2.35 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP m 197 HIS 0.003 0.001 HIS n 226 PHE 0.026 0.002 PHE m 157 TYR 0.015 0.002 TYR b 33 ARG 0.005 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 243 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 90 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8794 (mm) REVERT: f 111 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.7219 (m-80) REVERT: n 32 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.7957 (pp) REVERT: n 73 ILE cc_start: 0.8325 (mp) cc_final: 0.7709 (tp) REVERT: n 204 ASP cc_start: 0.7926 (p0) cc_final: 0.7564 (p0) REVERT: e 92 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8260 (mt0) REVERT: e 101 ARG cc_start: 0.6982 (mmm160) cc_final: 0.6511 (mmt180) outliers start: 49 outliers final: 36 residues processed: 224 average time/residue: 0.1863 time to fit residues: 58.8979 Evaluate side-chains 224 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 184 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain b residue 50 PHE Chi-restraints excluded: chain d residue 30 GLU 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 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 80 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 146 ASP Chi-restraints excluded: chain m residue 162 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 240 ASP 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: 2.9990 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8619 Z= 0.185 Angle : 0.603 8.991 11687 Z= 0.313 Chirality : 0.042 0.212 1309 Planarity : 0.003 0.036 1492 Dihedral : 5.763 52.449 1165 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 4.25 % Allowed : 19.13 % Favored : 76.62 % 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: -0.42 (0.26), residues: 1057 helix: 2.86 (0.31), residues: 268 sheet: 0.08 (0.32), residues: 255 loop : -2.27 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP m 197 HIS 0.005 0.001 HIS f 61 PHE 0.017 0.001 PHE m 55 TYR 0.016 0.001 TYR n 282 ARG 0.004 0.000 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 231 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 191 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 90 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8649 (mm) REVERT: f 111 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: g 84 MET cc_start: 0.7996 (mmp) cc_final: 0.7673 (mmt) REVERT: n 32 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7903 (pp) REVERT: n 73 ILE cc_start: 0.8361 (mp) cc_final: 0.7825 (tp) REVERT: n 204 ASP cc_start: 0.7882 (p0) cc_final: 0.7515 (p0) REVERT: e 92 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8196 (mt0) REVERT: e 101 ARG cc_start: 0.6889 (mmm160) cc_final: 0.6507 (mmt180) outliers start: 40 outliers final: 28 residues processed: 217 average time/residue: 0.1814 time to fit residues: 55.1260 Evaluate side-chains 218 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 186 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 29 LEU 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 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 47 ASP Chi-restraints excluded: chain g residue 80 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 m residue 106 SER Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain m residue 255 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.0370 chunk 11 optimal weight: 0.0770 chunk 56 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 94 GLN ** 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: 0.7780 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8619 Z= 0.152 Angle : 0.574 9.337 11687 Z= 0.300 Chirality : 0.041 0.215 1309 Planarity : 0.003 0.030 1492 Dihedral : 5.524 50.029 1165 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.96 % Favored : 93.85 % Rotamer: Outliers : 4.36 % Allowed : 19.34 % Favored : 76.30 % 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: -0.17 (0.27), residues: 1057 helix: 3.25 (0.31), residues: 265 sheet: 0.27 (0.33), residues: 251 loop : -2.21 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP n 178 HIS 0.005 0.001 HIS f 61 PHE 0.017 0.001 PHE m 55 TYR 0.017 0.001 TYR d 71 ARG 0.004 0.000 ARG d 72 *********************** 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 240 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7866 (t80) cc_final: 0.7592 (t80) REVERT: f 90 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8540 (mm) REVERT: f 111 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6982 (m-80) REVERT: g 38 GLU cc_start: 0.7037 (pm20) cc_final: 0.6119 (mp0) REVERT: g 84 MET cc_start: 0.7996 (mmp) cc_final: 0.7479 (mmt) REVERT: n 32 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7919 (pp) REVERT: n 73 ILE cc_start: 0.8357 (mp) cc_final: 0.7814 (tp) REVERT: e 58 LEU cc_start: 0.8822 (mm) cc_final: 0.8496 (mm) REVERT: e 92 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8134 (mt0) outliers start: 41 outliers final: 29 residues processed: 225 average time/residue: 0.2030 time to fit residues: 64.1310 Evaluate side-chains 222 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 189 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 45 ILE 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 73 CYS Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 39 SER 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 80 ASP Chi-restraints excluded: chain g residue 114 THR Chi-restraints excluded: chain g residue 127 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 106 SER Chi-restraints excluded: chain m residue 146 ASP 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 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 189 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** ** d 94 GLN ** 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: 0.7813 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8619 Z= 0.207 Angle : 0.610 11.322 11687 Z= 0.315 Chirality : 0.042 0.219 1309 Planarity : 0.003 0.032 1492 Dihedral : 5.478 43.428 1165 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.81 % Favored : 93.00 % Rotamer: Outliers : 3.72 % Allowed : 20.72 % Favored : 75.56 % 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: -0.14 (0.27), residues: 1057 helix: 3.33 (0.31), residues: 263 sheet: 0.29 (0.33), residues: 251 loop : -2.20 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP m 197 HIS 0.004 0.001 HIS f 61 PHE 0.022 0.001 PHE m 262 TYR 0.018 0.001 TYR d 71 ARG 0.005 0.001 ARG d 72 *********************** 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 221 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7975 (t80) cc_final: 0.7626 (t80) REVERT: f 90 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8600 (mm) REVERT: f 111 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.7059 (m-80) REVERT: g 38 GLU cc_start: 0.7087 (pm20) cc_final: 0.6710 (pm20) REVERT: g 84 MET cc_start: 0.8041 (mmp) cc_final: 0.7492 (mmp) REVERT: n 32 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.7923 (pp) REVERT: n 73 ILE cc_start: 0.8395 (mp) cc_final: 0.7839 (tp) REVERT: e 92 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8150 (mt0) outliers start: 35 outliers final: 27 residues processed: 211 average time/residue: 0.1909 time to fit residues: 56.3723 Evaluate side-chains 213 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 182 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 45 ILE 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 73 CYS Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 39 SER 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 80 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 m residue 106 SER Chi-restraints excluded: chain m residue 146 ASP 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 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 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: 2.9990 chunk 92 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 28 optimal weight: 0.0070 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- 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** ** d 94 GLN ** 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: 0.7815 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8619 Z= 0.202 Angle : 0.603 9.731 11687 Z= 0.312 Chirality : 0.042 0.227 1309 Planarity : 0.003 0.032 1492 Dihedral : 5.415 43.074 1165 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.72 % Favored : 93.09 % Rotamer: Outliers : 3.72 % Allowed : 20.94 % Favored : 75.35 % 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: -0.11 (0.27), residues: 1057 helix: 3.40 (0.31), residues: 263 sheet: 0.27 (0.33), residues: 253 loop : -2.20 (0.25), residues: 541 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 0.021 0.001 PHE m 262 TYR 0.020 0.001 TYR f 150 ARG 0.005 0.000 ARG d 72 *********************** 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 218 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7942 (t80) cc_final: 0.7621 (t80) REVERT: f 90 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8623 (mm) REVERT: f 111 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.7117 (m-80) REVERT: g 38 GLU cc_start: 0.7079 (pm20) cc_final: 0.6742 (pm20) REVERT: g 84 MET cc_start: 0.8032 (mmp) cc_final: 0.7484 (mmp) REVERT: n 32 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7895 (pp) REVERT: n 73 ILE cc_start: 0.8417 (mp) cc_final: 0.7844 (tp) outliers start: 35 outliers final: 29 residues processed: 206 average time/residue: 0.1845 time to fit residues: 53.4290 Evaluate side-chains 212 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 45 ILE 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 40 SER Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 39 SER 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 80 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 m residue 106 SER Chi-restraints excluded: chain m residue 146 ASP 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 270 LEU Chi-restraints excluded: chain m residue 272 SER 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 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER 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: 6.9990 chunk 46 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** ** d 94 GLN ** 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: 0.7864 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8619 Z= 0.296 Angle : 0.650 12.216 11687 Z= 0.335 Chirality : 0.043 0.232 1309 Planarity : 0.004 0.038 1492 Dihedral : 5.327 42.266 1162 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.57 % Favored : 92.24 % Rotamer: Outliers : 3.72 % Allowed : 21.68 % Favored : 74.60 % 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: -0.21 (0.27), residues: 1057 helix: 3.21 (0.31), residues: 263 sheet: 0.21 (0.33), residues: 253 loop : -2.19 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP m 197 HIS 0.002 0.001 HIS n 226 PHE 0.022 0.002 PHE m 262 TYR 0.023 0.002 TYR f 150 ARG 0.005 0.001 ARG e 101 ********************** 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 216 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.8009 (t80) cc_final: 0.7671 (t80) REVERT: f 90 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8774 (mm) REVERT: f 111 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.7221 (m-80) REVERT: f 128 MET cc_start: 0.6721 (ppp) cc_final: 0.6466 (ppp) REVERT: g 38 GLU cc_start: 0.7345 (pm20) cc_final: 0.7091 (pm20) REVERT: n 32 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7918 (pp) REVERT: n 73 ILE cc_start: 0.8481 (mp) cc_final: 0.7917 (tp) outliers start: 35 outliers final: 28 residues processed: 204 average time/residue: 0.1827 time to fit residues: 52.3776 Evaluate side-chains 209 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 178 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain b residue 45 ILE 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 73 CYS Chi-restraints excluded: chain d residue 93 CYS Chi-restraints excluded: chain f residue 39 SER 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 80 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 m residue 106 SER Chi-restraints excluded: chain m residue 146 ASP 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 270 LEU Chi-restraints excluded: chain m residue 272 SER 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 301 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER 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 25 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** ** d 94 GLN ** 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 = 0.3748 r_free = 0.3748 target = 0.134783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.104218 restraints weight = 13536.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105919 restraints weight = 9950.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108017 restraints weight = 7102.743| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8619 Z= 0.258 Angle : 0.641 11.365 11687 Z= 0.330 Chirality : 0.043 0.238 1309 Planarity : 0.004 0.040 1492 Dihedral : 5.301 42.186 1162 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.00 % Favored : 92.81 % Rotamer: Outliers : 3.93 % Allowed : 21.36 % Favored : 74.71 % 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: -0.22 (0.26), residues: 1057 helix: 3.18 (0.31), residues: 263 sheet: 0.19 (0.33), residues: 253 loop : -2.18 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP m 197 HIS 0.003 0.001 HIS f 61 PHE 0.021 0.001 PHE m 262 TYR 0.024 0.002 TYR f 150 ARG 0.005 0.000 ARG d 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2087.94 seconds wall clock time: 38 minutes 53.48 seconds (2333.48 seconds total)