Starting phenix.real_space_refine on Thu Feb 13 00:09:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fjf_31620/02_2025/7fjf_31620.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjf_31620/02_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_31620/02_2025/7fjf_31620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjf_31620/02_2025/7fjf_31620.map" model { file = "/net/cci-nas-00/data/ceres_data/7fjf_31620/02_2025/7fjf_31620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjf_31620/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.99, per 1000 atoms: 0.60 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: 2.14 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.00 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: 2.22 Time building geometry restraints manager: 2.46 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: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.360 Find NCS groups from input model: 0.140 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.700 ------------------------------------------------------------------------------- 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 : 0.010 0.177 8561 Z= 0.677 Angle : 1.345 30.884 11624 Z= 0.702 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 *********************** 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 : 0.896 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: 0.2200 time to fit residues: 57.0015 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 : 0.896 ------------------------------------------------------------------------------- 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: 4.9990 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 = 149)---------------| | r_work = 0.3511 r_free = 0.3511 target = 0.138055 restraints weight = 9699.051| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.83 r_work: 0.3176 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8561 Z= 0.237 Angle : 0.707 9.912 11624 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 *********************** 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 : 0.956 Fit side-chains REVERT: d 27 GLU cc_start: 0.8603 (pt0) cc_final: 0.8391 (pt0) REVERT: d 117 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8079 (tp) REVERT: e 51 GLN cc_start: 0.6531 (mt0) cc_final: 0.6317 (mp10) REVERT: e 125 MET cc_start: 0.8533 (mmt) cc_final: 0.8146 (mmt) REVERT: e 128 MET cc_start: 0.7589 (mmm) cc_final: 0.7273 (mmt) REVERT: f 111 TYR cc_start: 0.8731 (m-10) cc_final: 0.8497 (m-80) REVERT: g 30 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7420 (mp) REVERT: g 77 ASN cc_start: 0.8592 (p0) cc_final: 0.8141 (p0) REVERT: m 56 MET cc_start: 0.8081 (mpp) cc_final: 0.7861 (mpp) REVERT: m 145 ARG cc_start: 0.7969 (mtm180) cc_final: 0.7403 (ttm110) REVERT: n 80 PRO cc_start: 0.7142 (Cg_endo) cc_final: 0.6731 (Cg_exo) REVERT: n 151 GLU cc_start: 0.7596 (mp0) cc_final: 0.7144 (mp0) REVERT: n 252 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8068 (pt0) REVERT: n 261 ARG cc_start: 0.8438 (ppt-90) cc_final: 0.8082 (ptt180) outliers start: 25 outliers final: 6 residues processed: 171 average time/residue: 0.2383 time to fit residues: 53.5723 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 : 0.964 ------------------------------------------------------------------------------- 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: 0.5980 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.0170 chunk 9 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.181771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.148854 restraints weight = 9747.004| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.85 r_work: 0.3174 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8561 Z= 0.174 Angle : 0.617 9.559 11624 Z= 0.322 Chirality : 0.042 0.212 1308 Planarity : 0.004 0.043 1468 Dihedral : 6.109 56.843 1281 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.67 % Favored : 94.23 % Rotamer: Outliers : 2.27 % Allowed : 11.11 % Favored : 86.62 % 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: -0.89 (0.26), residues: 1040 helix: 2.78 (0.33), residues: 240 sheet: 0.20 (0.33), residues: 288 loop : -2.94 (0.22), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP n 259 HIS 0.005 0.001 HIS n 66 PHE 0.018 0.001 PHE n 29 TYR 0.017 0.001 TYR g 34 ARG 0.006 0.000 ARG d 91 *********************** 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 157 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.901 Fit side-chains REVERT: d 117 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8137 (tp) REVERT: e 128 MET cc_start: 0.7552 (mmm) cc_final: 0.7202 (mmt) REVERT: g 30 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7833 (pp) REVERT: g 77 ASN cc_start: 0.8674 (p0) cc_final: 0.8194 (p0) REVERT: m 145 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7477 (ttm110) REVERT: m 159 ASP cc_start: 0.6516 (p0) cc_final: 0.6154 (p0) REVERT: m 207 ASN cc_start: 0.7690 (m-40) cc_final: 0.7269 (p0) REVERT: n 80 PRO cc_start: 0.7291 (Cg_endo) cc_final: 0.6963 (Cg_exo) REVERT: n 151 GLU cc_start: 0.7817 (mp0) cc_final: 0.7531 (mp0) REVERT: n 252 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8177 (pt0) REVERT: n 261 ARG cc_start: 0.8465 (ppt-90) cc_final: 0.8075 (ptt180) REVERT: n 263 ASP cc_start: 0.7219 (m-30) cc_final: 0.7004 (m-30) outliers start: 21 outliers final: 8 residues processed: 151 average time/residue: 0.2320 time to fit residues: 47.0784 Evaluate side-chains 134 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU 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 184 GLU Chi-restraints excluded: chain n residue 215 VAL 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: 0.5980 chunk 35 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 7 optimal weight: 0.0050 chunk 65 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 0.0870 overall best weight: 0.3372 ------------------------------------------------------------------------------- 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 ** 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 = 0.4025 r_free = 0.4025 target = 0.183206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.148898 restraints weight = 9699.190| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.00 r_work: 0.3268 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 8561 Z= 0.135 Angle : 0.555 9.431 11624 Z= 0.288 Chirality : 0.041 0.185 1308 Planarity : 0.004 0.034 1468 Dihedral : 5.718 56.687 1281 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.23 % Favored : 95.67 % Rotamer: Outliers : 2.37 % Allowed : 11.22 % 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: 3.45 (0.32), residues: 236 sheet: 0.47 (0.33), residues: 282 loop : -2.61 (0.23), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP n 259 HIS 0.004 0.001 HIS n 66 PHE 0.014 0.001 PHE m 157 TYR 0.014 0.001 TYR n 50 ARG 0.002 0.000 ARG n 113 *********************** 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 149 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.917 Fit side-chains REVERT: d 99 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7362 (pp) REVERT: e 128 MET cc_start: 0.7227 (mmm) cc_final: 0.6920 (mmt) REVERT: g 30 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7753 (pp) REVERT: g 32 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8479 (mmtm) REVERT: g 77 ASN cc_start: 0.8579 (p0) cc_final: 0.8121 (p0) REVERT: m 145 ARG cc_start: 0.7890 (mtm180) cc_final: 0.7302 (ttm110) REVERT: m 159 ASP cc_start: 0.6001 (p0) cc_final: 0.5676 (p0) REVERT: m 207 ASN cc_start: 0.7823 (m-40) cc_final: 0.7289 (p0) REVERT: n 32 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8088 (pp) REVERT: n 50 TYR cc_start: 0.5503 (OUTLIER) cc_final: 0.5231 (p90) REVERT: n 80 PRO cc_start: 0.7206 (Cg_endo) cc_final: 0.6884 (Cg_exo) REVERT: n 252 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8203 (pt0) REVERT: n 261 ARG cc_start: 0.8366 (ppt-90) cc_final: 0.7996 (ptt180) outliers start: 22 outliers final: 11 residues processed: 143 average time/residue: 0.2153 time to fit residues: 41.7186 Evaluate side-chains 128 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 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 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 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: 4.9990 chunk 21 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 60 GLN g 52 ASN g 105 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 = 0.3844 r_free = 0.3844 target = 0.167534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.117179 restraints weight = 9233.580| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.57 r_work: 0.2949 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8561 Z= 0.388 Angle : 0.803 12.220 11624 Z= 0.413 Chirality : 0.049 0.213 1308 Planarity : 0.005 0.063 1468 Dihedral : 6.695 55.176 1281 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.31 % Favored : 92.50 % Rotamer: Outliers : 2.80 % Allowed : 10.90 % Favored : 86.30 % 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: -0.81 (0.26), residues: 1040 helix: 2.61 (0.32), residues: 243 sheet: 0.33 (0.33), residues: 280 loop : -2.81 (0.22), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP n 259 HIS 0.006 0.002 HIS n 226 PHE 0.018 0.002 PHE f 87 TYR 0.026 0.003 TYR g 34 ARG 0.007 0.001 ARG m 185 *********************** 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 159 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: d 84 SER cc_start: 0.8650 (p) cc_final: 0.8390 (t) REVERT: d 99 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7231 (pp) REVERT: e 37 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8503 (mttp) REVERT: e 128 MET cc_start: 0.7929 (mmm) cc_final: 0.7671 (mmm) REVERT: f 101 ARG cc_start: 0.7501 (tpt-90) cc_final: 0.6983 (tpt170) REVERT: f 104 LYS cc_start: 0.8829 (tttt) cc_final: 0.7986 (mttt) REVERT: g 92 ASN cc_start: 0.6932 (m110) cc_final: 0.5692 (t0) REVERT: g 103 MET cc_start: 0.7943 (mtp) cc_final: 0.7509 (mmm) REVERT: m 145 ARG cc_start: 0.8142 (mtm180) cc_final: 0.7868 (mtt90) REVERT: m 148 LYS cc_start: 0.7119 (mmtp) cc_final: 0.6871 (mttt) REVERT: m 207 ASN cc_start: 0.7899 (m-40) cc_final: 0.7422 (p0) REVERT: m 229 VAL cc_start: 0.8151 (t) cc_final: 0.7930 (m) REVERT: m 230 LYS cc_start: 0.8901 (mttt) cc_final: 0.8412 (mmtt) REVERT: n 28 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7620 (mtmm) REVERT: n 32 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7615 (pp) REVERT: n 50 TYR cc_start: 0.5356 (OUTLIER) cc_final: 0.4495 (p90) REVERT: n 80 PRO cc_start: 0.7366 (Cg_endo) cc_final: 0.7003 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8341 (tt) REVERT: n 252 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8140 (pt0) REVERT: n 261 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8709 (ptt180) outliers start: 26 outliers final: 13 residues processed: 152 average time/residue: 0.2097 time to fit residues: 43.4684 Evaluate side-chains 141 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 14 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 ** m 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 25 GLN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.170434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.118606 restraints weight = 9309.361| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.51 r_work: 0.2994 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8561 Z= 0.254 Angle : 0.679 10.156 11624 Z= 0.349 Chirality : 0.044 0.202 1308 Planarity : 0.004 0.037 1468 Dihedral : 6.163 55.769 1279 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.48 % Favored : 94.33 % Rotamer: Outliers : 2.70 % Allowed : 11.76 % Favored : 85.54 % 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: -0.53 (0.26), residues: 1040 helix: 3.10 (0.31), residues: 241 sheet: 0.39 (0.34), residues: 275 loop : -2.64 (0.22), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP n 259 HIS 0.004 0.001 HIS n 66 PHE 0.014 0.002 PHE f 87 TYR 0.016 0.002 TYR e 52 ARG 0.004 0.000 ARG d 91 *********************** 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 156 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.920 Fit side-chains REVERT: d 99 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7289 (pp) REVERT: e 37 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8399 (mttp) REVERT: e 128 MET cc_start: 0.7630 (mmm) cc_final: 0.7344 (mmm) REVERT: f 101 ARG cc_start: 0.7613 (tpt-90) cc_final: 0.6934 (tpt170) REVERT: f 104 LYS cc_start: 0.8876 (tttt) cc_final: 0.8062 (mttt) REVERT: f 125 MET cc_start: 0.7945 (mmp) cc_final: 0.7569 (mmt) REVERT: g 92 ASN cc_start: 0.7218 (m110) cc_final: 0.5760 (t0) REVERT: m 145 ARG cc_start: 0.8110 (mtm180) cc_final: 0.7421 (mtp-110) REVERT: m 148 LYS cc_start: 0.7007 (mmtp) cc_final: 0.6723 (mttt) REVERT: m 168 GLN cc_start: 0.7797 (mm110) cc_final: 0.7567 (mm110) REVERT: m 207 ASN cc_start: 0.7701 (m-40) cc_final: 0.7269 (p0) REVERT: m 229 VAL cc_start: 0.8093 (t) cc_final: 0.7798 (m) REVERT: m 230 LYS cc_start: 0.8817 (mttt) cc_final: 0.8332 (mmtt) REVERT: n 28 LYS cc_start: 0.8035 (mtmt) cc_final: 0.7666 (mtmm) REVERT: n 32 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8226 (pp) REVERT: n 50 TYR cc_start: 0.5366 (OUTLIER) cc_final: 0.4572 (p90) REVERT: n 80 PRO cc_start: 0.7451 (Cg_endo) cc_final: 0.7109 (Cg_exo) REVERT: n 252 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8151 (pt0) REVERT: n 261 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8591 (ptt180) outliers start: 25 outliers final: 17 residues processed: 151 average time/residue: 0.2134 time to fit residues: 43.8052 Evaluate side-chains 155 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 52 ASN 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 50 TYR Chi-restraints excluded: chain n residue 52 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.169977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121195 restraints weight = 9469.109| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.56 r_work: 0.3000 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8561 Z= 0.207 Angle : 0.644 9.348 11624 Z= 0.331 Chirality : 0.043 0.212 1308 Planarity : 0.004 0.033 1468 Dihedral : 5.947 55.905 1279 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.96 % Favored : 93.85 % Rotamer: Outliers : 2.91 % Allowed : 12.62 % 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: -0.28 (0.26), residues: 1040 helix: 3.53 (0.31), residues: 236 sheet: 0.47 (0.34), residues: 275 loop : -2.51 (0.22), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP n 259 HIS 0.003 0.001 HIS n 66 PHE 0.012 0.001 PHE f 87 TYR 0.014 0.001 TYR e 52 ARG 0.003 0.000 ARG d 91 *********************** 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 160 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: d 84 SER cc_start: 0.8480 (p) cc_final: 0.8137 (t) REVERT: d 99 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7372 (pp) REVERT: e 37 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8392 (mttp) REVERT: e 128 MET cc_start: 0.7571 (mmm) cc_final: 0.7304 (mmm) REVERT: f 101 ARG cc_start: 0.7592 (tpt-90) cc_final: 0.6903 (tpt170) REVERT: g 92 ASN cc_start: 0.7220 (m110) cc_final: 0.5751 (t0) REVERT: g 103 MET cc_start: 0.7679 (mtp) cc_final: 0.7291 (mmm) REVERT: m 145 ARG cc_start: 0.8132 (mtm180) cc_final: 0.7436 (mtp-110) REVERT: m 148 LYS cc_start: 0.7081 (mmtp) cc_final: 0.6796 (mttt) REVERT: m 168 GLN cc_start: 0.7847 (mm110) cc_final: 0.7610 (mm110) REVERT: m 207 ASN cc_start: 0.7628 (m-40) cc_final: 0.7274 (p0) REVERT: m 229 VAL cc_start: 0.8213 (t) cc_final: 0.7934 (m) REVERT: m 230 LYS cc_start: 0.8854 (mttt) cc_final: 0.8360 (mmtt) REVERT: n 28 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7746 (mtmm) REVERT: n 32 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8273 (pp) REVERT: n 50 TYR cc_start: 0.5424 (OUTLIER) cc_final: 0.4659 (p90) REVERT: n 80 PRO cc_start: 0.7496 (Cg_endo) cc_final: 0.7144 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8307 (tt) REVERT: n 252 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8081 (pt0) REVERT: n 261 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8546 (ptt180) REVERT: n 263 ASP cc_start: 0.7748 (m-30) cc_final: 0.7470 (m-30) outliers start: 27 outliers final: 19 residues processed: 155 average time/residue: 0.2027 time to fit residues: 43.2015 Evaluate side-chains 155 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 39 SER 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 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 182 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** n 66 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 = 0.3879 r_free = 0.3879 target = 0.171082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.118795 restraints weight = 9423.000| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.56 r_work: 0.3028 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8561 Z= 0.166 Angle : 0.606 9.381 11624 Z= 0.312 Chirality : 0.042 0.205 1308 Planarity : 0.004 0.033 1468 Dihedral : 5.715 56.382 1279 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 2.70 % Allowed : 13.27 % 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: -0.03 (0.27), residues: 1040 helix: 3.80 (0.31), residues: 236 sheet: 0.52 (0.33), residues: 285 loop : -2.37 (0.23), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP n 259 HIS 0.003 0.001 HIS n 66 PHE 0.010 0.001 PHE f 87 TYR 0.013 0.001 TYR e 52 ARG 0.002 0.000 ARG d 91 *********************** 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 154 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.965 Fit side-chains REVERT: d 27 GLU cc_start: 0.8205 (pt0) cc_final: 0.7997 (tt0) REVERT: d 82 LYS cc_start: 0.7824 (mttt) cc_final: 0.7555 (mttt) REVERT: d 99 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7412 (pp) REVERT: e 37 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8286 (mttp) REVERT: e 128 MET cc_start: 0.7310 (mmm) cc_final: 0.7079 (mmm) REVERT: f 101 ARG cc_start: 0.7618 (tpt-90) cc_final: 0.6832 (tpt170) REVERT: g 51 LYS cc_start: 0.6331 (pptt) cc_final: 0.6046 (mmmm) REVERT: g 52 ASN cc_start: 0.5992 (OUTLIER) cc_final: 0.5760 (t0) REVERT: g 92 ASN cc_start: 0.7285 (m110) cc_final: 0.5755 (t0) REVERT: m 145 ARG cc_start: 0.7847 (mtm180) cc_final: 0.7312 (mtt90) REVERT: m 148 LYS cc_start: 0.7069 (mmtp) cc_final: 0.6864 (mttt) REVERT: m 168 GLN cc_start: 0.7765 (mm110) cc_final: 0.7529 (mm110) REVERT: m 207 ASN cc_start: 0.7525 (m-40) cc_final: 0.7299 (p0) REVERT: m 229 VAL cc_start: 0.8220 (t) cc_final: 0.7947 (m) REVERT: m 230 LYS cc_start: 0.8755 (mttt) cc_final: 0.8304 (mmtt) REVERT: n 28 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7651 (mtmm) REVERT: n 32 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8199 (pp) REVERT: n 50 TYR cc_start: 0.5231 (OUTLIER) cc_final: 0.4609 (p90) REVERT: n 80 PRO cc_start: 0.7525 (Cg_endo) cc_final: 0.7199 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8333 (tt) REVERT: n 252 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8036 (pt0) REVERT: n 261 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8351 (ptt180) REVERT: n 263 ASP cc_start: 0.7829 (m-30) cc_final: 0.7546 (m-30) outliers start: 25 outliers final: 16 residues processed: 149 average time/residue: 0.2103 time to fit residues: 42.9383 Evaluate side-chains 146 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 39 SER 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 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 182 LEU Chi-restraints excluded: chain n residue 32 LEU 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 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: 1.9990 chunk 43 optimal weight: 0.6980 chunk 41 optimal weight: 0.0370 chunk 27 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.172701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.129114 restraints weight = 9485.247| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.96 r_work: 0.3131 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.6199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8561 Z= 0.160 Angle : 0.609 11.939 11624 Z= 0.313 Chirality : 0.042 0.208 1308 Planarity : 0.004 0.030 1468 Dihedral : 5.594 57.552 1279 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.00 % Favored : 94.90 % Rotamer: Outliers : 2.59 % Allowed : 13.38 % 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: 0.14 (0.27), residues: 1040 helix: 3.96 (0.31), residues: 236 sheet: 0.61 (0.33), residues: 286 loop : -2.25 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP n 259 HIS 0.004 0.001 HIS n 66 PHE 0.010 0.001 PHE m 157 TYR 0.013 0.001 TYR e 52 ARG 0.002 0.000 ARG d 91 *********************** 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 145 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.893 Fit side-chains REVERT: d 99 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7428 (pp) REVERT: e 37 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8322 (mttp) REVERT: e 128 MET cc_start: 0.7351 (mmm) cc_final: 0.7137 (mmm) REVERT: f 101 ARG cc_start: 0.7547 (tpt-90) cc_final: 0.6808 (tpt170) REVERT: g 51 LYS cc_start: 0.6425 (pptt) cc_final: 0.5995 (mmmm) REVERT: g 92 ASN cc_start: 0.7285 (m110) cc_final: 0.6814 (m-40) REVERT: m 121 THR cc_start: 0.7009 (m) cc_final: 0.6548 (p) REVERT: m 145 ARG cc_start: 0.7963 (mtm180) cc_final: 0.7424 (mtt90) REVERT: m 148 LYS cc_start: 0.7053 (mmtp) cc_final: 0.6829 (mttt) REVERT: m 168 GLN cc_start: 0.7838 (mm110) cc_final: 0.7632 (mm110) REVERT: m 229 VAL cc_start: 0.8160 (t) cc_final: 0.7898 (m) REVERT: n 28 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7686 (mtmm) REVERT: n 32 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8241 (pp) REVERT: n 50 TYR cc_start: 0.5191 (OUTLIER) cc_final: 0.4543 (p90) REVERT: n 80 PRO cc_start: 0.7613 (Cg_endo) cc_final: 0.7283 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8346 (tt) REVERT: n 261 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8419 (ptt180) REVERT: n 263 ASP cc_start: 0.7732 (m-30) cc_final: 0.7445 (m-30) outliers start: 24 outliers final: 16 residues processed: 141 average time/residue: 0.2105 time to fit residues: 40.3401 Evaluate side-chains 143 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 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 113 MET Chi-restraints excluded: chain m residue 182 LEU 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 250 VAL Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.0270 chunk 49 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.174587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.122378 restraints weight = 9301.060| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.77 r_work: 0.3034 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8561 Z= 0.159 Angle : 0.602 9.399 11624 Z= 0.306 Chirality : 0.042 0.211 1308 Planarity : 0.004 0.031 1468 Dihedral : 5.477 59.346 1279 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.42 % Favored : 95.38 % Rotamer: Outliers : 2.70 % Allowed : 13.48 % 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: 0.30 (0.27), residues: 1040 helix: 4.09 (0.31), residues: 236 sheet: 0.70 (0.33), residues: 286 loop : -2.15 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP n 259 HIS 0.004 0.001 HIS n 66 PHE 0.009 0.001 PHE n 29 TYR 0.013 0.001 TYR e 52 ARG 0.006 0.000 ARG m 99 ********************** 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 149 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.003 Fit side-chains REVERT: d 82 LYS cc_start: 0.7883 (mttt) cc_final: 0.7545 (mttt) REVERT: d 99 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7468 (pp) REVERT: e 37 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8322 (mttp) REVERT: e 128 MET cc_start: 0.7253 (mmm) cc_final: 0.6985 (mmm) REVERT: g 51 LYS cc_start: 0.6416 (pptt) cc_final: 0.6099 (mmmm) REVERT: g 92 ASN cc_start: 0.7195 (m110) cc_final: 0.6765 (m-40) REVERT: g 103 MET cc_start: 0.6990 (mtp) cc_final: 0.6744 (mmm) REVERT: m 121 THR cc_start: 0.7045 (m) cc_final: 0.6565 (p) REVERT: m 145 ARG cc_start: 0.7853 (mtm180) cc_final: 0.7355 (mtt90) REVERT: m 168 GLN cc_start: 0.7812 (mm110) cc_final: 0.7600 (mm110) REVERT: m 229 VAL cc_start: 0.8171 (t) cc_final: 0.7927 (m) REVERT: n 28 LYS cc_start: 0.8017 (mtmt) cc_final: 0.7716 (mtmm) REVERT: n 32 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8260 (pp) REVERT: n 50 TYR cc_start: 0.5130 (OUTLIER) cc_final: 0.4523 (p90) REVERT: n 80 PRO cc_start: 0.7632 (Cg_endo) cc_final: 0.7323 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8256 (tt) REVERT: n 252 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8025 (pt0) REVERT: n 261 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8364 (ptt180) outliers start: 25 outliers final: 19 residues processed: 144 average time/residue: 0.2294 time to fit residues: 45.1855 Evaluate side-chains 145 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 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 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 113 MET Chi-restraints excluded: chain m residue 161 ASP Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 32 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 34 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.173606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134690 restraints weight = 9452.204| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.44 r_work: 0.3050 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8561 Z= 0.157 Angle : 0.598 9.470 11624 Z= 0.306 Chirality : 0.042 0.210 1308 Planarity : 0.004 0.030 1468 Dihedral : 5.442 59.774 1279 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 2.91 % Allowed : 13.48 % Favored : 83.60 % 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: 4.08 (0.31), residues: 237 sheet: 0.73 (0.33), residues: 286 loop : -2.11 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP n 259 HIS 0.004 0.001 HIS n 66 PHE 0.009 0.001 PHE n 29 TYR 0.013 0.001 TYR e 52 ARG 0.004 0.000 ARG f 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4932.23 seconds wall clock time: 87 minutes 41.39 seconds (5261.39 seconds total)