Starting phenix.real_space_refine on Thu Mar 13 01:33:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fjf_31620/03_2025/7fjf_31620.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjf_31620/03_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_31620/03_2025/7fjf_31620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjf_31620/03_2025/7fjf_31620.map" model { file = "/net/cci-nas-00/data/ceres_data/7fjf_31620/03_2025/7fjf_31620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjf_31620/03_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-5624/modules/chem_data/mon_lib" Total number of atoms: 8377 Number of models: 1 Model: "" Number of chains: 10 Chain: "b" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "e" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "f" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 949 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "g" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "m" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1924 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 233} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2246 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "a" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 264 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "m" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'C3S': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'C3S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.13, per 1000 atoms: 0.61 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: 2.05 Conformation dependent library (CDL) restraints added in 989.2 milliseconds 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 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: 1.02 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: 2.11 Time building geometry restraints manager: 2.37 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.460 Find NCS groups from input model: 0.170 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.190 ------------------------------------------------------------------------------- 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 : 0.932 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: 0.2283 time to fit residues: 59.5785 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 : 0.924 ------------------------------------------------------------------------------- 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 = 89)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147959 restraints weight = 9699.014| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.70 r_work: 0.3356 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 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 : 0.912 Fit side-chains REVERT: d 27 GLU cc_start: 0.8567 (pt0) cc_final: 0.8356 (pt0) REVERT: d 117 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8137 (tp) REVERT: e 125 MET cc_start: 0.8522 (mmt) cc_final: 0.8129 (mmt) REVERT: e 128 MET cc_start: 0.7581 (mmm) cc_final: 0.7298 (mmt) REVERT: f 111 TYR cc_start: 0.8704 (m-10) cc_final: 0.8467 (m-80) REVERT: g 30 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7460 (mp) REVERT: g 77 ASN cc_start: 0.8604 (p0) cc_final: 0.8157 (p0) REVERT: m 56 MET cc_start: 0.8120 (mpp) cc_final: 0.7906 (mpp) REVERT: m 145 ARG cc_start: 0.7974 (mtm180) cc_final: 0.7426 (ttm110) REVERT: n 80 PRO cc_start: 0.7165 (Cg_endo) cc_final: 0.6770 (Cg_exo) REVERT: n 151 GLU cc_start: 0.7649 (mp0) cc_final: 0.7211 (mp0) REVERT: n 252 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8058 (pt0) REVERT: n 261 ARG cc_start: 0.8441 (ppt-90) cc_final: 0.8088 (ptt180) outliers start: 25 outliers final: 6 residues processed: 171 average time/residue: 0.2419 time to fit residues: 54.5205 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 : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 126 THR Chi-restraints excluded: chain n residue 252 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 25 GLN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.174709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.131652 restraints weight = 9710.203| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.95 r_work: 0.3255 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4425 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= 0.182 Angle : 0.633 9.593 11624 Z= 0.329 Chirality : 0.043 0.219 1308 Planarity : 0.005 0.054 1468 Dihedral : 6.073 56.698 1281 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.77 % Favored : 94.13 % 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: 2.89 (0.33), residues: 237 sheet: 0.25 (0.33), residues: 284 loop : -2.86 (0.22), residues: 519 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 m 157 TYR 0.018 0.002 TYR g 34 ARG 0.005 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 169 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.965 Fit side-chains REVERT: e 37 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8350 (mttp) REVERT: e 128 MET cc_start: 0.7552 (mmm) cc_final: 0.7189 (mmt) REVERT: g 30 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7888 (pp) REVERT: g 32 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8565 (mmtm) REVERT: g 77 ASN cc_start: 0.8719 (p0) cc_final: 0.8211 (p0) REVERT: m 145 ARG cc_start: 0.8104 (mtm180) cc_final: 0.7532 (ttm110) REVERT: m 159 ASP cc_start: 0.6541 (p0) cc_final: 0.6176 (p0) REVERT: m 173 ASP cc_start: 0.8248 (m-30) cc_final: 0.7967 (m-30) REVERT: m 207 ASN cc_start: 0.7877 (m-40) cc_final: 0.7322 (p0) REVERT: n 80 PRO cc_start: 0.7330 (Cg_endo) cc_final: 0.6992 (Cg_exo) REVERT: n 151 GLU cc_start: 0.7965 (mp0) cc_final: 0.7708 (mp0) REVERT: n 252 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8150 (pt0) REVERT: n 261 ARG cc_start: 0.8597 (ppt-90) cc_final: 0.8237 (ptt180) outliers start: 26 outliers final: 11 residues processed: 161 average time/residue: 0.2313 time to fit residues: 50.4412 Evaluate side-chains 132 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 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 n residue 184 GLU Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 252 GLN Chi-restraints excluded: chain n residue 300 VAL 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: 6.9990 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 65 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 105 GLN ** 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 = 0.3892 r_free = 0.3892 target = 0.171839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.134811 restraints weight = 9404.072| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.99 r_work: 0.3016 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8561 Z= 0.209 Angle : 0.638 9.714 11624 Z= 0.331 Chirality : 0.043 0.181 1308 Planarity : 0.004 0.032 1468 Dihedral : 6.058 56.215 1281 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.00 % Favored : 94.81 % Rotamer: Outliers : 2.37 % Allowed : 11.76 % Favored : 85.87 % 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: 3.20 (0.33), residues: 237 sheet: 0.47 (0.33), residues: 281 loop : -2.75 (0.22), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP n 259 HIS 0.004 0.001 HIS n 66 PHE 0.013 0.002 PHE f 87 TYR 0.017 0.002 TYR g 34 ARG 0.003 0.000 ARG d 91 *********************** 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 146 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: d 99 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7213 (pp) REVERT: e 37 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8397 (mttp) REVERT: e 109 ASN cc_start: 0.8566 (p0) cc_final: 0.8336 (p0) REVERT: f 101 ARG cc_start: 0.7160 (tpt-90) cc_final: 0.6742 (tpt170) REVERT: g 30 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7762 (pp) REVERT: g 92 ASN cc_start: 0.7024 (m110) cc_final: 0.5866 (t0) REVERT: m 145 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7355 (ttm110) REVERT: m 148 LYS cc_start: 0.7164 (mptt) cc_final: 0.6837 (mttt) REVERT: m 207 ASN cc_start: 0.7982 (m-40) cc_final: 0.7503 (p0) REVERT: m 229 VAL cc_start: 0.8080 (t) cc_final: 0.7815 (m) REVERT: n 32 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8240 (pp) REVERT: n 50 TYR cc_start: 0.5467 (OUTLIER) cc_final: 0.4938 (p90) REVERT: n 80 PRO cc_start: 0.7333 (Cg_endo) cc_final: 0.6982 (Cg_exo) REVERT: n 252 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8196 (pt0) REVERT: n 261 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8483 (ptt180) outliers start: 22 outliers final: 14 residues processed: 140 average time/residue: 0.2101 time to fit residues: 40.0154 Evaluate side-chains 135 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 99 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 m residue 62 SER Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 184 GLU Chi-restraints excluded: chain n residue 208 CYS Chi-restraints excluded: chain n residue 215 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.0570 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.7702 ------------------------------------------------------------------------------- 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** g 52 ASN g 105 GLN n 25 GLN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.176349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126056 restraints weight = 9280.266| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.75 r_work: 0.3063 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5434 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= 0.167 Angle : 0.593 9.437 11624 Z= 0.307 Chirality : 0.042 0.198 1308 Planarity : 0.004 0.037 1468 Dihedral : 5.723 55.994 1281 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 2.80 % Allowed : 11.00 % Favored : 86.19 % 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: -0.20 (0.27), residues: 1040 helix: 3.63 (0.32), residues: 235 sheet: 0.41 (0.32), residues: 302 loop : -2.53 (0.23), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP n 259 HIS 0.003 0.001 HIS n 66 PHE 0.011 0.001 PHE n 29 TYR 0.013 0.001 TYR n 50 ARG 0.002 0.000 ARG m 63 *********************** 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 144 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: d 99 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7151 (pp) REVERT: e 37 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8249 (mttp) REVERT: f 101 ARG cc_start: 0.7285 (tpt-90) cc_final: 0.6763 (tpt170) REVERT: g 92 ASN cc_start: 0.7018 (m110) cc_final: 0.5987 (t0) REVERT: m 145 ARG cc_start: 0.7787 (mtm180) cc_final: 0.7185 (ttm110) REVERT: m 148 LYS cc_start: 0.7130 (mptt) cc_final: 0.6845 (mttt) REVERT: m 168 GLN cc_start: 0.7764 (mm110) cc_final: 0.7558 (mm110) REVERT: m 207 ASN cc_start: 0.7881 (m-40) cc_final: 0.7375 (p0) REVERT: m 229 VAL cc_start: 0.7946 (t) cc_final: 0.7698 (m) REVERT: n 28 LYS cc_start: 0.7786 (mtmt) cc_final: 0.7392 (mtmm) REVERT: n 32 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8200 (pp) REVERT: n 50 TYR cc_start: 0.5447 (OUTLIER) cc_final: 0.4781 (p90) REVERT: n 80 PRO cc_start: 0.7380 (Cg_endo) cc_final: 0.7067 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8278 (tt) REVERT: n 252 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8027 (pt0) REVERT: n 261 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8315 (ptt180) outliers start: 26 outliers final: 13 residues processed: 137 average time/residue: 0.2080 time to fit residues: 38.9782 Evaluate side-chains 133 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 70 LYS Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 183 ASP Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 176 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 76 optimal weight: 0.0010 chunk 89 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 66 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 = 0.3935 r_free = 0.3935 target = 0.176276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.124703 restraints weight = 9383.159| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.60 r_work: 0.3089 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5710 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= 0.149 Angle : 0.575 9.298 11624 Z= 0.296 Chirality : 0.041 0.182 1308 Planarity : 0.004 0.027 1468 Dihedral : 5.478 56.109 1279 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.42 % Favored : 95.48 % Rotamer: Outliers : 2.80 % Allowed : 12.19 % Favored : 85.01 % 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: 0.06 (0.27), residues: 1040 helix: 3.91 (0.31), residues: 236 sheet: 0.60 (0.32), residues: 297 loop : -2.41 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP n 259 HIS 0.003 0.001 HIS n 66 PHE 0.010 0.001 PHE n 29 TYR 0.012 0.001 TYR n 50 ARG 0.002 0.000 ARG m 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: d 99 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7198 (pp) REVERT: e 37 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8215 (mttp) REVERT: f 101 ARG cc_start: 0.7478 (tpt-90) cc_final: 0.6846 (tpt170) REVERT: f 104 LYS cc_start: 0.8832 (tttt) cc_final: 0.8076 (mttt) REVERT: g 92 ASN cc_start: 0.7106 (m110) cc_final: 0.5951 (t0) REVERT: m 145 ARG cc_start: 0.7782 (mtm180) cc_final: 0.7129 (ttm110) REVERT: m 148 LYS cc_start: 0.7085 (mptt) cc_final: 0.6831 (mttt) REVERT: m 168 GLN cc_start: 0.7736 (mm110) cc_final: 0.7535 (mm110) REVERT: m 207 ASN cc_start: 0.7744 (m-40) cc_final: 0.7362 (p0) REVERT: m 229 VAL cc_start: 0.7945 (t) cc_final: 0.7715 (m) REVERT: n 28 LYS cc_start: 0.7829 (mtmt) cc_final: 0.7435 (mtmm) REVERT: n 32 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8157 (pp) REVERT: n 50 TYR cc_start: 0.5354 (OUTLIER) cc_final: 0.4698 (p90) REVERT: n 80 PRO cc_start: 0.7365 (Cg_endo) cc_final: 0.7049 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8223 (tt) REVERT: n 261 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8258 (ptt180) outliers start: 26 outliers final: 16 residues processed: 139 average time/residue: 0.2305 time to fit residues: 43.4200 Evaluate side-chains 139 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 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 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 215 VAL Chi-restraints excluded: chain n residue 250 VAL Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 16 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 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 = 0.3919 r_free = 0.3919 target = 0.174647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135242 restraints weight = 9506.341| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.37 r_work: 0.3038 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5865 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= 0.164 Angle : 0.585 9.438 11624 Z= 0.301 Chirality : 0.041 0.192 1308 Planarity : 0.004 0.033 1468 Dihedral : 5.432 55.488 1279 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.71 % Rotamer: Outliers : 2.91 % Allowed : 12.51 % Favored : 84.57 % 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: 3.99 (0.31), residues: 236 sheet: 0.61 (0.32), residues: 287 loop : -2.27 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP n 259 HIS 0.005 0.001 HIS n 66 PHE 0.010 0.001 PHE m 189 TYR 0.012 0.001 TYR n 50 ARG 0.003 0.000 ARG m 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: d 99 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7201 (pp) REVERT: e 37 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8279 (mttp) REVERT: f 101 ARG cc_start: 0.7536 (tpt-90) cc_final: 0.6878 (tpt170) REVERT: f 104 LYS cc_start: 0.8890 (tttt) cc_final: 0.8088 (mttt) REVERT: f 125 MET cc_start: 0.7666 (mmm) cc_final: 0.7457 (mmt) REVERT: g 92 ASN cc_start: 0.7075 (m110) cc_final: 0.5858 (t0) REVERT: m 145 ARG cc_start: 0.7889 (mtm180) cc_final: 0.7383 (mtt90) REVERT: m 148 LYS cc_start: 0.7088 (mptt) cc_final: 0.6798 (mttt) REVERT: m 168 GLN cc_start: 0.7767 (mm110) cc_final: 0.7566 (mm110) REVERT: m 207 ASN cc_start: 0.7688 (m-40) cc_final: 0.7325 (p0) REVERT: m 229 VAL cc_start: 0.8000 (t) cc_final: 0.7734 (m) REVERT: m 233 GLU cc_start: 0.8619 (tt0) cc_final: 0.8404 (tm-30) REVERT: n 28 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7556 (mtmm) REVERT: n 32 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8200 (pp) REVERT: n 50 TYR cc_start: 0.5111 (OUTLIER) cc_final: 0.4507 (p90) REVERT: n 80 PRO cc_start: 0.7461 (Cg_endo) cc_final: 0.7167 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8252 (tt) REVERT: n 252 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8075 (pt0) REVERT: n 261 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8386 (ptt180) REVERT: n 263 ASP cc_start: 0.7662 (m-30) cc_final: 0.7414 (m-30) outliers start: 27 outliers final: 16 residues processed: 145 average time/residue: 0.2124 time to fit residues: 41.9595 Evaluate side-chains 140 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 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 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 252 GLN Chi-restraints excluded: chain n residue 261 ARG 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: 0.8980 chunk 70 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** g 52 ASN m 211 ASN ** 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 = 0.3918 r_free = 0.3918 target = 0.174277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134705 restraints weight = 9421.592| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.40 r_work: 0.3020 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8561 Z= 0.177 Angle : 0.593 9.303 11624 Z= 0.304 Chirality : 0.042 0.178 1308 Planarity : 0.004 0.028 1468 Dihedral : 5.466 55.576 1279 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.00 % Favored : 94.90 % Rotamer: Outliers : 2.91 % Allowed : 12.51 % Favored : 84.57 % 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: 0.09 (0.27), residues: 1040 helix: 3.78 (0.31), residues: 242 sheet: 0.70 (0.33), residues: 287 loop : -2.38 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP n 259 HIS 0.005 0.001 HIS n 66 PHE 0.010 0.001 PHE m 189 TYR 0.012 0.001 TYR n 50 ARG 0.003 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 159 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: d 99 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7303 (pp) REVERT: e 37 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8339 (mttp) REVERT: f 101 ARG cc_start: 0.7554 (tpt-90) cc_final: 0.6865 (tpt170) REVERT: g 92 ASN cc_start: 0.7299 (m110) cc_final: 0.5854 (t0) REVERT: m 82 ARG cc_start: 0.5814 (mtm180) cc_final: 0.5504 (mtm-85) REVERT: m 121 THR cc_start: 0.7091 (m) cc_final: 0.6603 (p) REVERT: m 145 ARG cc_start: 0.7949 (mtm180) cc_final: 0.7450 (mtt90) REVERT: m 148 LYS cc_start: 0.7160 (mptt) cc_final: 0.6844 (mttt) REVERT: m 207 ASN cc_start: 0.7681 (m-40) cc_final: 0.7356 (p0) REVERT: m 229 VAL cc_start: 0.8053 (t) cc_final: 0.7777 (m) REVERT: n 28 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7596 (mtmm) REVERT: n 32 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8218 (pp) REVERT: n 50 TYR cc_start: 0.5158 (OUTLIER) cc_final: 0.4534 (p90) REVERT: n 67 TYR cc_start: 0.7409 (p90) cc_final: 0.7068 (p90) REVERT: n 80 PRO cc_start: 0.7546 (Cg_endo) cc_final: 0.7246 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8274 (tt) REVERT: n 252 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8063 (pt0) REVERT: n 261 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8480 (ptt180) REVERT: n 263 ASP cc_start: 0.7735 (m-30) cc_final: 0.7482 (m-30) outliers start: 27 outliers final: 19 residues processed: 152 average time/residue: 0.2089 time to fit residues: 43.6696 Evaluate side-chains 153 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 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 m residue 62 SER Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 40 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 60 GLN g 52 ASN m 211 ASN ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.172151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121835 restraints weight = 9484.462| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.52 r_work: 0.3041 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.6090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8561 Z= 0.181 Angle : 0.605 9.350 11624 Z= 0.310 Chirality : 0.042 0.187 1308 Planarity : 0.004 0.029 1468 Dihedral : 5.466 56.045 1279 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 3.02 % Allowed : 13.05 % Favored : 83.93 % 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: 0.13 (0.27), residues: 1040 helix: 3.81 (0.31), residues: 242 sheet: 0.75 (0.33), residues: 286 loop : -2.37 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP n 259 HIS 0.005 0.001 HIS n 66 PHE 0.010 0.001 PHE m 189 TYR 0.012 0.001 TYR e 52 ARG 0.003 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 155 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.030 Fit side-chains REVERT: d 99 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7353 (pp) REVERT: e 37 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8319 (mttp) REVERT: f 101 ARG cc_start: 0.7573 (tpt-90) cc_final: 0.6878 (tpt170) REVERT: g 51 LYS cc_start: 0.6841 (pttp) cc_final: 0.6575 (mttp) REVERT: g 92 ASN cc_start: 0.7284 (m110) cc_final: 0.5859 (t0) REVERT: m 82 ARG cc_start: 0.5913 (mtm180) cc_final: 0.5619 (mtm-85) REVERT: m 121 THR cc_start: 0.7045 (m) cc_final: 0.6569 (p) REVERT: m 145 ARG cc_start: 0.7864 (mtm180) cc_final: 0.7373 (mtt90) REVERT: m 148 LYS cc_start: 0.7164 (mptt) cc_final: 0.6869 (mttt) REVERT: m 207 ASN cc_start: 0.7594 (m-40) cc_final: 0.7343 (p0) REVERT: m 211 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.7955 (m110) REVERT: m 229 VAL cc_start: 0.8085 (t) cc_final: 0.7809 (m) REVERT: n 28 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7586 (mtmm) REVERT: n 32 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8233 (pp) REVERT: n 50 TYR cc_start: 0.5106 (OUTLIER) cc_final: 0.4527 (p90) REVERT: n 80 PRO cc_start: 0.7564 (Cg_endo) cc_final: 0.7279 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8273 (tt) REVERT: n 252 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8052 (pt0) REVERT: n 261 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8401 (ptt180) REVERT: n 263 ASP cc_start: 0.7783 (m-30) cc_final: 0.7517 (m-30) outliers start: 28 outliers final: 21 residues processed: 149 average time/residue: 0.2102 time to fit residues: 42.7603 Evaluate side-chains 153 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 m residue 211 ASN Chi-restraints excluded: chain n residue 32 LEU Chi-restraints excluded: chain n residue 40 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 297 SER 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: 0.0370 chunk 49 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 92 optimal weight: 0.0980 chunk 50 optimal weight: 0.5980 overall best weight: 0.3858 ------------------------------------------------------------------------------- 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** m 211 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 = 0.3909 r_free = 0.3909 target = 0.173548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.124811 restraints weight = 9381.632| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.64 r_work: 0.3065 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 8561 Z= 0.135 Angle : 0.566 9.437 11624 Z= 0.291 Chirality : 0.041 0.178 1308 Planarity : 0.003 0.028 1468 Dihedral : 5.294 58.133 1279 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.19 % Rotamer: Outliers : 2.59 % Allowed : 13.48 % Favored : 83.93 % 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: 0.29 (0.27), residues: 1040 helix: 3.99 (0.31), residues: 242 sheet: 0.73 (0.33), residues: 286 loop : -2.21 (0.24), residues: 512 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 0.010 0.001 PHE n 29 TYR 0.011 0.001 TYR n 50 ARG 0.001 0.000 ARG n 96 ********************** 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 148 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: d 27 GLU cc_start: 0.8277 (pt0) cc_final: 0.8040 (tt0) REVERT: d 99 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7284 (pp) REVERT: d 123 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6744 (t80) REVERT: e 37 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8273 (mttp) REVERT: f 101 ARG cc_start: 0.7534 (tpt-90) cc_final: 0.6766 (tpt170) REVERT: g 92 ASN cc_start: 0.7258 (m110) cc_final: 0.5842 (t0) REVERT: m 82 ARG cc_start: 0.5908 (mtm180) cc_final: 0.5634 (mtm-85) REVERT: m 121 THR cc_start: 0.6964 (m) cc_final: 0.6510 (p) REVERT: m 145 ARG cc_start: 0.7863 (mtm180) cc_final: 0.7405 (mtt90) REVERT: m 148 LYS cc_start: 0.7158 (mptt) cc_final: 0.6829 (mttt) REVERT: m 207 ASN cc_start: 0.7535 (m-40) cc_final: 0.7297 (p0) REVERT: m 229 VAL cc_start: 0.7986 (t) cc_final: 0.7695 (m) REVERT: n 28 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7614 (mtmm) REVERT: n 32 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8231 (pp) REVERT: n 50 TYR cc_start: 0.5013 (OUTLIER) cc_final: 0.4468 (p90) REVERT: n 80 PRO cc_start: 0.7564 (Cg_endo) cc_final: 0.7280 (Cg_exo) REVERT: n 176 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8232 (tt) REVERT: n 252 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8049 (pt0) REVERT: n 261 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8295 (ptt180) REVERT: n 263 ASP cc_start: 0.7737 (m-30) cc_final: 0.7462 (m-30) outliers start: 24 outliers final: 16 residues processed: 143 average time/residue: 0.2080 time to fit residues: 40.8849 Evaluate side-chains 144 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 135 PHE 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 40 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 297 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.171502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.120222 restraints weight = 9483.544| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.47 r_work: 0.3064 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8561 Z= 0.190 Angle : 0.609 9.350 11624 Z= 0.311 Chirality : 0.042 0.188 1308 Planarity : 0.004 0.028 1468 Dihedral : 5.467 57.564 1279 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.38 % Favored : 94.52 % Rotamer: Outliers : 2.91 % Allowed : 13.16 % Favored : 83.93 % 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: 0.23 (0.27), residues: 1040 helix: 3.90 (0.31), residues: 241 sheet: 0.75 (0.33), residues: 288 loop : -2.27 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP n 259 HIS 0.004 0.001 HIS n 66 PHE 0.010 0.001 PHE f 87 TYR 0.013 0.001 TYR e 52 ARG 0.003 0.000 ARG d 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5032.82 seconds wall clock time: 88 minutes 45.15 seconds (5325.15 seconds total)