Starting phenix.real_space_refine on Sat May 17 14:36:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spu_40686/05_2025/8spu_40686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spu_40686/05_2025/8spu_40686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8spu_40686/05_2025/8spu_40686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spu_40686/05_2025/8spu_40686.map" model { file = "/net/cci-nas-00/data/ceres_data/8spu_40686/05_2025/8spu_40686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spu_40686/05_2025/8spu_40686.cif" } resolution = 2.8 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= 0.003 sd= 0.054 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: 5 Type Number sf(0) Gaussians P 298 5.49 5 S 35 5.16 5 C 9259 2.51 5 N 2928 2.21 5 O 3661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16181 Number of models: 1 Model: "" Number of chains: 13 Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3011 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "I" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3098 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "L" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 559 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1759 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 9.02, per 1000 atoms: 0.56 Number of scatterers: 16181 At special positions: 0 Unit cell: (128.832, 121.44, 134.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 298 15.00 O 3661 8.00 N 2928 7.00 C 9259 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 Simple disulfide: pdb=" SG CYS K 44 " - pdb=" SG CYS K 118 " distance=2.03 Simple disulfide: pdb=" SG CYS K 181 " - pdb=" SG CYS K 246 " distance=2.03 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: 3.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 21 sheets defined 49.5% alpha, 18.6% beta 144 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 7.20 Creating SS restraints... Processing helix chain 'L' and resid 140 through 161 Processing helix chain 'L' and resid 163 through 176 removed outlier: 3.952A pdb=" N GLY L 172 " --> pdb=" O GLY L 168 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL L 173 " --> pdb=" O LEU L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 190 Processing helix chain 'L' and resid 193 through 214 Proline residue: L 202 - end of helix removed outlier: 3.555A pdb=" N GLU L 209 " --> pdb=" O GLN L 205 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN L 213 " --> pdb=" O GLU L 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.591A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.802A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.646A pdb=" N LEU G 55 " --> pdb=" O MET G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.549A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 removed outlier: 3.609A pdb=" N TYR H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 123 Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.530A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.746A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.511A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.620A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 removed outlier: 3.548A pdb=" N ASN D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 109 through 113 removed outlier: 4.115A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 52 No H-bonds generated for 'chain 'K' and resid 50 through 52' Processing helix chain 'K' and resid 84 through 87 removed outlier: 3.828A pdb=" N LYS K 87 " --> pdb=" O GLU K 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 84 through 87' Processing helix chain 'K' and resid 109 through 113 removed outlier: 3.673A pdb=" N ASP K 112 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER K 113 " --> pdb=" O SER K 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 109 through 113' Processing helix chain 'K' and resid 237 through 241 removed outlier: 3.709A pdb=" N ASP K 240 " --> pdb=" O GLU K 237 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR K 241 " --> pdb=" O SER K 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 237 through 241' Processing sheet with id=AA1, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.970A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.573A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.153A pdb=" N ARG G 42 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.501A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.139A pdb=" N ARG C 42 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'N' and resid 25 through 28 removed outlier: 3.563A pdb=" N VAL N 101 " --> pdb=" O CYS N 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 32 through 34 removed outlier: 7.998A pdb=" N TYR N 54 " --> pdb=" O TYR N 74 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR N 74 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE N 56 " --> pdb=" O TYR N 72 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR N 72 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP N 58 " --> pdb=" O ILE N 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 168 through 171 removed outlier: 3.502A pdb=" N MET N 169 " --> pdb=" O LYS N 261 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU N 263 " --> pdb=" O MET N 169 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA N 171 " --> pdb=" O GLU N 263 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 168 through 171 removed outlier: 3.502A pdb=" N MET N 169 " --> pdb=" O LYS N 261 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU N 263 " --> pdb=" O MET N 169 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA N 171 " --> pdb=" O GLU N 263 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR N 255 " --> pdb=" O GLN N 248 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 177 through 180 Processing sheet with id=AB7, first strand: chain 'K' and resid 25 through 27 Processing sheet with id=AB8, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.274A pdb=" N LYS K 60 " --> pdb=" O TRP K 69 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP K 69 " --> pdb=" O LYS K 60 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR K 62 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU K 67 " --> pdb=" O THR K 62 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 32 through 34 removed outlier: 4.029A pdb=" N TYR K 131 " --> pdb=" O ARG K 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 39 through 43 Processing sheet with id=AC2, first strand: chain 'K' and resid 162 through 164 removed outlier: 3.956A pdb=" N PHE K 229 " --> pdb=" O CYS K 181 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP K 228 " --> pdb=" O SER K 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 168 through 171 removed outlier: 6.817A pdb=" N LEU K 191 " --> pdb=" O TYR K 207 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR K 207 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TRP K 193 " --> pdb=" O LEU K 205 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 365 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 6.83 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 15 1.20 - 1.36: 4743 1.36 - 1.51: 7218 1.51 - 1.67: 5065 1.67 - 1.83: 55 Bond restraints: 17096 Sorted by residual: bond pdb=" C LEU F 90 " pdb=" O LEU F 90 " ideal model delta sigma weight residual 1.237 1.053 0.184 1.19e-02 7.06e+03 2.39e+02 bond pdb=" C MET G 51 " pdb=" O MET G 51 " ideal model delta sigma weight residual 1.236 1.044 0.192 1.29e-02 6.01e+03 2.22e+02 bond pdb=" C LEU G 93 " pdb=" O LEU G 93 " ideal model delta sigma weight residual 1.237 1.070 0.167 1.17e-02 7.31e+03 2.04e+02 bond pdb=" C ASN G 94 " pdb=" O ASN G 94 " ideal model delta sigma weight residual 1.237 1.087 0.150 1.17e-02 7.31e+03 1.64e+02 bond pdb=" CA MET G 51 " pdb=" C MET G 51 " ideal model delta sigma weight residual 1.523 1.362 0.161 1.37e-02 5.33e+03 1.38e+02 ... (remaining 17091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.96: 24319 5.96 - 11.91: 54 11.91 - 17.87: 11 17.87 - 23.82: 2 23.82 - 29.78: 1 Bond angle restraints: 24387 Sorted by residual: angle pdb=" N SER D 33 " pdb=" CA SER D 33 " pdb=" C SER D 33 " ideal model delta sigma weight residual 110.61 126.86 -16.25 1.25e+00 6.40e-01 1.69e+02 angle pdb=" CB MET G 51 " pdb=" CG MET G 51 " pdb=" SD MET G 51 " ideal model delta sigma weight residual 112.70 82.92 29.78 3.00e+00 1.11e-01 9.85e+01 angle pdb=" N LYS G 13 " pdb=" CA LYS G 13 " pdb=" C LYS G 13 " ideal model delta sigma weight residual 110.80 128.75 -17.95 2.13e+00 2.20e-01 7.10e+01 angle pdb=" C LYS G 13 " pdb=" N ALA G 14 " pdb=" CA ALA G 14 " ideal model delta sigma weight residual 121.54 134.10 -12.56 1.91e+00 2.74e-01 4.33e+01 angle pdb=" CA GLN F 93 " pdb=" CB GLN F 93 " pdb=" CG GLN F 93 " ideal model delta sigma weight residual 114.10 101.76 12.34 2.00e+00 2.50e-01 3.81e+01 ... (remaining 24382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 7841 34.97 - 69.95: 1631 69.95 - 104.92: 28 104.92 - 139.89: 3 139.89 - 174.87: 3 Dihedral angle restraints: 9506 sinusoidal: 5777 harmonic: 3729 Sorted by residual: dihedral pdb=" C LEU A 82 " pdb=" N LEU A 82 " pdb=" CA LEU A 82 " pdb=" CB LEU A 82 " ideal model delta harmonic sigma weight residual -122.60 -108.43 -14.17 0 2.50e+00 1.60e-01 3.21e+01 dihedral pdb=" C SER D 33 " pdb=" N SER D 33 " pdb=" CA SER D 33 " pdb=" CB SER D 33 " ideal model delta harmonic sigma weight residual -122.60 -134.47 11.87 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" CA PRO H 104 " pdb=" C PRO H 104 " pdb=" N GLY H 105 " pdb=" CA GLY H 105 " ideal model delta harmonic sigma weight residual -180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 9503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2720 0.137 - 0.274: 27 0.274 - 0.410: 6 0.410 - 0.547: 2 0.547 - 0.684: 2 Chirality restraints: 2757 Sorted by residual: chirality pdb=" CA SER D 33 " pdb=" N SER D 33 " pdb=" C SER D 33 " pdb=" CB SER D 33 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CG LEU G 93 " pdb=" CB LEU G 93 " pdb=" CD1 LEU G 93 " pdb=" CD2 LEU G 93 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA LYS G 13 " pdb=" N LYS G 13 " pdb=" C LYS G 13 " pdb=" CB LYS G 13 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.73e+00 ... (remaining 2754 not shown) Planarity restraints: 2046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 92 " 0.035 2.00e-02 2.50e+03 7.35e-02 5.40e+01 pdb=" C GLU G 92 " -0.127 2.00e-02 2.50e+03 pdb=" O GLU G 92 " 0.049 2.00e-02 2.50e+03 pdb=" N LEU G 93 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 51 " 0.026 2.00e-02 2.50e+03 5.34e-02 2.85e+01 pdb=" C MET G 51 " -0.092 2.00e-02 2.50e+03 pdb=" O MET G 51 " 0.035 2.00e-02 2.50e+03 pdb=" N ALA G 52 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR K 62 " 0.084 5.00e-02 4.00e+02 1.27e-01 2.56e+01 pdb=" N PRO K 63 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO K 63 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO K 63 " 0.067 5.00e-02 4.00e+02 ... (remaining 2043 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 40 2.48 - 3.08: 9878 3.08 - 3.69: 27048 3.69 - 4.29: 41559 4.29 - 4.90: 61617 Nonbonded interactions: 140142 Sorted by model distance: nonbonded pdb=" C7 DT J 11 " pdb=" NH2 ARG L 186 " model vdw 1.874 3.540 nonbonded pdb=" O SER D 33 " pdb=" OG SER D 33 " model vdw 2.087 3.040 nonbonded pdb=" CG LYS G 13 " pdb=" N ALA G 14 " model vdw 2.181 3.520 nonbonded pdb=" OP1 DG I 163 " pdb=" NH1 ARG A 42 " model vdw 2.247 3.120 nonbonded pdb=" O GLN L 155 " pdb=" OG1 THR L 159 " model vdw 2.254 3.040 ... (remaining 140137 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 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 12 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = (chain 'D' and resid 32 through 125) selection = (chain 'H' and resid 32 through 125) } ncs_group { reference = (chain 'K' and (resid 23 through 187 or (resid 188 and (name N or name CA or nam \ e C or name O or name CB )) or resid 189 through 264 or (resid 265 and (name N o \ r name CA or name C or name O or name CB )))) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 40.940 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.192 17100 Z= 0.484 Angle : 0.906 29.775 24395 Z= 0.503 Chirality : 0.050 0.684 2757 Planarity : 0.007 0.127 2046 Dihedral : 27.152 174.865 7102 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 0.47 % Allowed : 21.88 % Favored : 77.65 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1259 helix: -0.12 (0.18), residues: 603 sheet: -0.23 (0.34), residues: 234 loop : -1.27 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 58 HIS 0.006 0.002 HIS G 31 PHE 0.029 0.003 PHE E 78 TYR 0.046 0.002 TYR D 41 ARG 0.012 0.000 ARG H 100 Details of bonding type rmsd hydrogen bonds : bond 0.12129 ( 943) hydrogen bonds : angle 5.40658 ( 2398) SS BOND : bond 0.00315 ( 4) SS BOND : angle 1.24302 ( 8) covalent geometry : bond 0.00806 (17096) covalent geometry : angle 0.90567 (24387) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 329 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7768 (mm-30) REVERT: E 120 MET cc_start: 0.8446 (mmm) cc_final: 0.8198 (mpp) REVERT: G 51 MET cc_start: 0.8050 (tpt) cc_final: 0.7798 (tpp) REVERT: G 91 GLU cc_start: 0.8050 (tp30) cc_final: 0.7826 (tp30) REVERT: C 73 ASN cc_start: 0.8266 (t0) cc_final: 0.7985 (t0) REVERT: D 69 ASP cc_start: 0.8106 (t70) cc_final: 0.7833 (t0) REVERT: D 72 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7296 (mt-10) REVERT: N 130 ASP cc_start: 0.8258 (p0) cc_final: 0.8032 (p0) REVERT: K 42 MET cc_start: 0.8231 (mtm) cc_final: 0.8022 (mtp) REVERT: K 103 MET cc_start: 0.8178 (ttt) cc_final: 0.7795 (ttt) REVERT: K 235 ASN cc_start: 0.7834 (p0) cc_final: 0.7433 (p0) outliers start: 5 outliers final: 1 residues processed: 332 average time/residue: 1.7599 time to fit residues: 627.1368 Evaluate side-chains 223 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 178 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 164 GLN E 39 HIS G 31 HIS H 64 ASN H 85 ASN B 64 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN N 196 GLN K 134 GLN ** K 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.110008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.067439 restraints weight = 33111.436| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.67 r_work: 0.2850 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17100 Z= 0.149 Angle : 0.603 16.009 24395 Z= 0.340 Chirality : 0.036 0.158 2757 Planarity : 0.005 0.080 2046 Dihedral : 29.526 171.237 4686 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.17 % Allowed : 25.79 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.73 (0.23), residues: 1259 helix: 1.59 (0.20), residues: 612 sheet: 0.19 (0.34), residues: 232 loop : -0.97 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 58 HIS 0.007 0.001 HIS K 170 PHE 0.009 0.001 PHE L 149 TYR 0.014 0.001 TYR D 41 ARG 0.008 0.001 ARG N 64 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 943) hydrogen bonds : angle 3.64350 ( 2398) SS BOND : bond 0.00273 ( 4) SS BOND : angle 0.91563 ( 8) covalent geometry : bond 0.00326 (17096) covalent geometry : angle 0.60288 (24387) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 1.288 Fit side-chains REVERT: E 59 GLU cc_start: 0.8331 (pm20) cc_final: 0.8026 (pm20) REVERT: F 79 LYS cc_start: 0.8920 (mtmm) cc_final: 0.8537 (mtmm) REVERT: G 41 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7951 (tm-30) REVERT: G 73 ASN cc_start: 0.8785 (t0) cc_final: 0.8381 (t0) REVERT: G 92 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8508 (mt-10) REVERT: H 40 ILE cc_start: 0.9161 (tt) cc_final: 0.8772 (pt) REVERT: H 72 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8337 (tm-30) REVERT: H 114 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8759 (mm-30) REVERT: A 90 MET cc_start: 0.9029 (mtm) cc_final: 0.8802 (mtp) REVERT: A 99 TYR cc_start: 0.9507 (t80) cc_final: 0.9247 (t80) REVERT: A 133 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7786 (mt-10) REVERT: B 24 ASP cc_start: 0.7805 (p0) cc_final: 0.7062 (p0) REVERT: C 36 LYS cc_start: 0.9130 (mmpt) cc_final: 0.8845 (mmtt) REVERT: C 73 ASN cc_start: 0.8480 (t0) cc_final: 0.8266 (t160) REVERT: C 74 LYS cc_start: 0.9044 (mppt) cc_final: 0.8837 (mmtp) REVERT: C 91 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: D 69 ASP cc_start: 0.8973 (t70) cc_final: 0.8521 (t0) REVERT: D 72 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8579 (mt-10) REVERT: N 27 GLN cc_start: 0.8837 (tp40) cc_final: 0.8435 (tp40) REVERT: N 95 ASP cc_start: 0.8270 (t0) cc_final: 0.8002 (t0) REVERT: N 240 ASP cc_start: 0.8950 (m-30) cc_final: 0.8414 (m-30) REVERT: K 35 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8058 (mm-30) REVERT: K 68 GLU cc_start: 0.8978 (pt0) cc_final: 0.8451 (pm20) REVERT: K 103 MET cc_start: 0.8500 (ttt) cc_final: 0.7914 (ttt) REVERT: K 111 GLU cc_start: 0.8822 (pp20) cc_final: 0.8516 (pp20) REVERT: K 139 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8932 (p) REVERT: K 219 ARG cc_start: 0.8467 (mtm110) cc_final: 0.7778 (mtp-110) REVERT: K 235 ASN cc_start: 0.8259 (p0) cc_final: 0.7177 (p0) REVERT: K 237 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7365 (mp0) outliers start: 34 outliers final: 13 residues processed: 271 average time/residue: 1.5623 time to fit residues: 457.7219 Evaluate side-chains 242 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 226 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 247 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 32 optimal weight: 50.0000 chunk 102 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 31 optimal weight: 30.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN B 93 GLN C 104 GLN ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN N 164 GLN K 164 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.104042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.060431 restraints weight = 33088.503| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.73 r_work: 0.2706 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 17100 Z= 0.296 Angle : 0.656 12.450 24395 Z= 0.367 Chirality : 0.040 0.187 2757 Planarity : 0.005 0.066 2046 Dihedral : 30.007 171.139 4685 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.91 % Allowed : 25.42 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.31 (0.24), residues: 1259 helix: 2.12 (0.21), residues: 609 sheet: 0.60 (0.34), residues: 238 loop : -0.89 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 58 HIS 0.006 0.001 HIS K 170 PHE 0.011 0.002 PHE E 84 TYR 0.016 0.002 TYR C 50 ARG 0.007 0.001 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.04611 ( 943) hydrogen bonds : angle 3.65687 ( 2398) SS BOND : bond 0.00607 ( 4) SS BOND : angle 1.13783 ( 8) covalent geometry : bond 0.00673 (17096) covalent geometry : angle 0.65553 (24387) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 1.365 Fit side-chains REVERT: E 59 GLU cc_start: 0.8611 (pm20) cc_final: 0.8300 (pm20) REVERT: F 84 MET cc_start: 0.9197 (mmm) cc_final: 0.8841 (mmm) REVERT: G 41 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7832 (tm-30) REVERT: G 64 GLU cc_start: 0.8918 (tt0) cc_final: 0.8714 (tt0) REVERT: G 91 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8285 (tp30) REVERT: G 92 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8645 (mt-10) REVERT: H 52 ASP cc_start: 0.8689 (m-30) cc_final: 0.8378 (OUTLIER) REVERT: H 60 MET cc_start: 0.9045 (tpp) cc_final: 0.8811 (tpp) REVERT: H 93 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8143 (mtp85) REVERT: A 59 GLU cc_start: 0.9189 (pm20) cc_final: 0.8894 (pm20) REVERT: A 131 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8903 (mtp85) REVERT: A 133 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7644 (mt-10) REVERT: B 77 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9035 (mmtp) REVERT: B 92 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8435 (ttp80) REVERT: C 36 LYS cc_start: 0.9238 (mmpt) cc_final: 0.8890 (mmpt) REVERT: C 73 ASN cc_start: 0.8704 (t0) cc_final: 0.8389 (t0) REVERT: C 74 LYS cc_start: 0.9180 (mppt) cc_final: 0.8940 (mmtp) REVERT: C 91 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: C 95 LYS cc_start: 0.9165 (tmtm) cc_final: 0.8928 (ttmt) REVERT: C 104 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8787 (mm110) REVERT: D 52 ASP cc_start: 0.8422 (p0) cc_final: 0.7927 (p0) REVERT: D 69 ASP cc_start: 0.9277 (t70) cc_final: 0.9015 (t0) REVERT: D 87 ARG cc_start: 0.8749 (mpt-90) cc_final: 0.8531 (mmt90) REVERT: N 27 GLN cc_start: 0.8940 (tp40) cc_final: 0.8644 (tp40) REVERT: N 32 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8951 (mm-30) REVERT: N 64 ARG cc_start: 0.8891 (ttp80) cc_final: 0.8497 (ttp80) REVERT: N 65 GLN cc_start: 0.8713 (mp10) cc_final: 0.8310 (mm-40) REVERT: N 95 ASP cc_start: 0.8578 (t0) cc_final: 0.8254 (OUTLIER) REVERT: N 175 GLU cc_start: 0.8816 (tp30) cc_final: 0.8527 (mm-30) REVERT: N 189 SER cc_start: 0.8890 (m) cc_final: 0.8541 (p) REVERT: N 234 ASN cc_start: 0.8494 (t0) cc_final: 0.8110 (t0) REVERT: N 237 GLU cc_start: 0.8594 (mm-30) cc_final: 0.7955 (mp0) REVERT: N 240 ASP cc_start: 0.8869 (m-30) cc_final: 0.8510 (m-30) REVERT: K 103 MET cc_start: 0.8836 (ttt) cc_final: 0.8473 (ttt) REVERT: K 111 GLU cc_start: 0.9006 (pp20) cc_final: 0.8526 (pp20) REVERT: K 112 ASP cc_start: 0.8668 (m-30) cc_final: 0.8421 (m-30) REVERT: K 263 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7429 (tm-30) outliers start: 42 outliers final: 15 residues processed: 257 average time/residue: 1.6940 time to fit residues: 468.6156 Evaluate side-chains 223 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 34 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 81 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN A 68 GLN ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 GLN K 27 GLN ** K 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.107291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.064194 restraints weight = 33051.985| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.68 r_work: 0.2794 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17100 Z= 0.140 Angle : 0.573 12.228 24395 Z= 0.327 Chirality : 0.035 0.174 2757 Planarity : 0.004 0.054 2046 Dihedral : 29.507 171.551 4685 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.98 % Allowed : 26.91 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.24), residues: 1259 helix: 2.59 (0.21), residues: 612 sheet: 0.64 (0.36), residues: 214 loop : -0.78 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 199 HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE L 149 TYR 0.011 0.001 TYR K 72 ARG 0.008 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 943) hydrogen bonds : angle 3.33964 ( 2398) SS BOND : bond 0.00243 ( 4) SS BOND : angle 1.00989 ( 8) covalent geometry : bond 0.00306 (17096) covalent geometry : angle 0.57326 (24387) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8479 (pm20) cc_final: 0.8199 (pm20) REVERT: F 84 MET cc_start: 0.9154 (mmm) cc_final: 0.8925 (mmm) REVERT: G 92 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8561 (mt-10) REVERT: H 40 ILE cc_start: 0.9127 (tt) cc_final: 0.8758 (pt) REVERT: H 60 MET cc_start: 0.8917 (tpp) cc_final: 0.8588 (tpp) REVERT: H 72 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8393 (tp30) REVERT: A 59 GLU cc_start: 0.9141 (pm20) cc_final: 0.8703 (pm20) REVERT: A 99 TYR cc_start: 0.9461 (t80) cc_final: 0.9219 (t80) REVERT: A 133 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8020 (mt-10) REVERT: B 77 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8956 (mmtp) REVERT: B 92 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8533 (ttp80) REVERT: C 35 ARG cc_start: 0.8536 (mtm110) cc_final: 0.8310 (mtp-110) REVERT: C 36 LYS cc_start: 0.9212 (mmpt) cc_final: 0.8938 (mmpt) REVERT: C 73 ASN cc_start: 0.8619 (t0) cc_final: 0.8280 (t160) REVERT: C 95 LYS cc_start: 0.9127 (tmtm) cc_final: 0.8887 (ttmt) REVERT: C 104 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8615 (mm110) REVERT: D 52 ASP cc_start: 0.8293 (p0) cc_final: 0.8038 (p0) REVERT: D 69 ASP cc_start: 0.9184 (t70) cc_final: 0.8887 (t0) REVERT: N 27 GLN cc_start: 0.8897 (tp40) cc_final: 0.8562 (tp40) REVERT: N 32 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8938 (mm-30) REVERT: N 95 ASP cc_start: 0.8518 (t0) cc_final: 0.8177 (OUTLIER) REVERT: K 64 ARG cc_start: 0.8800 (ttp80) cc_final: 0.8595 (ttp80) REVERT: K 111 GLU cc_start: 0.9094 (pp20) cc_final: 0.8628 (pp20) outliers start: 32 outliers final: 11 residues processed: 258 average time/residue: 1.6944 time to fit residues: 471.3299 Evaluate side-chains 224 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 247 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 119 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN A 68 GLN ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN N 196 GLN K 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.103838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.060512 restraints weight = 33281.858| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.57 r_work: 0.2706 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 17100 Z= 0.301 Angle : 0.642 12.102 24395 Z= 0.361 Chirality : 0.040 0.216 2757 Planarity : 0.004 0.048 2046 Dihedral : 29.839 171.410 4685 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.72 % Allowed : 25.61 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.67 (0.24), residues: 1259 helix: 2.50 (0.21), residues: 608 sheet: 0.56 (0.34), residues: 238 loop : -0.70 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 58 HIS 0.004 0.001 HIS B 75 PHE 0.010 0.002 PHE L 149 TYR 0.016 0.002 TYR K 72 ARG 0.009 0.001 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 943) hydrogen bonds : angle 3.50683 ( 2398) SS BOND : bond 0.00637 ( 4) SS BOND : angle 1.01205 ( 8) covalent geometry : bond 0.00689 (17096) covalent geometry : angle 0.64234 (24387) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 1.382 Fit side-chains REVERT: E 59 GLU cc_start: 0.8672 (pm20) cc_final: 0.8364 (pm20) REVERT: F 84 MET cc_start: 0.9215 (mmm) cc_final: 0.8888 (mmm) REVERT: F 91 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.9017 (ttmt) REVERT: G 91 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: G 92 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8632 (mt-10) REVERT: H 52 ASP cc_start: 0.8662 (m-30) cc_final: 0.8372 (OUTLIER) REVERT: H 93 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8067 (mtp85) REVERT: A 56 LYS cc_start: 0.9398 (ptmm) cc_final: 0.9073 (ptpp) REVERT: A 59 GLU cc_start: 0.9190 (pm20) cc_final: 0.8659 (pm20) REVERT: A 106 ASP cc_start: 0.8763 (m-30) cc_final: 0.8540 (m-30) REVERT: A 131 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8771 (mtp85) REVERT: A 133 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: B 77 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9043 (mmtp) REVERT: B 92 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8452 (ttp80) REVERT: C 35 ARG cc_start: 0.8536 (mtm110) cc_final: 0.8299 (mtp-110) REVERT: C 36 LYS cc_start: 0.9229 (mmpt) cc_final: 0.8941 (mmpt) REVERT: C 73 ASN cc_start: 0.8696 (t0) cc_final: 0.8324 (t0) REVERT: C 91 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: C 104 GLN cc_start: 0.9232 (mm-40) cc_final: 0.8977 (mm110) REVERT: D 52 ASP cc_start: 0.8397 (p0) cc_final: 0.7918 (p0) REVERT: N 27 GLN cc_start: 0.8833 (tp40) cc_final: 0.8518 (tp-100) REVERT: N 32 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8985 (mm-30) REVERT: N 95 ASP cc_start: 0.8609 (t0) cc_final: 0.8242 (t0) REVERT: N 162 MET cc_start: 0.9105 (mmm) cc_final: 0.8722 (mmm) REVERT: N 176 ARG cc_start: 0.8811 (tpp-160) cc_final: 0.8344 (tpp-160) outliers start: 40 outliers final: 21 residues processed: 236 average time/residue: 1.8137 time to fit residues: 460.9935 Evaluate side-chains 230 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 197 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 221 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 30 optimal weight: 50.0000 chunk 19 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 73 ASN A 68 GLN C 38 ASN ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.106205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.063284 restraints weight = 33036.946| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.59 r_work: 0.2769 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17100 Z= 0.165 Angle : 0.583 11.989 24395 Z= 0.332 Chirality : 0.035 0.202 2757 Planarity : 0.004 0.045 2046 Dihedral : 29.430 171.714 4685 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.89 % Allowed : 26.54 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.90 (0.24), residues: 1259 helix: 2.73 (0.21), residues: 612 sheet: 0.58 (0.34), residues: 238 loop : -0.63 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 199 HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE L 149 TYR 0.011 0.001 TYR K 72 ARG 0.012 0.001 ARG N 64 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 943) hydrogen bonds : angle 3.27809 ( 2398) SS BOND : bond 0.00299 ( 4) SS BOND : angle 0.89205 ( 8) covalent geometry : bond 0.00369 (17096) covalent geometry : angle 0.58304 (24387) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 1.409 Fit side-chains revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8606 (pm20) cc_final: 0.8293 (pm20) REVERT: F 84 MET cc_start: 0.9168 (mmm) cc_final: 0.8936 (mmm) REVERT: G 91 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: G 92 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8606 (mt-10) REVERT: H 36 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8373 (mt-10) REVERT: H 60 MET cc_start: 0.8931 (tpp) cc_final: 0.8640 (tpp) REVERT: H 72 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8527 (tp30) REVERT: A 56 LYS cc_start: 0.9351 (ptmm) cc_final: 0.9015 (ptpp) REVERT: A 59 GLU cc_start: 0.9230 (pm20) cc_final: 0.8732 (pm20) REVERT: A 131 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8793 (mtp85) REVERT: B 77 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8945 (mmtp) REVERT: B 92 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8520 (ttp80) REVERT: C 35 ARG cc_start: 0.8569 (mtm110) cc_final: 0.8324 (mtp-110) REVERT: C 36 LYS cc_start: 0.9224 (mmpt) cc_final: 0.8949 (mmpt) REVERT: C 73 ASN cc_start: 0.8700 (t0) cc_final: 0.8354 (t160) REVERT: C 91 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8309 (tt0) REVERT: C 95 LYS cc_start: 0.9147 (tmtm) cc_final: 0.8943 (ttmt) REVERT: C 104 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8908 (mm110) REVERT: D 52 ASP cc_start: 0.8241 (p0) cc_final: 0.8027 (p0) REVERT: D 69 ASP cc_start: 0.9245 (t70) cc_final: 0.8998 (t0) REVERT: N 27 GLN cc_start: 0.8798 (tp40) cc_final: 0.8483 (tp-100) REVERT: N 32 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8995 (mm-30) REVERT: N 95 ASP cc_start: 0.8569 (t0) cc_final: 0.8188 (t0) REVERT: N 162 MET cc_start: 0.9171 (mmm) cc_final: 0.8864 (mmm) REVERT: N 237 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8104 (mm-30) outliers start: 31 outliers final: 12 residues processed: 239 average time/residue: 1.7015 time to fit residues: 437.8541 Evaluate side-chains 226 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 221 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 102 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 0.0970 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 73 ASN A 68 GLN ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN K 164 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.107147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.064021 restraints weight = 33010.516| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.64 r_work: 0.2784 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17100 Z= 0.146 Angle : 0.573 11.827 24395 Z= 0.326 Chirality : 0.035 0.231 2757 Planarity : 0.004 0.043 2046 Dihedral : 29.346 173.094 4685 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.07 % Allowed : 26.16 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.97 (0.24), residues: 1259 helix: 2.84 (0.21), residues: 612 sheet: 0.57 (0.36), residues: 214 loop : -0.60 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 199 HIS 0.002 0.001 HIS B 75 PHE 0.009 0.001 PHE L 149 TYR 0.009 0.001 TYR K 72 ARG 0.009 0.000 ARG N 64 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 943) hydrogen bonds : angle 3.19554 ( 2398) SS BOND : bond 0.00309 ( 4) SS BOND : angle 0.76628 ( 8) covalent geometry : bond 0.00323 (17096) covalent geometry : angle 0.57247 (24387) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8582 (pm20) cc_final: 0.8218 (pm20) REVERT: F 91 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8949 (ttmt) REVERT: G 91 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: G 92 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8563 (mt-10) REVERT: H 36 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8369 (mt-10) REVERT: H 40 ILE cc_start: 0.9137 (tt) cc_final: 0.8747 (pp) REVERT: A 56 LYS cc_start: 0.9331 (ptmm) cc_final: 0.8997 (ptpp) REVERT: A 59 GLU cc_start: 0.9209 (pm20) cc_final: 0.8816 (pm20) REVERT: A 131 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8886 (mtp85) REVERT: B 24 ASP cc_start: 0.7914 (p0) cc_final: 0.7628 (p0) REVERT: B 92 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8596 (ttp80) REVERT: C 35 ARG cc_start: 0.8570 (mtm110) cc_final: 0.8317 (mtp-110) REVERT: C 36 LYS cc_start: 0.9219 (mmpt) cc_final: 0.8956 (mmpt) REVERT: C 73 ASN cc_start: 0.8671 (t0) cc_final: 0.8343 (t160) REVERT: C 91 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: C 95 LYS cc_start: 0.9123 (tmtm) cc_final: 0.8912 (ttmt) REVERT: C 104 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8909 (mm110) REVERT: D 69 ASP cc_start: 0.9215 (t70) cc_final: 0.8868 (t0) REVERT: N 27 GLN cc_start: 0.8797 (tp40) cc_final: 0.8481 (tp-100) REVERT: N 32 GLU cc_start: 0.9268 (mm-30) cc_final: 0.9020 (mm-30) REVERT: N 95 ASP cc_start: 0.8543 (t0) cc_final: 0.8144 (t0) REVERT: N 162 MET cc_start: 0.9178 (mmm) cc_final: 0.8866 (mmm) REVERT: N 176 ARG cc_start: 0.8784 (tpp-160) cc_final: 0.8498 (tpp-160) REVERT: K 176 ARG cc_start: 0.9243 (mtm-85) cc_final: 0.8419 (mtp85) outliers start: 33 outliers final: 15 residues processed: 239 average time/residue: 1.6568 time to fit residues: 427.4549 Evaluate side-chains 222 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 65 GLN Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 221 SER Chi-restraints excluded: chain K residue 247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 100 optimal weight: 2.9990 chunk 29 optimal weight: 50.0000 chunk 116 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 90 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 73 ASN A 68 GLN ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.106497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.063507 restraints weight = 32851.937| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.60 r_work: 0.2765 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17100 Z= 0.173 Angle : 0.595 11.797 24395 Z= 0.335 Chirality : 0.036 0.272 2757 Planarity : 0.004 0.043 2046 Dihedral : 29.378 172.921 4685 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.89 % Allowed : 27.19 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.90 (0.24), residues: 1259 helix: 2.77 (0.21), residues: 613 sheet: 0.56 (0.36), residues: 214 loop : -0.64 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 199 HIS 0.003 0.001 HIS D 50 PHE 0.008 0.001 PHE L 149 TYR 0.012 0.001 TYR K 72 ARG 0.009 0.000 ARG K 64 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 943) hydrogen bonds : angle 3.22201 ( 2398) SS BOND : bond 0.00362 ( 4) SS BOND : angle 0.78163 ( 8) covalent geometry : bond 0.00391 (17096) covalent geometry : angle 0.59503 (24387) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 1.465 Fit side-chains REVERT: E 59 GLU cc_start: 0.8578 (pm20) cc_final: 0.8251 (pm20) REVERT: F 84 MET cc_start: 0.9198 (mmm) cc_final: 0.8945 (mmm) REVERT: F 91 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8952 (ttmt) REVERT: G 91 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: G 92 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8598 (mt-10) REVERT: H 36 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8369 (mt-10) REVERT: H 40 ILE cc_start: 0.9149 (tt) cc_final: 0.8730 (pp) REVERT: H 72 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8401 (tp30) REVERT: A 56 LYS cc_start: 0.9365 (ptmm) cc_final: 0.9050 (ptpp) REVERT: A 59 GLU cc_start: 0.9227 (pm20) cc_final: 0.8710 (pm20) REVERT: A 131 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8880 (mtp85) REVERT: B 77 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8928 (mmtp) REVERT: B 92 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8559 (ttp80) REVERT: C 35 ARG cc_start: 0.8556 (mtm110) cc_final: 0.8297 (mtp-110) REVERT: C 36 LYS cc_start: 0.9229 (mmpt) cc_final: 0.8942 (mmpt) REVERT: C 73 ASN cc_start: 0.8683 (t0) cc_final: 0.8362 (t160) REVERT: C 91 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: C 95 LYS cc_start: 0.9136 (tmtm) cc_final: 0.8925 (ttmt) REVERT: C 104 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8852 (mm110) REVERT: D 69 ASP cc_start: 0.9231 (t70) cc_final: 0.8940 (t0) REVERT: N 27 GLN cc_start: 0.8838 (tp40) cc_final: 0.8528 (tp-100) REVERT: N 95 ASP cc_start: 0.8546 (t0) cc_final: 0.8138 (t0) REVERT: N 162 MET cc_start: 0.9144 (mmm) cc_final: 0.8898 (mmm) REVERT: N 176 ARG cc_start: 0.8780 (tpp-160) cc_final: 0.8346 (tpp-160) REVERT: K 65 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8905 (pm20) REVERT: K 176 ARG cc_start: 0.9241 (mtm-85) cc_final: 0.8395 (mtp85) outliers start: 31 outliers final: 18 residues processed: 224 average time/residue: 1.6244 time to fit residues: 393.3726 Evaluate side-chains 234 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 65 GLN Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 221 SER Chi-restraints excluded: chain K residue 247 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 62 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 73 ASN A 68 GLN C 38 ASN ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.104301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.060954 restraints weight = 32869.430| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.57 r_work: 0.2703 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17100 Z= 0.265 Angle : 0.640 11.729 24395 Z= 0.359 Chirality : 0.039 0.286 2757 Planarity : 0.004 0.060 2046 Dihedral : 29.651 171.989 4685 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.89 % Allowed : 27.47 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.67 (0.24), residues: 1259 helix: 2.58 (0.21), residues: 610 sheet: 0.52 (0.36), residues: 214 loop : -0.76 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 58 HIS 0.004 0.001 HIS B 75 PHE 0.008 0.002 PHE B 61 TYR 0.015 0.002 TYR C 50 ARG 0.010 0.001 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 943) hydrogen bonds : angle 3.38608 ( 2398) SS BOND : bond 0.00560 ( 4) SS BOND : angle 0.88697 ( 8) covalent geometry : bond 0.00607 (17096) covalent geometry : angle 0.63956 (24387) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8631 (pm20) cc_final: 0.8295 (pm20) REVERT: F 91 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8975 (ttmt) REVERT: G 91 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: G 92 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8597 (mt-10) REVERT: H 36 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8352 (mt-10) REVERT: H 52 ASP cc_start: 0.8625 (m-30) cc_final: 0.8325 (OUTLIER) REVERT: H 93 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8060 (mtp85) REVERT: A 56 LYS cc_start: 0.9392 (ptmm) cc_final: 0.9080 (ptpp) REVERT: A 59 GLU cc_start: 0.9155 (pm20) cc_final: 0.8605 (pm20) REVERT: A 131 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8778 (mtp85) REVERT: B 77 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8947 (mmtp) REVERT: B 92 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8437 (ttp80) REVERT: C 36 LYS cc_start: 0.9237 (mmpt) cc_final: 0.8912 (mmpt) REVERT: C 73 ASN cc_start: 0.8755 (t0) cc_final: 0.8395 (t160) REVERT: C 91 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: C 95 LYS cc_start: 0.9146 (tmtm) cc_final: 0.8903 (ttmt) REVERT: C 104 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8858 (mm110) REVERT: D 43 TYR cc_start: 0.8577 (t80) cc_final: 0.8357 (t80) REVERT: D 69 ASP cc_start: 0.9327 (t70) cc_final: 0.9039 (t0) REVERT: D 114 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8622 (mm-30) REVERT: N 27 GLN cc_start: 0.8840 (tp40) cc_final: 0.8556 (tp-100) REVERT: N 32 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8936 (mm-30) REVERT: N 64 ARG cc_start: 0.8903 (ttp80) cc_final: 0.8641 (ttp80) REVERT: N 95 ASP cc_start: 0.8543 (t0) cc_final: 0.8106 (t0) REVERT: N 162 MET cc_start: 0.9164 (mmm) cc_final: 0.8887 (mmm) outliers start: 31 outliers final: 17 residues processed: 231 average time/residue: 1.7596 time to fit residues: 439.3832 Evaluate side-chains 221 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 221 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 107 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 73 ASN A 68 GLN ** N 25 GLN ** 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 = 0.3739 r_free = 0.3739 target = 0.106915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.063929 restraints weight = 33125.196| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.58 r_work: 0.2771 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17100 Z= 0.155 Angle : 0.594 11.684 24395 Z= 0.336 Chirality : 0.036 0.248 2757 Planarity : 0.004 0.053 2046 Dihedral : 29.305 172.614 4685 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.42 % Allowed : 27.84 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.88 (0.24), residues: 1259 helix: 2.75 (0.21), residues: 613 sheet: 0.48 (0.34), residues: 238 loop : -0.66 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 199 HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE L 149 TYR 0.012 0.001 TYR F 88 ARG 0.013 0.001 ARG K 64 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 943) hydrogen bonds : angle 3.22458 ( 2398) SS BOND : bond 0.00290 ( 4) SS BOND : angle 0.82008 ( 8) covalent geometry : bond 0.00347 (17096) covalent geometry : angle 0.59410 (24387) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 1.351 Fit side-chains REVERT: E 59 GLU cc_start: 0.8568 (pm20) cc_final: 0.8244 (pm20) REVERT: G 91 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: G 92 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8591 (mt-10) REVERT: H 40 ILE cc_start: 0.9144 (tt) cc_final: 0.8706 (pp) REVERT: H 72 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8446 (tp30) REVERT: A 56 LYS cc_start: 0.9356 (ptmm) cc_final: 0.9048 (ptpp) REVERT: A 59 GLU cc_start: 0.9156 (pm20) cc_final: 0.8647 (pm20) REVERT: A 131 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8883 (mtp85) REVERT: B 92 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8522 (ttp80) REVERT: C 36 LYS cc_start: 0.9233 (mmpt) cc_final: 0.8940 (mmpt) REVERT: C 73 ASN cc_start: 0.8700 (t0) cc_final: 0.8376 (t160) REVERT: C 90 ASP cc_start: 0.9104 (t0) cc_final: 0.8790 (t0) REVERT: C 91 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: C 95 LYS cc_start: 0.9118 (tmtm) cc_final: 0.8909 (ttmt) REVERT: C 104 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8883 (mm110) REVERT: D 69 ASP cc_start: 0.9227 (t70) cc_final: 0.8959 (t0) REVERT: N 27 GLN cc_start: 0.8818 (tp40) cc_final: 0.8533 (tp-100) REVERT: N 64 ARG cc_start: 0.8850 (ttp80) cc_final: 0.8579 (ttp80) REVERT: N 95 ASP cc_start: 0.8516 (t0) cc_final: 0.8081 (t0) REVERT: N 161 LYS cc_start: 0.9470 (tppp) cc_final: 0.9260 (tppp) REVERT: N 176 ARG cc_start: 0.8651 (tpp-160) cc_final: 0.8332 (tpp-160) REVERT: K 176 ARG cc_start: 0.9248 (mtm-85) cc_final: 0.8525 (mtp85) outliers start: 26 outliers final: 15 residues processed: 226 average time/residue: 1.6452 time to fit residues: 401.3918 Evaluate side-chains 232 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 221 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 118 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 132 optimal weight: 7.9990 chunk 145 optimal weight: 0.0870 chunk 148 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 73 ASN A 68 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.108203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.065484 restraints weight = 32948.183| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.63 r_work: 0.2817 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17100 Z= 0.135 Angle : 0.579 11.650 24395 Z= 0.327 Chirality : 0.035 0.253 2757 Planarity : 0.004 0.054 2046 Dihedral : 29.205 173.874 4685 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.96 % Allowed : 28.58 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.98 (0.24), residues: 1259 helix: 2.85 (0.20), residues: 613 sheet: 0.60 (0.36), residues: 214 loop : -0.64 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 199 HIS 0.003 0.001 HIS D 50 PHE 0.007 0.001 PHE L 149 TYR 0.009 0.001 TYR K 72 ARG 0.012 0.001 ARG K 64 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 943) hydrogen bonds : angle 3.16559 ( 2398) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.70681 ( 8) covalent geometry : bond 0.00295 (17096) covalent geometry : angle 0.57848 (24387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12353.85 seconds wall clock time: 212 minutes 33.56 seconds (12753.56 seconds total)