Starting phenix.real_space_refine (version: dev) on Sat Feb 18 16:10:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/02_2023/6jxr_9895.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/02_2023/6jxr_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_2023/6jxr_9895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/02_2023/6jxr_9895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/02_2023/6jxr_9895.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxr_9895/02_2023/6jxr_9895.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 5.33, per 1000 atoms: 0.63 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: 3.19 Conformation dependent library (CDL) restraints added in 1.3 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: 0.51 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: 2.34 Time building geometry restraints manager: 3.48 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 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. 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: 0.010 Normalize map: mean=0, sd=1: 1.130 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: 5.350 Check model and map are aligned: 0.110 Process input model: 25.040 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 1.010 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 % 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 *********************** 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 : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 356 average time/residue: 0.2027 time to fit residues: 97.8107 Evaluate side-chains 208 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 205 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0942 time to fit residues: 1.9534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 93 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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: 0.7919 moved from start: 0.3193 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= 0.196 Angle : 0.681 12.344 11687 Z= 0.351 Chirality : 0.045 0.282 1309 Planarity : 0.005 0.048 1492 Dihedral : 5.789 40.519 1159 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.68 % Favored : 94.13 % Rotamer Outliers : 3.29 % 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: -2.02 (0.24), residues: 1057 helix: 1.18 (0.30), residues: 267 sheet: -1.14 (0.29), residues: 272 loop : -2.95 (0.23), residues: 518 *********************** 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 267 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 236 time to evaluate : 1.007 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 22 residues processed: 250 average time/residue: 0.1900 time to fit residues: 65.8753 Evaluate side-chains 229 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 207 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.0822 time to fit residues: 4.7921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 92 optimal weight: 0.0170 chunk 31 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.7622 ------------------------------------------------------------------------------- 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 m 211 ASN n 221 GLN ** n 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 8619 Z= 0.208 Angle : 0.642 9.556 11687 Z= 0.333 Chirality : 0.044 0.249 1309 Planarity : 0.004 0.040 1492 Dihedral : 5.534 39.437 1159 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.43 % Favored : 93.47 % Rotamer Outliers : 2.44 % 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: -1.28 (0.25), residues: 1057 helix: 2.12 (0.31), residues: 267 sheet: -0.67 (0.29), residues: 275 loop : -2.71 (0.24), residues: 515 *********************** 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 240 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 217 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 234 average time/residue: 0.1897 time to fit residues: 61.8186 Evaluate side-chains 209 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0822 time to fit residues: 3.3812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 94 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 89 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ** 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: 0.7934 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 8619 Z= 0.163 Angle : 0.598 9.258 11687 Z= 0.310 Chirality : 0.043 0.263 1309 Planarity : 0.004 0.051 1492 Dihedral : 5.200 40.401 1159 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.05 % Favored : 93.85 % Rotamer Outliers : 2.13 % 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: -0.84 (0.25), residues: 1057 helix: 2.60 (0.31), residues: 267 sheet: -0.34 (0.31), residues: 263 loop : -2.52 (0.24), residues: 527 *********************** 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 224 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 204 time to evaluate : 1.050 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 216 average time/residue: 0.1911 time to fit residues: 58.4757 Evaluate side-chains 204 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0853 time to fit residues: 3.3105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 0 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ** 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: 0.7983 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8619 Z= 0.222 Angle : 0.626 9.147 11687 Z= 0.323 Chirality : 0.043 0.205 1309 Planarity : 0.004 0.040 1492 Dihedral : 5.144 39.437 1159 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.34 % Favored : 93.57 % Rotamer Outliers : 2.02 % 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: -0.63 (0.26), residues: 1057 helix: 2.74 (0.31), residues: 268 sheet: -0.19 (0.31), residues: 263 loop : -2.38 (0.24), residues: 526 *********************** 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 213 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 206 average time/residue: 0.1996 time to fit residues: 57.5415 Evaluate side-chains 196 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0811 time to fit residues: 3.1372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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: 0.8002 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 8619 Z= 0.237 Angle : 0.618 9.032 11687 Z= 0.321 Chirality : 0.042 0.218 1309 Planarity : 0.004 0.037 1492 Dihedral : 5.203 42.444 1159 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.62 % Favored : 93.28 % Rotamer Outliers : 2.13 % 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: -0.51 (0.26), residues: 1057 helix: 2.86 (0.31), residues: 268 sheet: -0.09 (0.32), residues: 257 loop : -2.31 (0.24), residues: 532 *********************** 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 216 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 205 average time/residue: 0.1953 time to fit residues: 55.4403 Evaluate side-chains 197 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 184 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1019 time to fit residues: 3.6481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4718 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= 0.205 Angle : 0.620 10.636 11687 Z= 0.319 Chirality : 0.042 0.220 1309 Planarity : 0.004 0.033 1492 Dihedral : 5.100 39.046 1159 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.34 % Favored : 93.47 % Rotamer Outliers : 1.91 % 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: -0.35 (0.26), residues: 1057 helix: 3.14 (0.31), residues: 262 sheet: 0.08 (0.32), residues: 259 loop : -2.29 (0.24), residues: 536 *********************** 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 213 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 206 average time/residue: 0.1963 time to fit residues: 56.1448 Evaluate side-chains 195 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0807 time to fit residues: 3.0242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 0.0060 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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: 0.7952 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 8619 Z= 0.160 Angle : 0.588 8.874 11687 Z= 0.306 Chirality : 0.042 0.226 1309 Planarity : 0.003 0.030 1492 Dihedral : 4.910 39.930 1159 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.77 % Favored : 94.04 % Rotamer Outliers : 1.06 % 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: -0.18 (0.26), residues: 1057 helix: 3.37 (0.30), residues: 262 sheet: 0.18 (0.33), residues: 253 loop : -2.21 (0.24), residues: 542 *********************** 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 209 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 199 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 205 average time/residue: 0.2102 time to fit residues: 58.9724 Evaluate side-chains 197 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0784 time to fit residues: 2.3139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.1183 > 50: distance: 77 - 81: 22.490 distance: 81 - 82: 32.899 distance: 82 - 83: 40.512 distance: 82 - 85: 26.185 distance: 83 - 84: 10.784 distance: 83 - 86: 31.029 distance: 86 - 87: 10.506 distance: 87 - 88: 45.220 distance: 87 - 90: 32.072 distance: 88 - 89: 27.776 distance: 88 - 92: 40.175 distance: 90 - 91: 12.436 distance: 92 - 93: 14.159 distance: 93 - 94: 38.612 distance: 93 - 96: 24.252 distance: 94 - 95: 24.683 distance: 94 - 103: 24.903 distance: 96 - 97: 20.520 distance: 97 - 98: 31.515 distance: 98 - 99: 26.150 distance: 99 - 100: 34.901 distance: 100 - 101: 17.511 distance: 100 - 102: 24.433 distance: 103 - 104: 58.424 distance: 104 - 105: 45.386 distance: 104 - 107: 38.437 distance: 105 - 106: 21.593 distance: 105 - 114: 46.449 distance: 107 - 108: 27.666 distance: 108 - 109: 23.929 distance: 109 - 110: 15.274 distance: 110 - 111: 17.037 distance: 111 - 112: 10.389 distance: 111 - 113: 10.174 distance: 114 - 115: 56.927 distance: 115 - 116: 44.984 distance: 115 - 118: 44.116 distance: 116 - 117: 29.143 distance: 116 - 119: 53.082 distance: 119 - 120: 22.267 distance: 120 - 121: 15.307 distance: 120 - 123: 20.767 distance: 121 - 122: 45.766 distance: 121 - 128: 18.229 distance: 123 - 124: 7.408 distance: 124 - 125: 31.094 distance: 125 - 126: 19.937 distance: 125 - 127: 25.509 distance: 128 - 129: 7.994 distance: 129 - 130: 20.438 distance: 130 - 131: 45.724 distance: 130 - 132: 23.854 distance: 132 - 133: 34.139 distance: 133 - 134: 25.817 distance: 133 - 136: 52.867 distance: 134 - 135: 20.731 distance: 134 - 137: 37.428 distance: 137 - 138: 14.045 distance: 138 - 139: 41.075 distance: 138 - 141: 17.128 distance: 139 - 140: 60.695 distance: 139 - 143: 9.307 distance: 141 - 142: 44.723 distance: 143 - 144: 41.536 distance: 144 - 145: 34.937 distance: 145 - 146: 26.155 distance: 145 - 147: 12.406