Starting phenix.real_space_refine on Sun May 11 22:29:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fjd_31618/05_2025/7fjd_31618.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjd_31618/05_2025/7fjd_31618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fjd_31618/05_2025/7fjd_31618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjd_31618/05_2025/7fjd_31618.map" model { file = "/net/cci-nas-00/data/ceres_data/7fjd_31618/05_2025/7fjd_31618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjd_31618/05_2025/7fjd_31618.cif" } resolution = 3.2 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= 0.006 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 5341 2.51 5 N 1368 2.21 5 O 1589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8352 Number of models: 1 Model: "" Number of chains: 10 Chain: "a" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 264 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "b" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 103} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 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} Chain: "f" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 946 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "g" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 887 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1923 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 233} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2241 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.19, per 1000 atoms: 0.62 Number of scatterers: 8352 At special positions: 0 Unit cell: (89.1, 99, 144.1, 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 1589 8.00 N 1368 7.00 C 5341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, 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=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.04 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.04 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 111 " distance=2.04 Simple disulfide: pdb=" SG CYS m 155 " - pdb=" SG CYS m 205 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS n 164 " - pdb=" SG CYS n 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 999.2 milliseconds 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 18 sheets defined 26.4% alpha, 28.7% 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 29 through 54 removed outlier: 4.480A pdb=" N LEU a 39 " --> pdb=" O LEU a 35 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS a 54 " --> pdb=" O PHE a 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 54 removed outlier: 3.685A pdb=" N ASP b 36 " --> pdb=" O CYS b 32 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE b 38 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU b 39 " --> pdb=" O LEU b 35 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR b 47 " --> pdb=" O GLY b 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 66 No H-bonds generated for 'chain 'd' and resid 64 through 66' Processing helix chain 'd' and resid 76 through 80 Processing helix chain 'd' and resid 102 through 126 removed outlier: 4.076A pdb=" N PHE d 123 " --> pdb=" O ALA d 119 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS d 124 " --> pdb=" O LEU d 120 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE d 125 " --> pdb=" O GLY d 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 108 removed outlier: 3.830A pdb=" N ASP e 107 " --> pdb=" O LYS e 104 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 154 removed outlier: 4.180A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA e 131 " --> pdb=" O VAL e 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 removed outlier: 3.967A pdb=" N ASP f 107 " --> pdb=" O LYS f 104 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA f 108 " --> pdb=" O PRO f 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 104 through 108' Processing helix chain 'f' and resid 128 through 142 Processing helix chain 'f' and resid 143 through 154 Processing helix chain 'g' and resid 78 through 80 No H-bonds generated for 'chain 'g' and resid 78 through 80' Processing helix chain 'g' and resid 111 through 138 removed outlier: 3.729A pdb=" N ILE g 115 " --> pdb=" O ASN g 111 " (cutoff:3.500A) Processing helix chain 'm' and resid 231 through 235 removed outlier: 3.540A pdb=" N LYS m 234 " --> pdb=" O LEU m 231 " (cutoff:3.500A) Processing helix chain 'm' and resid 240 through 273 removed outlier: 4.008A pdb=" N ILE m 254 " --> pdb=" O ILE m 250 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER m 273 " --> pdb=" O ARG m 269 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 105 removed outlier: 3.628A pdb=" N THR n 105 " --> pdb=" O PRO n 102 " (cutoff:3.500A) Processing helix chain 'n' and resid 150 through 157 removed outlier: 3.641A pdb=" N ILE n 154 " --> pdb=" O SER n 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 217 through 221 Processing helix chain 'n' and resid 269 through 308 removed outlier: 4.172A pdb=" N GLN n 273 " --> pdb=" O GLU n 269 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS n 308 " --> pdb=" O MET n 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 27 removed outlier: 6.075A 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: 6.842A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLY d 46 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG d 68 " --> pdb=" O GLY d 46 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN e 60 " --> pdb=" O VAL e 97 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TRP e 59 " --> pdb=" O ILE e 66 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE e 66 " --> pdb=" O TRP e 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 40 removed outlier: 3.656A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER e 83 " --> pdb=" O GLY e 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 41 removed outlier: 3.510A pdb=" N THR f 44 " --> pdb=" O SER f 41 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU f 47 " --> pdb=" O LEU f 82 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY f 76 " --> pdb=" O SER f 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 57 through 61 removed outlier: 3.513A pdb=" N LEU f 114 " --> pdb=" O GLY f 94 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG f 115 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG g 102 " --> pdb=" O ARG f 115 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY g 83 " --> pdb=" O VAL g 99 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE g 53 " --> pdb=" O PHE g 64 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N PHE g 64 " --> pdb=" O ILE g 53 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE g 62 " --> pdb=" O TRP g 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 122 through 124 removed outlier: 3.616A pdb=" N ILE g 108 " --> pdb=" O MET f 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.785A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'm' and resid 33 through 36 removed outlier: 3.554A pdb=" N LEU m 33 " --> pdb=" O MET m 127 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR m 54 " --> pdb=" O SER m 114 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE m 55 " --> pdb=" O TYR m 71 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR m 71 " --> pdb=" O PHE m 55 " (cutoff:3.500A) removed outlier: 6.948A 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: 3.554A pdb=" N LEU m 33 " --> pdb=" O MET m 127 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 41 through 46 Processing sheet with id=AB3, first strand: chain 'm' and resid 140 through 143 removed outlier: 4.093A pdb=" N ALA m 140 " --> pdb=" O THR m 158 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER m 153 " --> pdb=" O SER m 198 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER m 198 " --> pdb=" O SER m 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 180 through 184 Processing sheet with id=AB5, first strand: chain 'n' and resid 24 through 26 removed outlier: 3.632A pdb=" N MET n 38 " --> pdb=" O LEU n 97 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN n 84 " --> pdb=" O ARG n 96 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'n' and resid 29 through 33 removed outlier: 6.856A pdb=" N GLN n 30 " --> pdb=" O THR n 131 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR n 133 " --> pdb=" O GLN n 30 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU n 32 " --> pdb=" O THR n 133 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL n 107 " --> pdb=" O GLN n 56 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE n 109 " --> pdb=" O TYR n 54 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET n 51 " --> pdb=" O TYR n 67 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR n 67 " --> pdb=" O MET n 51 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TRP n 53 " --> pdb=" O ILE n 65 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL n 69 " --> pdb=" O ILE n 73 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE n 73 " --> pdb=" O VAL n 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'n' and resid 143 through 147 removed outlier: 3.543A pdb=" N VAL n 163 " --> pdb=" O PHE n 147 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'n' and resid 143 through 147 removed outlier: 3.543A pdb=" N VAL n 163 " --> pdb=" O PHE n 147 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'n' and resid 183 through 184 372 hydrogen bonds defined for protein. 1026 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: 2.22 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2067 1.33 - 1.46: 2117 1.46 - 1.58: 4275 1.58 - 1.71: 0 1.71 - 1.84: 76 Bond restraints: 8535 Sorted by residual: bond pdb=" CG LEU a 27 " pdb=" CD2 LEU a 27 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.90e+00 bond pdb=" N ILE d 78 " pdb=" CA ILE d 78 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.30e-02 5.92e+03 7.41e+00 bond pdb=" N ILE n 253 " pdb=" CA ILE n 253 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.29e-02 6.01e+03 6.39e+00 bond pdb=" N CYS b 32 " pdb=" CA CYS b 32 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.26e-02 6.30e+03 6.23e+00 bond pdb=" CB ARG e 117 " pdb=" CG ARG e 117 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.12e+00 ... (remaining 8530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 11369 3.60 - 7.20: 185 7.20 - 10.80: 26 10.80 - 14.40: 4 14.40 - 18.00: 2 Bond angle restraints: 11586 Sorted by residual: angle pdb=" C PHE m 160 " pdb=" N ASP m 161 " pdb=" CA ASP m 161 " ideal model delta sigma weight residual 121.54 133.64 -12.10 1.91e+00 2.74e-01 4.02e+01 angle pdb=" C LYS g 79 " pdb=" N ASP g 80 " pdb=" CA ASP g 80 " ideal model delta sigma weight residual 121.80 134.79 -12.99 2.44e+00 1.68e-01 2.83e+01 angle pdb=" CA TYR n 50 " pdb=" CB TYR n 50 " pdb=" CG TYR n 50 " ideal model delta sigma weight residual 113.90 123.18 -9.28 1.80e+00 3.09e-01 2.66e+01 angle pdb=" N ASP m 159 " pdb=" CA ASP m 159 " pdb=" C ASP m 159 " ideal model delta sigma weight residual 110.42 117.93 -7.51 1.46e+00 4.69e-01 2.65e+01 angle pdb=" CA LEU m 182 " pdb=" CB LEU m 182 " pdb=" CG LEU m 182 " ideal model delta sigma weight residual 116.30 134.30 -18.00 3.50e+00 8.16e-02 2.65e+01 ... (remaining 11581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 4888 17.13 - 34.26: 236 34.26 - 51.39: 70 51.39 - 68.52: 16 68.52 - 85.65: 9 Dihedral angle restraints: 5219 sinusoidal: 2143 harmonic: 3076 Sorted by residual: dihedral pdb=" CA GLU n 49 " pdb=" C GLU n 49 " pdb=" N TYR n 50 " pdb=" CA TYR n 50 " ideal model delta harmonic sigma weight residual 180.00 127.81 52.19 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual 93.00 178.65 -85.65 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CA MET g 103 " pdb=" C MET g 103 " pdb=" N CYS g 104 " pdb=" CA CYS g 104 " ideal model delta harmonic sigma weight residual 180.00 -135.19 -44.81 0 5.00e+00 4.00e-02 8.03e+01 ... (remaining 5216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1113 0.095 - 0.191: 181 0.191 - 0.286: 9 0.286 - 0.382: 1 0.382 - 0.477: 1 Chirality restraints: 1305 Sorted by residual: chirality pdb=" CB ILE m 134 " pdb=" CA ILE m 134 " pdb=" CG1 ILE m 134 " pdb=" CG2 ILE m 134 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" CA ASP g 80 " pdb=" N ASP g 80 " pdb=" C ASP g 80 " pdb=" CB ASP g 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+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 -2.32 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1302 not shown) Planarity restraints: 1466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR n 50 " -0.043 2.00e-02 2.50e+03 2.67e-02 1.42e+01 pdb=" CG TYR n 50 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR n 50 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR n 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR n 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR n 50 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR n 50 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR n 50 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR e 111 " -0.027 2.00e-02 2.50e+03 2.60e-02 1.35e+01 pdb=" CG TYR e 111 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR e 111 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR e 111 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR e 111 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR e 111 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR e 111 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR e 111 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 90 " -0.026 2.00e-02 2.50e+03 2.56e-02 1.31e+01 pdb=" CG TYR d 90 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR d 90 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR d 90 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR d 90 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR d 90 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR d 90 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR d 90 " -0.002 2.00e-02 2.50e+03 ... (remaining 1463 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1302 2.76 - 3.30: 6821 3.30 - 3.83: 12089 3.83 - 4.37: 13423 4.37 - 4.90: 24896 Nonbonded interactions: 58531 Sorted by model distance: nonbonded pdb=" NZ LYS b 30 " pdb=" O1 CLR b 201 " model vdw 2.229 3.120 nonbonded pdb=" N ASP m 159 " pdb=" OD1 ASP m 159 " model vdw 2.305 3.120 nonbonded pdb=" OG SER m 118 " pdb=" OE1 GLN n 116 " model vdw 2.310 3.040 nonbonded pdb=" O TYR m 71 " pdb=" NZ LYS m 78 " model vdw 2.408 3.120 nonbonded pdb=" N ASP g 39 " pdb=" OD1 ASP g 39 " model vdw 2.409 3.120 ... (remaining 58526 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and (resid 26 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 54)) selection = (chain 'b' and resid 26 through 54) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 77 or (resid 78 and (nam \ e N or name CA or name C or name O or name CB )) or resid 79 through 155)) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.140 Find NCS groups from input model: 0.160 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.011 0.120 8548 Z= 0.450 Angle : 1.251 18.002 11612 Z= 0.670 Chirality : 0.068 0.477 1305 Planarity : 0.008 0.073 1466 Dihedral : 11.941 82.404 3206 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.94 % Favored : 90.87 % Rotamer: Outliers : 0.87 % Allowed : 6.19 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -3.57 (0.22), residues: 1040 helix: -1.03 (0.28), residues: 237 sheet: -1.35 (0.29), residues: 292 loop : -3.79 (0.19), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP e 59 HIS 0.018 0.005 HIS f 61 PHE 0.041 0.005 PHE f 110 TYR 0.063 0.005 TYR d 90 ARG 0.015 0.002 ARG d 63 Details of bonding type rmsd hydrogen bonds : bond 0.26212 ( 353) hydrogen bonds : angle 7.52542 ( 1026) SS BOND : bond 0.00549 ( 13) SS BOND : angle 3.74477 ( 26) covalent geometry : bond 0.01061 ( 8535) covalent geometry : angle 1.24022 (11586) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 0.859 Fit side-chains REVERT: e 41 SER cc_start: 0.9071 (t) cc_final: 0.8756 (p) REVERT: e 57 ILE cc_start: 0.8760 (mp) cc_final: 0.8355 (tt) REVERT: f 117 ARG cc_start: 0.8506 (ttm170) cc_final: 0.8258 (ttm170) REVERT: g 32 LYS cc_start: 0.8422 (mmtp) cc_final: 0.8215 (mptt) REVERT: g 53 ILE cc_start: 0.7888 (mm) cc_final: 0.7685 (mt) REVERT: m 99 ARG cc_start: 0.7189 (ptp90) cc_final: 0.6860 (mtm-85) REVERT: m 173 ASP cc_start: 0.7734 (m-30) cc_final: 0.7082 (p0) REVERT: m 211 ASN cc_start: 0.8609 (t160) cc_final: 0.8401 (t0) REVERT: n 33 LYS cc_start: 0.7903 (ttpt) cc_final: 0.7531 (ptmt) REVERT: n 92 ASP cc_start: 0.7574 (m-30) cc_final: 0.6680 (t70) REVERT: n 96 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7403 (mtt90) REVERT: n 113 ARG cc_start: 0.6255 (mtp180) cc_final: 0.5994 (mtm180) REVERT: n 121 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6581 (mp0) REVERT: n 183 LYS cc_start: 0.7914 (mttt) cc_final: 0.7421 (mtpp) outliers start: 8 outliers final: 1 residues processed: 202 average time/residue: 0.2480 time to fit residues: 64.6826 Evaluate side-chains 135 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 30 optimal weight: 0.0270 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 36 ASN ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 65 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 136 ASN m 168 GLN n 25 GLN n 47 ASN ** n 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.153868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.118360 restraints weight = 9937.232| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.06 r_work: 0.3013 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8548 Z= 0.129 Angle : 0.607 8.475 11612 Z= 0.324 Chirality : 0.043 0.216 1305 Planarity : 0.005 0.049 1466 Dihedral : 7.128 55.981 1275 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.71 % Allowed : 7.93 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.71 (0.25), residues: 1040 helix: 1.78 (0.33), residues: 241 sheet: -0.06 (0.32), residues: 273 loop : -3.38 (0.21), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP m 197 HIS 0.004 0.001 HIS f 81 PHE 0.016 0.001 PHE m 157 TYR 0.030 0.001 TYR n 50 ARG 0.003 0.000 ARG f 115 Details of bonding type rmsd hydrogen bonds : bond 0.06715 ( 353) hydrogen bonds : angle 4.84455 ( 1026) SS BOND : bond 0.00319 ( 13) SS BOND : angle 1.20596 ( 26) covalent geometry : bond 0.00244 ( 8535) covalent geometry : angle 0.60545 (11586) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.890 Fit side-chains REVERT: b 34 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7688 (mt) REVERT: d 99 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7233 (pp) REVERT: e 41 SER cc_start: 0.9091 (t) cc_final: 0.8863 (p) REVERT: e 57 ILE cc_start: 0.8834 (mp) cc_final: 0.8446 (tt) REVERT: e 80 ASP cc_start: 0.8454 (p0) cc_final: 0.8132 (p0) REVERT: f 39 SER cc_start: 0.8432 (t) cc_final: 0.8173 (m) REVERT: f 80 ASP cc_start: 0.8114 (t70) cc_final: 0.7688 (t0) REVERT: f 101 ARG cc_start: 0.7821 (tpp-160) cc_final: 0.7606 (tpp-160) REVERT: g 30 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7456 (mp) REVERT: m 100 ASP cc_start: 0.6999 (m-30) cc_final: 0.6788 (t0) REVERT: m 173 ASP cc_start: 0.7823 (m-30) cc_final: 0.7139 (p0) REVERT: m 211 ASN cc_start: 0.8717 (t160) cc_final: 0.8361 (t0) REVERT: n 33 LYS cc_start: 0.7887 (ttpt) cc_final: 0.7462 (ptmt) REVERT: n 92 ASP cc_start: 0.7616 (m-30) cc_final: 0.6764 (t70) REVERT: n 96 ARG cc_start: 0.7780 (mtt180) cc_final: 0.7332 (mtt90) REVERT: n 121 GLU cc_start: 0.7514 (mt-10) cc_final: 0.6687 (mp0) REVERT: n 302 MET cc_start: 0.7392 (ttp) cc_final: 0.5774 (mmt) outliers start: 25 outliers final: 13 residues processed: 176 average time/residue: 0.2149 time to fit residues: 50.4534 Evaluate side-chains 140 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 71 LYS Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 95 SER Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 86 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 128 HIS ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS m 28 GLN ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.107886 restraints weight = 10223.604| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.18 r_work: 0.2830 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 8548 Z= 0.270 Angle : 0.787 12.206 11612 Z= 0.410 Chirality : 0.049 0.222 1305 Planarity : 0.006 0.055 1466 Dihedral : 7.041 48.996 1275 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.75 % Favored : 91.15 % Rotamer: Outliers : 5.54 % Allowed : 9.99 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.50 (0.25), residues: 1040 helix: 1.93 (0.32), residues: 241 sheet: 0.07 (0.32), residues: 290 loop : -3.32 (0.21), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP d 43 HIS 0.009 0.002 HIS n 173 PHE 0.020 0.003 PHE m 157 TYR 0.031 0.003 TYR n 50 ARG 0.004 0.001 ARG n 114 Details of bonding type rmsd hydrogen bonds : bond 0.09473 ( 353) hydrogen bonds : angle 4.93757 ( 1026) SS BOND : bond 0.00540 ( 13) SS BOND : angle 1.73811 ( 26) covalent geometry : bond 0.00662 ( 8535) covalent geometry : angle 0.78392 (11586) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 136 time to evaluate : 0.888 Fit side-chains REVERT: b 34 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7702 (mt) REVERT: d 29 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8066 (mm) REVERT: d 99 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.6866 (pp) REVERT: d 117 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7639 (tm) REVERT: e 41 SER cc_start: 0.9165 (t) cc_final: 0.8899 (p) REVERT: e 57 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8484 (tt) REVERT: e 79 GLU cc_start: 0.8174 (pm20) cc_final: 0.7141 (tp30) REVERT: e 114 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8426 (pt) REVERT: e 144 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7475 (tp) REVERT: f 80 ASP cc_start: 0.8174 (t70) cc_final: 0.7748 (t0) REVERT: f 101 ARG cc_start: 0.7781 (tpp-160) cc_final: 0.7556 (tpp-160) REVERT: m 100 ASP cc_start: 0.6994 (m-30) cc_final: 0.6736 (t0) REVERT: m 173 ASP cc_start: 0.7976 (m-30) cc_final: 0.7265 (p0) REVERT: m 211 ASN cc_start: 0.8802 (t160) cc_final: 0.8553 (t0) REVERT: n 33 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7585 (ptmt) REVERT: n 46 MET cc_start: 0.4456 (tmm) cc_final: 0.3810 (tmm) REVERT: n 50 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.5779 (p90) REVERT: n 92 ASP cc_start: 0.7637 (m-30) cc_final: 0.6705 (t70) REVERT: n 96 ARG cc_start: 0.7892 (mtt180) cc_final: 0.7414 (mtt90) REVERT: n 121 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6565 (mp0) REVERT: n 183 LYS cc_start: 0.8076 (mttt) cc_final: 0.7590 (mtpp) REVERT: n 252 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7996 (pt0) outliers start: 51 outliers final: 29 residues processed: 170 average time/residue: 0.2119 time to fit residues: 48.1709 Evaluate side-chains 167 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 141 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 149 SER Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain m residue 267 THR Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 290 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.0970 chunk 57 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 ASN n 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.152827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.115950 restraints weight = 10085.494| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.20 r_work: 0.2955 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8548 Z= 0.114 Angle : 0.552 8.586 11612 Z= 0.294 Chirality : 0.042 0.184 1305 Planarity : 0.004 0.044 1466 Dihedral : 5.859 46.406 1275 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.47 % Allowed : 12.70 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.77 (0.26), residues: 1040 helix: 2.96 (0.32), residues: 241 sheet: 0.23 (0.31), residues: 317 loop : -3.07 (0.23), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP d 43 HIS 0.005 0.001 HIS n 173 PHE 0.014 0.001 PHE m 157 TYR 0.022 0.001 TYR n 50 ARG 0.002 0.000 ARG b 52 Details of bonding type rmsd hydrogen bonds : bond 0.05603 ( 353) hydrogen bonds : angle 4.27911 ( 1026) SS BOND : bond 0.00292 ( 13) SS BOND : angle 1.39664 ( 26) covalent geometry : bond 0.00225 ( 8535) covalent geometry : angle 0.54860 (11586) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.896 Fit side-chains REVERT: d 29 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7806 (mm) REVERT: d 99 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7035 (pp) REVERT: d 117 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7555 (tp) REVERT: e 144 LEU cc_start: 0.7642 (mm) cc_final: 0.7420 (tp) REVERT: f 80 ASP cc_start: 0.8058 (t70) cc_final: 0.7647 (t0) REVERT: f 106 GLU cc_start: 0.8162 (pt0) cc_final: 0.7638 (pt0) REVERT: g 108 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7586 (tp) REVERT: m 100 ASP cc_start: 0.7032 (m-30) cc_final: 0.6768 (t0) REVERT: m 145 ARG cc_start: 0.7779 (mtm180) cc_final: 0.7517 (mtp85) REVERT: m 200 LYS cc_start: 0.8230 (ptmt) cc_final: 0.7949 (ptpt) REVERT: m 211 ASN cc_start: 0.8750 (t160) cc_final: 0.8380 (t0) REVERT: n 33 LYS cc_start: 0.7907 (ttpt) cc_final: 0.7568 (ptmt) REVERT: n 38 MET cc_start: 0.7930 (tpt) cc_final: 0.7515 (tmm) REVERT: n 50 TYR cc_start: 0.6473 (OUTLIER) cc_final: 0.5371 (p90) REVERT: n 92 ASP cc_start: 0.7573 (m-30) cc_final: 0.6678 (t70) REVERT: n 96 ARG cc_start: 0.7804 (mtt180) cc_final: 0.7318 (mtt90) REVERT: n 121 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6638 (mp0) REVERT: n 252 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8005 (pt0) REVERT: n 302 MET cc_start: 0.6977 (ttp) cc_final: 0.6724 (ttm) outliers start: 32 outliers final: 17 residues processed: 161 average time/residue: 0.2391 time to fit residues: 51.1329 Evaluate side-chains 150 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 0.7980 chunk 88 optimal weight: 0.4980 chunk 51 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.147438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.110642 restraints weight = 9903.199| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.04 r_work: 0.2917 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8548 Z= 0.138 Angle : 0.579 8.901 11612 Z= 0.304 Chirality : 0.042 0.190 1305 Planarity : 0.004 0.043 1466 Dihedral : 5.543 44.581 1273 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.80 % Allowed : 13.25 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.55 (0.27), residues: 1040 helix: 3.15 (0.32), residues: 241 sheet: 0.46 (0.32), residues: 309 loop : -2.97 (0.23), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP d 43 HIS 0.004 0.001 HIS n 173 PHE 0.014 0.001 PHE m 157 TYR 0.023 0.001 TYR n 50 ARG 0.002 0.000 ARG b 52 Details of bonding type rmsd hydrogen bonds : bond 0.06290 ( 353) hydrogen bonds : angle 4.25684 ( 1026) SS BOND : bond 0.00315 ( 13) SS BOND : angle 1.30272 ( 26) covalent geometry : bond 0.00305 ( 8535) covalent geometry : angle 0.57667 (11586) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.924 Fit side-chains REVERT: d 29 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7868 (mm) REVERT: d 99 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.6930 (pp) REVERT: d 117 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7643 (tp) REVERT: d 123 PHE cc_start: 0.6840 (OUTLIER) cc_final: 0.6063 (t80) REVERT: e 57 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8520 (tt) REVERT: e 80 ASP cc_start: 0.8384 (p0) cc_final: 0.8086 (p0) REVERT: e 90 LEU cc_start: 0.8593 (tp) cc_final: 0.8303 (tp) REVERT: e 104 LYS cc_start: 0.7973 (mmtp) cc_final: 0.7333 (ttpt) REVERT: e 144 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7466 (tp) REVERT: f 80 ASP cc_start: 0.8095 (t70) cc_final: 0.7672 (t0) REVERT: f 106 GLU cc_start: 0.8243 (pt0) cc_final: 0.7743 (pt0) REVERT: m 100 ASP cc_start: 0.7058 (m-30) cc_final: 0.6758 (t0) REVERT: m 200 LYS cc_start: 0.8278 (ptmt) cc_final: 0.7974 (ptpt) REVERT: m 211 ASN cc_start: 0.8812 (t160) cc_final: 0.8484 (t0) REVERT: n 33 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7517 (ptmt) REVERT: n 50 TYR cc_start: 0.6567 (OUTLIER) cc_final: 0.5410 (p90) REVERT: n 92 ASP cc_start: 0.7607 (m-30) cc_final: 0.6706 (t70) REVERT: n 96 ARG cc_start: 0.7944 (mtt180) cc_final: 0.7427 (mtt90) REVERT: n 121 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6560 (mp0) REVERT: n 252 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8002 (pt0) outliers start: 35 outliers final: 24 residues processed: 162 average time/residue: 0.2113 time to fit residues: 46.2118 Evaluate side-chains 164 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 162 SER Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 ASN ** n 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.150693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114221 restraints weight = 9983.472| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.05 r_work: 0.2886 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8548 Z= 0.142 Angle : 0.593 9.060 11612 Z= 0.308 Chirality : 0.043 0.193 1305 Planarity : 0.004 0.042 1466 Dihedral : 5.532 44.192 1273 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.23 % Allowed : 13.46 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.40 (0.26), residues: 1040 helix: 3.26 (0.31), residues: 241 sheet: 0.68 (0.33), residues: 289 loop : -2.83 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP d 43 HIS 0.004 0.001 HIS n 173 PHE 0.011 0.002 PHE m 157 TYR 0.025 0.001 TYR n 50 ARG 0.003 0.000 ARG b 52 Details of bonding type rmsd hydrogen bonds : bond 0.06449 ( 353) hydrogen bonds : angle 4.25255 ( 1026) SS BOND : bond 0.00332 ( 13) SS BOND : angle 1.34321 ( 26) covalent geometry : bond 0.00318 ( 8535) covalent geometry : angle 0.58980 (11586) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.926 Fit side-chains REVERT: d 29 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7843 (mm) REVERT: d 99 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.6963 (pp) REVERT: d 117 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7680 (tp) REVERT: d 123 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.6017 (t80) REVERT: e 57 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8461 (tt) REVERT: e 80 ASP cc_start: 0.8392 (p0) cc_final: 0.8065 (p0) REVERT: e 90 LEU cc_start: 0.8581 (tp) cc_final: 0.8318 (tp) REVERT: e 104 LYS cc_start: 0.8003 (mmtp) cc_final: 0.7381 (ttpt) REVERT: e 123 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8108 (ptp) REVERT: e 144 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7464 (tp) REVERT: f 80 ASP cc_start: 0.8172 (t70) cc_final: 0.7649 (t0) REVERT: f 106 GLU cc_start: 0.8212 (pt0) cc_final: 0.7666 (pt0) REVERT: g 52 ASN cc_start: 0.6036 (OUTLIER) cc_final: 0.5595 (t0) REVERT: m 100 ASP cc_start: 0.7136 (m-30) cc_final: 0.6806 (t0) REVERT: m 143 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: m 200 LYS cc_start: 0.8294 (ptmt) cc_final: 0.7979 (ptpt) REVERT: m 211 ASN cc_start: 0.8796 (t0) cc_final: 0.8477 (t0) REVERT: n 33 LYS cc_start: 0.7875 (ttpt) cc_final: 0.7536 (ptmt) REVERT: n 50 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.5494 (p90) REVERT: n 92 ASP cc_start: 0.7624 (m-30) cc_final: 0.6711 (t70) REVERT: n 96 ARG cc_start: 0.7968 (mtt180) cc_final: 0.7415 (mtt90) REVERT: n 121 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6517 (mp0) REVERT: n 252 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8040 (pt0) outliers start: 39 outliers final: 24 residues processed: 164 average time/residue: 0.2094 time to fit residues: 46.2640 Evaluate side-chains 161 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 52 ASN Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 143 GLN Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 0.0970 chunk 38 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.153325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116608 restraints weight = 9721.992| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.77 r_work: 0.2939 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8548 Z= 0.114 Angle : 0.542 8.582 11612 Z= 0.283 Chirality : 0.041 0.182 1305 Planarity : 0.004 0.040 1466 Dihedral : 5.217 42.611 1273 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.02 % Allowed : 14.12 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.15 (0.27), residues: 1040 helix: 3.56 (0.31), residues: 242 sheet: 0.74 (0.32), residues: 304 loop : -2.78 (0.24), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP m 197 HIS 0.003 0.001 HIS n 173 PHE 0.012 0.001 PHE m 157 TYR 0.022 0.001 TYR n 50 ARG 0.002 0.000 ARG n 261 Details of bonding type rmsd hydrogen bonds : bond 0.05255 ( 353) hydrogen bonds : angle 4.03082 ( 1026) SS BOND : bond 0.00255 ( 13) SS BOND : angle 1.43214 ( 26) covalent geometry : bond 0.00238 ( 8535) covalent geometry : angle 0.53822 (11586) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.940 Fit side-chains REVERT: d 29 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7737 (mm) REVERT: d 99 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7013 (pp) REVERT: d 117 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7561 (tp) REVERT: d 123 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.5838 (t80) REVERT: e 79 GLU cc_start: 0.8234 (pm20) cc_final: 0.7972 (pm20) REVERT: e 104 LYS cc_start: 0.7932 (mmtp) cc_final: 0.7221 (ttpt) REVERT: e 144 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7270 (tp) REVERT: f 80 ASP cc_start: 0.8265 (t70) cc_final: 0.7618 (t0) REVERT: g 52 ASN cc_start: 0.5833 (OUTLIER) cc_final: 0.5436 (t0) REVERT: m 100 ASP cc_start: 0.7214 (m-30) cc_final: 0.6952 (t0) REVERT: m 200 LYS cc_start: 0.8105 (ptmt) cc_final: 0.7787 (ptpt) REVERT: n 33 LYS cc_start: 0.7851 (ttpt) cc_final: 0.7552 (ptmt) REVERT: n 50 TYR cc_start: 0.6377 (OUTLIER) cc_final: 0.5395 (p90) REVERT: n 92 ASP cc_start: 0.7529 (m-30) cc_final: 0.6706 (t70) REVERT: n 96 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7379 (mtt90) REVERT: n 121 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6514 (mp0) REVERT: n 252 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8065 (pt0) outliers start: 37 outliers final: 23 residues processed: 161 average time/residue: 0.2141 time to fit residues: 46.4601 Evaluate side-chains 158 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 125 MET Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 52 ASN Chi-restraints excluded: chain g residue 71 LYS Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 146 ASP Chi-restraints excluded: chain m residue 180 THR Chi-restraints excluded: chain m residue 217 ASP Chi-restraints excluded: chain n residue 26 THR Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 57 ASP Chi-restraints excluded: chain n residue 86 SER Chi-restraints excluded: chain n residue 131 THR Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 299 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7192 > 50: distance: 19 - 148: 25.020 distance: 29 - 151: 32.595 distance: 76 - 81: 28.391 distance: 81 - 82: 44.309 distance: 82 - 83: 54.937 distance: 83 - 84: 53.552 distance: 83 - 85: 52.813 distance: 85 - 86: 38.935 distance: 86 - 87: 54.220 distance: 86 - 89: 33.810 distance: 87 - 88: 52.185 distance: 87 - 91: 3.028 distance: 89 - 90: 41.761 distance: 91 - 92: 12.159 distance: 92 - 93: 9.041 distance: 92 - 95: 46.175 distance: 93 - 94: 42.246 distance: 93 - 100: 57.819 distance: 95 - 96: 38.110 distance: 96 - 97: 45.241 distance: 97 - 98: 23.562 distance: 98 - 99: 19.685 distance: 100 - 101: 38.866 distance: 100 - 106: 14.457 distance: 101 - 102: 41.104 distance: 101 - 104: 48.720 distance: 102 - 103: 29.395 distance: 102 - 107: 35.298 distance: 103 - 124: 25.919 distance: 104 - 105: 47.883 distance: 105 - 106: 10.214 distance: 107 - 108: 20.678 distance: 108 - 109: 19.193 distance: 108 - 111: 23.803 distance: 109 - 110: 23.995 distance: 109 - 116: 20.397 distance: 111 - 112: 8.358 distance: 112 - 113: 9.188 distance: 113 - 114: 24.126 distance: 113 - 115: 19.391 distance: 116 - 117: 27.371 distance: 117 - 118: 26.430 distance: 117 - 120: 27.378 distance: 118 - 119: 37.380 distance: 118 - 124: 10.628 distance: 120 - 121: 6.579 distance: 121 - 122: 18.500 distance: 121 - 123: 12.693 distance: 124 - 125: 29.469 distance: 125 - 126: 40.239 distance: 125 - 128: 35.429 distance: 126 - 127: 38.351 distance: 126 - 129: 41.562 distance: 129 - 130: 46.981 distance: 130 - 131: 56.525 distance: 130 - 133: 49.870 distance: 131 - 132: 59.682 distance: 131 - 137: 57.841 distance: 133 - 134: 33.340 distance: 134 - 135: 20.425 distance: 134 - 136: 24.354 distance: 137 - 138: 56.353 distance: 138 - 139: 70.719 distance: 138 - 141: 46.141 distance: 139 - 140: 57.412 distance: 139 - 148: 57.831 distance: 141 - 142: 11.175 distance: 142 - 143: 15.467 distance: 142 - 144: 11.839 distance: 143 - 145: 18.047 distance: 144 - 146: 13.389 distance: 145 - 147: 9.268 distance: 146 - 147: 15.725 distance: 148 - 149: 22.360 distance: 149 - 150: 39.973 distance: 149 - 152: 25.151 distance: 150 - 151: 40.900 distance: 150 - 160: 26.542 distance: 152 - 153: 21.714 distance: 153 - 154: 30.866 distance: 153 - 155: 23.411 distance: 154 - 156: 11.649 distance: 155 - 157: 29.747 distance: 156 - 158: 8.905 distance: 157 - 158: 13.490 distance: 158 - 159: 21.300