Starting phenix.real_space_refine on Sat Jun 7 05:13:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fjf_31620/06_2025/7fjf_31620.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjf_31620/06_2025/7fjf_31620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fjf_31620/06_2025/7fjf_31620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjf_31620/06_2025/7fjf_31620.map" model { file = "/net/cci-nas-00/data/ceres_data/7fjf_31620/06_2025/7fjf_31620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjf_31620/06_2025/7fjf_31620.cif" } resolution = 3.1 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 56 5.16 5 C 5352 2.51 5 N 1370 2.21 5 O 1599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8377 Number of models: 1 Model: "" Number of chains: 10 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: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} 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: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 949 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "g" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "m" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1924 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 233} 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: "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: "m" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'C3S': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'C3S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.55, per 1000 atoms: 0.66 Number of scatterers: 8377 At special positions: 0 Unit cell: (91.3, 97.9, 140.8, 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 56 16.00 O 1599 8.00 N 1370 7.00 C 5352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS b 32 " - pdb=" SG CYS a 32 " distance=2.14 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=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.04 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=2.04 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: 2.20 Conformation dependent library (CDL) restraints added in 914.9 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: 17 helices and 21 sheets defined 25.9% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'b' and resid 29 through 53 removed outlier: 3.529A pdb=" N LEU b 39 " --> pdb=" O LEU b 35 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY b 43 " --> pdb=" O LEU b 39 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL b 44 " --> pdb=" O PHE b 40 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE b 45 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU b 46 " --> pdb=" O TYR b 42 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL b 53 " --> pdb=" O LEU b 49 " (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 102 through 124 removed outlier: 4.496A pdb=" N PHE d 123 " --> pdb=" O ALA d 119 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N CYS d 124 " --> pdb=" O LEU d 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 108 removed outlier: 3.709A pdb=" N ASP e 107 " --> pdb=" O LYS e 104 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA e 108 " --> pdb=" O PRO e 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 104 through 108' Processing helix chain 'e' and resid 127 through 154 removed outlier: 3.608A pdb=" N ALA e 131 " --> pdb=" O VAL e 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 removed outlier: 3.599A pdb=" N ASP f 107 " --> pdb=" O LYS f 104 " (cutoff:3.500A) removed outlier: 3.896A 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 154 removed outlier: 4.551A pdb=" N GLY f 143 " --> pdb=" O CYS f 139 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU f 144 " --> pdb=" O ILE f 140 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU f 145 " --> pdb=" O THR f 141 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU f 146 " --> pdb=" O GLY f 142 " (cutoff:3.500A) 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: 4.055A pdb=" N ILE g 115 " --> pdb=" O ASN g 111 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY g 138 " --> pdb=" O TYR g 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 102 through 106 removed outlier: 3.818A pdb=" N ASP m 105 " --> pdb=" O GLN m 102 " (cutoff:3.500A) removed outlier: 4.188A 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 231 through 235 removed outlier: 3.573A pdb=" N LYS m 234 " --> pdb=" O LEU m 231 " (cutoff:3.500A) Processing helix chain 'm' and resid 240 through 272 removed outlier: 3.846A pdb=" N ILE m 254 " --> pdb=" O ILE m 250 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 105 removed outlier: 3.949A pdb=" N THR n 105 " --> pdb=" O PRO n 102 " (cutoff:3.500A) Processing helix chain 'n' and resid 150 through 158 removed outlier: 3.755A 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 270 through 308 removed outlier: 4.452A pdb=" N LYS n 308 " --> pdb=" O MET n 304 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 54 removed outlier: 4.434A pdb=" N LEU a 39 " --> pdb=" O LEU a 35 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS a 54 " --> pdb=" O PHE a 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 28 removed outlier: 5.977A 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: 6.851A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS d 73 " --> pdb=" O SER d 84 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER d 84 " --> pdb=" O CYS d 73 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN e 60 " --> pdb=" O VAL e 97 " (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 'e' and resid 39 through 40 removed outlier: 3.551A pdb=" N LEU e 82 " --> pdb=" O LEU e 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 40 removed outlier: 3.513A pdb=" N VAL f 45 " --> pdb=" O LEU f 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 65 through 66 removed outlier: 3.514A pdb=" N ILE f 66 " --> pdb=" O TRP f 59 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TRP f 59 " --> pdb=" O ILE f 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 111 through 117 removed outlier: 6.875A pdb=" N TYR f 111 " --> pdb=" O GLN g 98 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N TYR g 100 " --> pdb=" O TYR f 111 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ARG g 102 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG f 115 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU g 97 " --> pdb=" O TYR g 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY g 83 " --> pdb=" O VAL g 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 122 through 124 Processing sheet with id=AA9, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.641A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'g' and resid 60 through 65 removed outlier: 3.583A pdb=" N ILE g 62 " --> pdb=" O TRP g 55 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE g 64 " --> pdb=" O ILE g 53 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE g 53 " --> pdb=" O PHE g 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 33 through 36 removed outlier: 3.839A pdb=" N TYR m 109 " --> pdb=" O THR m 126 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR m 54 " --> pdb=" O SER m 114 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET m 70 " --> pdb=" O TRP m 57 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG m 59 " --> pdb=" O LEU m 68 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU m 68 " --> pdb=" O ARG m 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'm' and resid 33 through 36 removed outlier: 3.839A pdb=" N TYR m 109 " --> pdb=" O THR m 126 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 40 through 46 removed outlier: 3.626A pdb=" N ILE m 98 " --> pdb=" O VAL m 41 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU m 96 " --> pdb=" O LEU m 43 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR m 93 " --> pdb=" O ASP m 88 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN m 86 " --> pdb=" O SER m 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'm' and resid 141 through 143 removed outlier: 3.519A pdb=" N SER m 153 " --> pdb=" O SER m 198 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER m 198 " --> pdb=" O SER m 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 180 through 184 removed outlier: 3.549A pdb=" N THR m 180 " --> pdb=" O SER m 193 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU m 182 " --> pdb=" O SER m 191 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE m 189 " --> pdb=" O MET m 184 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'n' and resid 29 through 33 removed outlier: 3.588A pdb=" N THR n 131 " --> pdb=" O GLN n 30 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU n 32 " --> pdb=" O THR n 131 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR n 133 " --> pdb=" O LEU n 32 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'n' and resid 38 through 40 removed outlier: 3.800A pdb=" N MET n 38 " --> pdb=" O LEU n 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'n' and resid 73 through 76 removed outlier: 7.348A pdb=" N ILE n 73 " --> pdb=" O VAL n 69 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL n 69 " --> pdb=" O ILE n 73 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR n 67 " --> pdb=" O ASP n 75 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY n 61 " --> pdb=" O ASP n 57 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP n 57 " --> pdb=" O GLY n 61 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP n 53 " --> pdb=" O ILE n 65 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR n 67 " --> pdb=" O MET n 51 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET n 51 " --> pdb=" O TYR n 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER n 52 " --> pdb=" O ALA n 111 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE n 109 " --> pdb=" O TYR n 54 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL n 107 " --> pdb=" O GLN n 56 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'n' and resid 143 through 147 removed outlier: 5.583A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'n' and resid 143 through 147 removed outlier: 5.583A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'n' and resid 183 through 184 removed outlier: 3.619A pdb=" N LYS n 183 " --> pdb=" O VAL n 180 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 972 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: 2.16 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2281 1.33 - 1.46: 2075 1.46 - 1.58: 4126 1.58 - 1.71: 3 1.71 - 1.83: 76 Bond restraints: 8561 Sorted by residual: bond pdb=" O3 C3S m1001 " pdb=" S1 C3S m1001 " ideal model delta sigma weight residual 1.467 1.644 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" O3 C3S n 401 " pdb=" S1 C3S n 401 " ideal model delta sigma weight residual 1.467 1.632 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" C SER f 103 " pdb=" N LYS f 104 " ideal model delta sigma weight residual 1.331 1.220 0.111 2.07e-02 2.33e+03 2.88e+01 bond pdb=" O6 C3S n 401 " pdb=" S1 C3S n 401 " ideal model delta sigma weight residual 1.637 1.536 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" O6 C3S m1001 " pdb=" S1 C3S m1001 " ideal model delta sigma weight residual 1.637 1.545 0.092 2.00e-02 2.50e+03 2.10e+01 ... (remaining 8556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.18: 11576 6.18 - 12.35: 38 12.35 - 18.53: 7 18.53 - 24.71: 1 24.71 - 30.88: 2 Bond angle restraints: 11624 Sorted by residual: angle pdb=" O2 C3S m1001 " pdb=" S1 C3S m1001 " pdb=" O4 C3S m1001 " ideal model delta sigma weight residual 114.52 83.64 30.88 3.00e+00 1.11e-01 1.06e+02 angle pdb=" O3 C3S m1001 " pdb=" S1 C3S m1001 " pdb=" O4 C3S m1001 " ideal model delta sigma weight residual 113.45 84.47 28.98 3.00e+00 1.11e-01 9.33e+01 angle pdb=" N ILE d 78 " pdb=" CA ILE d 78 " pdb=" C ILE d 78 " ideal model delta sigma weight residual 109.34 125.01 -15.67 2.08e+00 2.31e-01 5.67e+01 angle pdb=" O4 C3S m1001 " pdb=" S1 C3S m1001 " pdb=" O6 C3S m1001 " ideal model delta sigma weight residual 105.67 84.46 21.21 3.00e+00 1.11e-01 5.00e+01 angle pdb=" CG LYS b 30 " pdb=" CD LYS b 30 " pdb=" CE LYS b 30 " ideal model delta sigma weight residual 111.30 126.51 -15.21 2.30e+00 1.89e-01 4.37e+01 ... (remaining 11619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 4844 16.50 - 33.00: 278 33.00 - 49.50: 82 49.50 - 66.00: 21 66.00 - 82.50: 10 Dihedral angle restraints: 5235 sinusoidal: 2159 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 180.00 127.09 52.91 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ASP d 77 " pdb=" C ASP d 77 " pdb=" N ILE d 78 " pdb=" CA ILE d 78 " ideal model delta harmonic sigma weight residual -180.00 -133.97 -46.03 0 5.00e+00 4.00e-02 8.48e+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 -134.18 -45.82 0 5.00e+00 4.00e-02 8.40e+01 ... (remaining 5232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1100 0.094 - 0.189: 194 0.189 - 0.283: 11 0.283 - 0.377: 2 0.377 - 0.472: 1 Chirality restraints: 1308 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 0.47 2.00e-01 2.50e+01 5.56e+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 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CG LEU d 29 " pdb=" CB LEU d 29 " pdb=" CD1 LEU d 29 " pdb=" CD2 LEU d 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1305 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN n 222 " -0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO n 223 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO n 223 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO n 223 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 90 " -0.026 2.00e-02 2.50e+03 2.13e-02 9.08e+00 pdb=" CG TYR d 90 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR d 90 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR d 90 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR d 90 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR d 90 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR d 90 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR d 90 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN m 102 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.41e+00 pdb=" N PRO m 103 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO m 103 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO m 103 " -0.040 5.00e-02 4.00e+02 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1730 2.78 - 3.31: 6761 3.31 - 3.84: 12261 3.84 - 4.37: 13401 4.37 - 4.90: 24676 Nonbonded interactions: 58829 Sorted by model distance: nonbonded pdb=" O VAL f 148 " pdb=" OG SER f 152 " model vdw 2.256 3.040 nonbonded pdb=" NH2 ARG m 253 " pdb=" OD1 ASP a 36 " model vdw 2.258 3.120 nonbonded pdb=" NE1 TRP m 271 " pdb=" O4 C3S m1001 " model vdw 2.289 3.120 nonbonded pdb=" OE1 GLN d 94 " pdb=" OG SER a 23 " model vdw 2.292 3.040 nonbonded pdb=" O TYR e 149 " pdb=" OG SER e 152 " model vdw 2.318 3.040 ... (remaining 58824 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' } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 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: 0.010 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.830 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: 26.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 0.177 8574 Z= 0.473 Angle : 1.348 30.884 11650 Z= 0.704 Chirality : 0.070 0.472 1308 Planarity : 0.008 0.075 1468 Dihedral : 12.223 75.568 3222 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.94 % Favored : 90.77 % Rotamer: Outliers : 1.73 % Allowed : 5.29 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.70 % 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: -3.59 (0.21), residues: 1040 helix: -1.06 (0.29), residues: 229 sheet: -1.40 (0.30), residues: 277 loop : -3.68 (0.19), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP n 179 HIS 0.017 0.004 HIS n 173 PHE 0.040 0.004 PHE m 157 TYR 0.051 0.005 TYR d 90 ARG 0.018 0.002 ARG m 253 Details of bonding type rmsd hydrogen bonds : bond 0.24154 ( 325) hydrogen bonds : angle 8.04943 ( 972) SS BOND : bond 0.03071 ( 13) SS BOND : angle 2.31005 ( 26) covalent geometry : bond 0.01045 ( 8561) covalent geometry : angle 1.34460 (11624) *********************** 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 198 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.784 Fit side-chains REVERT: b 39 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7845 (mp) REVERT: b 54 LYS cc_start: 0.5481 (OUTLIER) cc_final: 0.5059 (tttm) REVERT: d 27 GLU cc_start: 0.7935 (pt0) cc_final: 0.7688 (pt0) REVERT: d 56 THR cc_start: 0.8023 (p) cc_final: 0.7796 (p) REVERT: e 74 ASN cc_start: 0.8041 (m-40) cc_final: 0.7730 (m-40) REVERT: e 85 LYS cc_start: 0.8654 (mttt) cc_final: 0.8441 (mmtt) REVERT: e 124 GLU cc_start: 0.7486 (tt0) cc_final: 0.6965 (tt0) REVERT: e 128 MET cc_start: 0.7294 (mmm) cc_final: 0.7080 (mmm) REVERT: f 51 GLN cc_start: 0.6480 (mt0) cc_final: 0.5822 (mp10) REVERT: f 83 SER cc_start: 0.8253 (m) cc_final: 0.7960 (p) REVERT: g 30 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7167 (pp) REVERT: m 104 SER cc_start: 0.7053 (m) cc_final: 0.6531 (p) REVERT: m 145 ARG cc_start: 0.7432 (mtm180) cc_final: 0.7048 (ttm110) REVERT: m 184 MET cc_start: 0.8549 (ptm) cc_final: 0.8308 (ptm) REVERT: n 80 PRO cc_start: 0.7073 (Cg_endo) cc_final: 0.6721 (Cg_exo) REVERT: n 261 ARG cc_start: 0.7142 (ppt-90) cc_final: 0.6680 (ptt180) outliers start: 16 outliers final: 1 residues processed: 196 average time/residue: 0.2356 time to fit residues: 61.4702 Evaluate side-chains 121 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain g residue 30 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: 3.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 0.0070 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- 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 f 65 ASN g 29 HIS m 102 GLN n 47 ASN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 272 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.183941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147959 restraints weight = 9699.014| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.70 r_work: 0.3356 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8574 Z= 0.169 Angle : 0.708 9.912 11650 Z= 0.370 Chirality : 0.045 0.210 1308 Planarity : 0.005 0.045 1468 Dihedral : 7.025 56.534 1289 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.48 % Favored : 94.33 % Rotamer: Outliers : 2.70 % Allowed : 8.63 % Favored : 88.67 % 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: -1.81 (0.25), residues: 1040 helix: 1.61 (0.33), residues: 245 sheet: -0.42 (0.32), residues: 290 loop : -3.30 (0.21), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP d 43 HIS 0.006 0.001 HIS d 89 PHE 0.028 0.002 PHE m 157 TYR 0.019 0.002 TYR n 50 ARG 0.005 0.001 ARG d 91 Details of bonding type rmsd hydrogen bonds : bond 0.06929 ( 325) hydrogen bonds : angle 4.82871 ( 972) SS BOND : bond 0.00598 ( 13) SS BOND : angle 1.12324 ( 26) covalent geometry : bond 0.00362 ( 8561) covalent geometry : angle 0.70693 (11624) *********************** 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 179 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.853 Fit side-chains REVERT: d 27 GLU cc_start: 0.8567 (pt0) cc_final: 0.8356 (pt0) REVERT: d 117 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8137 (tp) REVERT: e 125 MET cc_start: 0.8522 (mmt) cc_final: 0.8129 (mmt) REVERT: e 128 MET cc_start: 0.7581 (mmm) cc_final: 0.7298 (mmt) REVERT: f 111 TYR cc_start: 0.8704 (m-10) cc_final: 0.8467 (m-80) REVERT: g 30 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7460 (mp) REVERT: g 77 ASN cc_start: 0.8604 (p0) cc_final: 0.8157 (p0) REVERT: m 56 MET cc_start: 0.8120 (mpp) cc_final: 0.7906 (mpp) REVERT: m 145 ARG cc_start: 0.7974 (mtm180) cc_final: 0.7426 (ttm110) REVERT: n 80 PRO cc_start: 0.7165 (Cg_endo) cc_final: 0.6770 (Cg_exo) REVERT: n 151 GLU cc_start: 0.7649 (mp0) cc_final: 0.7211 (mp0) REVERT: n 252 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8058 (pt0) REVERT: n 261 ARG cc_start: 0.8441 (ppt-90) cc_final: 0.8088 (ptt180) outliers start: 25 outliers final: 6 residues processed: 171 average time/residue: 0.2727 time to fit residues: 61.3026 Evaluate side-chains 133 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 126 THR Chi-restraints excluded: chain n residue 252 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 85 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 105 GLN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.182106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.146132 restraints weight = 9690.119| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.22 r_work: 0.3185 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8574 Z= 0.122 Angle : 0.607 9.611 11650 Z= 0.317 Chirality : 0.042 0.210 1308 Planarity : 0.004 0.045 1468 Dihedral : 6.090 56.830 1281 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.71 % Rotamer: Outliers : 1.83 % Allowed : 11.33 % Favored : 86.84 % 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: -0.88 (0.26), residues: 1040 helix: 2.80 (0.33), residues: 240 sheet: 0.26 (0.33), residues: 279 loop : -2.93 (0.22), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP n 259 HIS 0.005 0.001 HIS n 66 PHE 0.017 0.001 PHE m 157 TYR 0.016 0.001 TYR g 34 ARG 0.005 0.000 ARG d 91 Details of bonding type rmsd hydrogen bonds : bond 0.05714 ( 325) hydrogen bonds : angle 4.41918 ( 972) SS BOND : bond 0.00382 ( 13) SS BOND : angle 0.91992 ( 26) covalent geometry : bond 0.00256 ( 8561) covalent geometry : angle 0.60621 (11624) *********************** 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 151 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.967 Fit side-chains REVERT: d 117 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8137 (tp) REVERT: e 128 MET cc_start: 0.7577 (mmm) cc_final: 0.7235 (mmt) REVERT: g 30 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7839 (pp) REVERT: g 77 ASN cc_start: 0.8655 (p0) cc_final: 0.8200 (p0) REVERT: m 145 ARG cc_start: 0.8110 (mtm180) cc_final: 0.7464 (ttm110) REVERT: m 159 ASP cc_start: 0.6534 (p0) cc_final: 0.6182 (p0) REVERT: m 185 ARG cc_start: 0.8623 (mtp-110) cc_final: 0.8283 (mtm-85) REVERT: m 207 ASN cc_start: 0.7689 (m-40) cc_final: 0.7214 (p0) REVERT: n 80 PRO cc_start: 0.7278 (Cg_endo) cc_final: 0.6933 (Cg_exo) REVERT: n 151 GLU cc_start: 0.7881 (mp0) cc_final: 0.7555 (mp0) REVERT: n 252 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8041 (pt0) REVERT: n 261 ARG cc_start: 0.8496 (ppt-90) cc_final: 0.8138 (ptt180) REVERT: n 263 ASP cc_start: 0.7215 (m-30) cc_final: 0.7002 (m-30) outliers start: 17 outliers final: 7 residues processed: 145 average time/residue: 0.2293 time to fit residues: 44.2224 Evaluate side-chains 134 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain n residue 252 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 0.0970 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 65 optimal weight: 0.9980 chunk 4 optimal weight: 0.0170 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.3654 ------------------------------------------------------------------------------- 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 25 GLN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.183140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148853 restraints weight = 9496.724| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 3.21 r_work: 0.3233 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 8574 Z= 0.102 Angle : 0.553 9.395 11650 Z= 0.288 Chirality : 0.041 0.184 1308 Planarity : 0.004 0.032 1468 Dihedral : 5.691 56.697 1281 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.23 % Favored : 95.67 % Rotamer: Outliers : 2.48 % Allowed : 11.11 % Favored : 86.41 % 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: -0.35 (0.27), residues: 1040 helix: 3.49 (0.32), residues: 236 sheet: 0.55 (0.34), residues: 273 loop : -2.62 (0.22), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP n 259 HIS 0.004 0.001 HIS n 66 PHE 0.013 0.001 PHE m 157 TYR 0.014 0.001 TYR n 50 ARG 0.002 0.000 ARG n 113 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 325) hydrogen bonds : angle 4.01483 ( 972) SS BOND : bond 0.00322 ( 13) SS BOND : angle 0.71034 ( 26) covalent geometry : bond 0.00214 ( 8561) covalent geometry : angle 0.55288 (11624) *********************** 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 151 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.743 Fit side-chains REVERT: d 99 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7395 (pp) REVERT: e 128 MET cc_start: 0.7297 (mmm) cc_final: 0.6985 (mmt) REVERT: f 125 MET cc_start: 0.8035 (mmp) cc_final: 0.7610 (mmt) REVERT: g 30 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7735 (pp) REVERT: g 32 LYS cc_start: 0.8747 (mmtt) cc_final: 0.8525 (mmtm) REVERT: g 77 ASN cc_start: 0.8600 (p0) cc_final: 0.8245 (p0) REVERT: m 145 ARG cc_start: 0.7989 (mtm180) cc_final: 0.7381 (ttm110) REVERT: m 159 ASP cc_start: 0.5978 (p0) cc_final: 0.5650 (p0) REVERT: m 173 ASP cc_start: 0.8316 (m-30) cc_final: 0.8105 (m-30) REVERT: m 207 ASN cc_start: 0.7858 (m-40) cc_final: 0.7306 (p0) REVERT: n 32 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8135 (pp) REVERT: n 50 TYR cc_start: 0.5464 (OUTLIER) cc_final: 0.5176 (p90) REVERT: n 80 PRO cc_start: 0.7208 (Cg_endo) cc_final: 0.6866 (Cg_exo) REVERT: n 252 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8220 (pt0) REVERT: n 261 ARG cc_start: 0.8377 (ppt-90) cc_final: 0.8010 (ptt180) outliers start: 23 outliers final: 11 residues processed: 147 average time/residue: 0.2503 time to fit residues: 49.9628 Evaluate side-chains 130 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 208 CYS Chi-restraints excluded: chain n residue 252 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 51 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 60 GLN g 52 ASN g 105 GLN m 102 GLN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.168505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.118435 restraints weight = 9315.319| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.45 r_work: 0.2974 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8574 Z= 0.188 Angle : 0.706 11.898 11650 Z= 0.364 Chirality : 0.046 0.198 1308 Planarity : 0.005 0.047 1468 Dihedral : 6.241 55.662 1281 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.63 % Favored : 93.27 % Rotamer: Outliers : 3.13 % Allowed : 10.79 % Favored : 86.08 % 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: -0.54 (0.26), residues: 1040 helix: 2.94 (0.32), residues: 244 sheet: 0.44 (0.34), residues: 277 loop : -2.64 (0.23), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP n 259 HIS 0.004 0.001 HIS n 66 PHE 0.016 0.002 PHE f 87 TYR 0.021 0.002 TYR g 34 ARG 0.006 0.001 ARG d 91 Details of bonding type rmsd hydrogen bonds : bond 0.07716 ( 325) hydrogen bonds : angle 4.48822 ( 972) SS BOND : bond 0.00608 ( 13) SS BOND : angle 1.34906 ( 26) covalent geometry : bond 0.00439 ( 8561) covalent geometry : angle 0.70430 (11624) *********************** 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 162 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 84 SER cc_start: 0.8496 (p) cc_final: 0.8192 (t) REVERT: d 99 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7274 (pp) REVERT: e 37 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8384 (mttp) REVERT: f 101 ARG cc_start: 0.7295 (tpt-90) cc_final: 0.6805 (tpt170) REVERT: g 58 ASP cc_start: 0.8265 (m-30) cc_final: 0.7976 (m-30) REVERT: g 92 ASN cc_start: 0.6948 (m110) cc_final: 0.5750 (t0) REVERT: m 145 ARG cc_start: 0.7985 (mtm180) cc_final: 0.7297 (ttm110) REVERT: m 207 ASN cc_start: 0.7873 (m-40) cc_final: 0.7393 (p0) REVERT: m 230 LYS cc_start: 0.8824 (mttt) cc_final: 0.8345 (mmtt) REVERT: n 28 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7481 (mtmm) REVERT: n 50 TYR cc_start: 0.5358 (OUTLIER) cc_final: 0.4722 (p90) REVERT: n 67 TYR cc_start: 0.7162 (p90) cc_final: 0.6908 (p90) REVERT: n 80 PRO cc_start: 0.7271 (Cg_endo) cc_final: 0.6935 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8279 (tt) REVERT: n 252 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8140 (pt0) REVERT: n 261 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8537 (ptt180) outliers start: 29 outliers final: 13 residues processed: 154 average time/residue: 0.2882 time to fit residues: 60.1679 Evaluate side-chains 141 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 ASN g 105 GLN n 25 GLN ** n 48 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 = 0.3894 r_free = 0.3894 target = 0.172166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.120395 restraints weight = 9408.401| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.67 r_work: 0.3046 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8574 Z= 0.121 Angle : 0.601 9.314 11650 Z= 0.309 Chirality : 0.042 0.188 1308 Planarity : 0.004 0.029 1468 Dihedral : 5.687 56.135 1279 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 2.37 % Allowed : 12.19 % Favored : 85.44 % 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: -0.16 (0.27), residues: 1040 helix: 3.63 (0.31), residues: 236 sheet: 0.48 (0.33), residues: 283 loop : -2.43 (0.23), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP n 259 HIS 0.004 0.001 HIS n 66 PHE 0.010 0.001 PHE m 189 TYR 0.012 0.001 TYR n 50 ARG 0.003 0.000 ARG n 228 Details of bonding type rmsd hydrogen bonds : bond 0.05617 ( 325) hydrogen bonds : angle 4.08394 ( 972) SS BOND : bond 0.00402 ( 13) SS BOND : angle 0.88767 ( 26) covalent geometry : bond 0.00261 ( 8561) covalent geometry : angle 0.60062 (11624) *********************** 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 146 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: d 82 LYS cc_start: 0.7845 (mttt) cc_final: 0.7546 (mttt) REVERT: d 99 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7175 (pp) REVERT: e 37 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8258 (mttp) REVERT: f 101 ARG cc_start: 0.7397 (tpt-90) cc_final: 0.6872 (tpt170) REVERT: g 58 ASP cc_start: 0.8217 (m-30) cc_final: 0.7926 (m-30) REVERT: g 92 ASN cc_start: 0.7040 (m110) cc_final: 0.5869 (t0) REVERT: m 145 ARG cc_start: 0.7887 (mtm180) cc_final: 0.7189 (ttm110) REVERT: m 207 ASN cc_start: 0.7719 (m-40) cc_final: 0.7341 (p0) REVERT: m 230 LYS cc_start: 0.8741 (mttt) cc_final: 0.8273 (mmtt) REVERT: n 28 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7477 (mtmm) REVERT: n 32 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8162 (pp) REVERT: n 50 TYR cc_start: 0.5385 (OUTLIER) cc_final: 0.4737 (p90) REVERT: n 80 PRO cc_start: 0.7361 (Cg_endo) cc_final: 0.7038 (Cg_exo) REVERT: n 252 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8064 (pt0) REVERT: n 261 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8314 (ptt180) outliers start: 22 outliers final: 15 residues processed: 140 average time/residue: 0.3027 time to fit residues: 58.4485 Evaluate side-chains 136 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 52 ASN Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 161 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 16 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 ASN ** n 48 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 = 0.3914 r_free = 0.3914 target = 0.173989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124031 restraints weight = 9483.275| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.49 r_work: 0.3078 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8574 Z= 0.119 Angle : 0.596 9.426 11650 Z= 0.306 Chirality : 0.041 0.186 1308 Planarity : 0.004 0.030 1468 Dihedral : 5.565 55.880 1279 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 2.80 % Allowed : 12.73 % 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: -0.01 (0.27), residues: 1040 helix: 3.83 (0.31), residues: 236 sheet: 0.55 (0.33), residues: 283 loop : -2.36 (0.23), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP n 259 HIS 0.004 0.001 HIS n 66 PHE 0.010 0.001 PHE m 189 TYR 0.013 0.001 TYR n 50 ARG 0.003 0.000 ARG n 96 Details of bonding type rmsd hydrogen bonds : bond 0.05382 ( 325) hydrogen bonds : angle 3.97060 ( 972) SS BOND : bond 0.00379 ( 13) SS BOND : angle 0.85579 ( 26) covalent geometry : bond 0.00256 ( 8561) covalent geometry : angle 0.59538 (11624) *********************** 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 151 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: d 99 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7156 (pp) REVERT: e 37 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8290 (mttp) REVERT: f 101 ARG cc_start: 0.7489 (tpt-90) cc_final: 0.6837 (tpt170) REVERT: f 104 LYS cc_start: 0.8940 (tttt) cc_final: 0.8053 (mttt) REVERT: g 92 ASN cc_start: 0.7031 (m110) cc_final: 0.5812 (t0) REVERT: m 145 ARG cc_start: 0.8029 (mtm180) cc_final: 0.7501 (mtt90) REVERT: m 207 ASN cc_start: 0.7624 (m-40) cc_final: 0.7181 (p0) REVERT: m 230 LYS cc_start: 0.8799 (mttt) cc_final: 0.8282 (mmtt) REVERT: n 28 LYS cc_start: 0.7936 (mtmt) cc_final: 0.7584 (mtmm) REVERT: n 32 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8173 (pp) REVERT: n 50 TYR cc_start: 0.5347 (OUTLIER) cc_final: 0.4714 (p90) REVERT: n 80 PRO cc_start: 0.7395 (Cg_endo) cc_final: 0.7057 (Cg_exo) REVERT: n 261 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8531 (ptt180) outliers start: 26 outliers final: 19 residues processed: 144 average time/residue: 0.2151 time to fit residues: 41.6893 Evaluate side-chains 144 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 52 ASN Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 161 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 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 = 0.3925 r_free = 0.3925 target = 0.175171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.124249 restraints weight = 9449.172| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.52 r_work: 0.3075 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 8574 Z= 0.114 Angle : 0.591 9.354 11650 Z= 0.303 Chirality : 0.041 0.184 1308 Planarity : 0.003 0.030 1468 Dihedral : 5.463 55.798 1279 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.19 % Rotamer: Outliers : 2.91 % Allowed : 12.94 % Favored : 84.14 % 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: 0.16 (0.27), residues: 1040 helix: 4.00 (0.31), residues: 236 sheet: 0.59 (0.33), residues: 287 loop : -2.25 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP n 259 HIS 0.005 0.001 HIS n 66 PHE 0.009 0.001 PHE m 189 TYR 0.012 0.001 TYR n 50 ARG 0.002 0.000 ARG n 228 Details of bonding type rmsd hydrogen bonds : bond 0.05061 ( 325) hydrogen bonds : angle 3.84321 ( 972) SS BOND : bond 0.00356 ( 13) SS BOND : angle 0.80398 ( 26) covalent geometry : bond 0.00244 ( 8561) covalent geometry : angle 0.59023 (11624) *********************** REFINEMENT MACRO_CYCLE 8 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 147 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.878 Fit side-chains REVERT: d 99 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7136 (pp) REVERT: e 37 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8277 (mttp) REVERT: f 101 ARG cc_start: 0.7562 (tpt-90) cc_final: 0.6899 (tpt170) REVERT: g 92 ASN cc_start: 0.7004 (m110) cc_final: 0.5777 (t0) REVERT: m 145 ARG cc_start: 0.8039 (mtm180) cc_final: 0.7538 (mtt90) REVERT: m 207 ASN cc_start: 0.7574 (m-40) cc_final: 0.7170 (p0) REVERT: n 28 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7595 (mtmm) REVERT: n 32 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8167 (pp) REVERT: n 50 TYR cc_start: 0.5163 (OUTLIER) cc_final: 0.4495 (p90) REVERT: n 80 PRO cc_start: 0.7420 (Cg_endo) cc_final: 0.7084 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8244 (tt) REVERT: n 252 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8309 (pt0) REVERT: n 261 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8510 (ptt180) REVERT: n 263 ASP cc_start: 0.7704 (m-30) cc_final: 0.7445 (m-30) outliers start: 27 outliers final: 19 residues processed: 141 average time/residue: 0.2256 time to fit residues: 43.1702 Evaluate side-chains 138 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 161 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 0.0000 chunk 27 optimal weight: 0.0670 chunk 77 optimal weight: 6.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 ASN ** n 48 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 = 0.3969 r_free = 0.3969 target = 0.178779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.141541 restraints weight = 9461.282| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.29 r_work: 0.3123 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 8574 Z= 0.093 Angle : 0.547 9.547 11650 Z= 0.279 Chirality : 0.040 0.179 1308 Planarity : 0.003 0.028 1468 Dihedral : 5.174 59.527 1279 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 2.27 % Allowed : 13.92 % Favored : 83.82 % 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: 0.32 (0.27), residues: 1040 helix: 4.00 (0.31), residues: 243 sheet: 0.79 (0.33), residues: 277 loop : -2.18 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP n 259 HIS 0.005 0.001 HIS n 66 PHE 0.011 0.001 PHE n 29 TYR 0.011 0.001 TYR n 50 ARG 0.002 0.000 ARG e 117 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 325) hydrogen bonds : angle 3.59560 ( 972) SS BOND : bond 0.00215 ( 13) SS BOND : angle 0.57959 ( 26) covalent geometry : bond 0.00196 ( 8561) covalent geometry : angle 0.54714 (11624) *********************** REFINEMENT MACRO_CYCLE 9 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 144 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.883 Fit side-chains REVERT: d 99 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7204 (pp) REVERT: d 123 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6858 (t80) REVERT: e 37 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8220 (mttp) REVERT: f 101 ARG cc_start: 0.7466 (tpt-90) cc_final: 0.6802 (tpt170) REVERT: g 77 ASN cc_start: 0.8621 (p0) cc_final: 0.8112 (p0) REVERT: g 92 ASN cc_start: 0.7081 (m110) cc_final: 0.5917 (t0) REVERT: m 121 THR cc_start: 0.6899 (m) cc_final: 0.6477 (p) REVERT: m 145 ARG cc_start: 0.7903 (mtm180) cc_final: 0.7489 (mtt90) REVERT: m 207 ASN cc_start: 0.7546 (m-40) cc_final: 0.7304 (p0) REVERT: n 28 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7666 (mtmm) REVERT: n 50 TYR cc_start: 0.5412 (OUTLIER) cc_final: 0.4773 (p90) REVERT: n 80 PRO cc_start: 0.7563 (Cg_endo) cc_final: 0.7267 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8275 (tt) REVERT: n 261 ARG cc_start: 0.8547 (ppt-90) cc_final: 0.8203 (ptt180) REVERT: n 263 ASP cc_start: 0.7568 (m-30) cc_final: 0.7323 (m-30) outliers start: 21 outliers final: 12 residues processed: 139 average time/residue: 0.2323 time to fit residues: 42.6771 Evaluate side-chains 132 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 52 ASN Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 161 ASP Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 250 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.4980 chunk 49 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.175151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135832 restraints weight = 9355.851| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.40 r_work: 0.3060 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8574 Z= 0.122 Angle : 0.605 9.368 11650 Z= 0.307 Chirality : 0.042 0.178 1308 Planarity : 0.004 0.029 1468 Dihedral : 5.329 58.227 1279 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 1.73 % Allowed : 14.24 % Favored : 84.03 % 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: 0.32 (0.27), residues: 1040 helix: 3.86 (0.31), residues: 243 sheet: 0.78 (0.33), residues: 286 loop : -2.14 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP n 259 HIS 0.004 0.001 HIS n 66 PHE 0.012 0.001 PHE m 189 TYR 0.013 0.001 TYR n 50 ARG 0.003 0.000 ARG n 96 Details of bonding type rmsd hydrogen bonds : bond 0.04916 ( 325) hydrogen bonds : angle 3.74470 ( 972) SS BOND : bond 0.00375 ( 13) SS BOND : angle 0.88492 ( 26) covalent geometry : bond 0.00271 ( 8561) covalent geometry : angle 0.60384 (11624) ********************** REFINEMENT MACRO_CYCLE 10 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 138 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.870 Fit side-chains REVERT: d 99 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7194 (pp) REVERT: e 37 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8311 (mttp) REVERT: f 101 ARG cc_start: 0.7571 (tpt-90) cc_final: 0.6890 (tpt170) REVERT: g 51 LYS cc_start: 0.6374 (pttp) cc_final: 0.6162 (mttp) REVERT: g 92 ASN cc_start: 0.7282 (m110) cc_final: 0.5887 (t0) REVERT: m 82 ARG cc_start: 0.5917 (mtm180) cc_final: 0.5319 (mtm-85) REVERT: m 121 THR cc_start: 0.7008 (m) cc_final: 0.6545 (p) REVERT: m 145 ARG cc_start: 0.7928 (mtm180) cc_final: 0.7460 (mtt90) REVERT: m 207 ASN cc_start: 0.7535 (m-40) cc_final: 0.7297 (p0) REVERT: m 211 ASN cc_start: 0.8474 (m-40) cc_final: 0.8155 (t0) REVERT: n 28 LYS cc_start: 0.7957 (mtmt) cc_final: 0.7656 (mtmm) REVERT: n 50 TYR cc_start: 0.5163 (OUTLIER) cc_final: 0.4506 (p90) REVERT: n 80 PRO cc_start: 0.7619 (Cg_endo) cc_final: 0.7383 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8221 (tt) REVERT: n 261 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8356 (ptt180) REVERT: n 263 ASP cc_start: 0.7684 (m-30) cc_final: 0.7398 (m-30) outliers start: 16 outliers final: 11 residues processed: 134 average time/residue: 0.2250 time to fit residues: 40.7023 Evaluate side-chains 136 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 161 ASP Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 176 LEU Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 88 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 ASN ** n 48 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 = 0.3928 r_free = 0.3928 target = 0.174958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127433 restraints weight = 9477.083| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.46 r_work: 0.3110 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.6284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8574 Z= 0.117 Angle : 0.591 9.371 11650 Z= 0.300 Chirality : 0.041 0.183 1308 Planarity : 0.003 0.031 1468 Dihedral : 5.353 59.513 1279 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 2.05 % Allowed : 14.46 % Favored : 83.50 % 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: 0.36 (0.27), residues: 1040 helix: 3.93 (0.31), residues: 242 sheet: 0.76 (0.33), residues: 286 loop : -2.09 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP n 259 HIS 0.005 0.001 HIS n 66 PHE 0.009 0.001 PHE m 189 TYR 0.013 0.001 TYR e 52 ARG 0.003 0.000 ARG n 96 Details of bonding type rmsd hydrogen bonds : bond 0.04950 ( 325) hydrogen bonds : angle 3.75377 ( 972) SS BOND : bond 0.00336 ( 13) SS BOND : angle 0.84637 ( 26) covalent geometry : bond 0.00257 ( 8561) covalent geometry : angle 0.58986 (11624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5495.88 seconds wall clock time: 97 minutes 20.88 seconds (5840.88 seconds total)