Starting phenix.real_space_refine on Mon Nov 18 07:31:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spu_40686/11_2024/8spu_40686.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spu_40686/11_2024/8spu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spu_40686/11_2024/8spu_40686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spu_40686/11_2024/8spu_40686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spu_40686/11_2024/8spu_40686.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spu_40686/11_2024/8spu_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 9.84, per 1000 atoms: 0.61 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: 3.96 Conformation dependent library (CDL) restraints added in 1.3 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: 7.72 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: 6.78 Time building geometry restraints manager: 4.64 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.840 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 41.340 Find NCS groups from input model: 0.440 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:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.830 ------------------------------------------------------------------------------- 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 17096 Z= 0.514 Angle : 0.906 29.775 24387 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 *********************** 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 : 1.297 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: 1.8404 time to fit residues: 655.9914 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 : 1.383 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 17096 Z= 0.183 Angle : 0.603 16.009 24387 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 *********************** 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 : 1.345 Fit side-chains REVERT: F 79 LYS cc_start: 0.8919 (mtmm) cc_final: 0.8716 (mtmm) REVERT: G 41 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7230 (tm-30) REVERT: G 73 ASN cc_start: 0.8629 (t0) cc_final: 0.8272 (t0) REVERT: G 92 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8022 (mt-10) REVERT: H 100 ARG cc_start: 0.8368 (mmt90) cc_final: 0.8115 (mtt180) REVERT: A 99 TYR cc_start: 0.9068 (t80) cc_final: 0.8842 (t80) REVERT: A 133 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7631 (mt-10) REVERT: B 24 ASP cc_start: 0.7460 (p0) cc_final: 0.6680 (p0) REVERT: C 36 LYS cc_start: 0.8634 (mmpt) cc_final: 0.8405 (mmtt) REVERT: C 74 LYS cc_start: 0.8795 (mppt) cc_final: 0.8594 (mmtp) REVERT: C 91 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: N 27 GLN cc_start: 0.8325 (tp40) cc_final: 0.8123 (tp40) REVERT: N 240 ASP cc_start: 0.8581 (m-30) cc_final: 0.8300 (m-30) REVERT: K 103 MET cc_start: 0.8230 (ttt) cc_final: 0.7753 (ttt) REVERT: K 111 GLU cc_start: 0.8421 (pp20) cc_final: 0.8149 (pp20) REVERT: K 219 ARG cc_start: 0.8484 (mtm110) cc_final: 0.8125 (mtp-110) REVERT: K 235 ASN cc_start: 0.8138 (p0) cc_final: 0.7359 (p0) outliers start: 34 outliers final: 13 residues processed: 271 average time/residue: 1.6560 time to fit residues: 485.4838 Evaluate side-chains 233 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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 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 247 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 147 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 GLN ** K 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17096 Z= 0.258 Angle : 0.611 12.531 24387 Z= 0.344 Chirality : 0.037 0.167 2757 Planarity : 0.004 0.067 2046 Dihedral : 29.687 172.255 4685 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.07 % Allowed : 25.98 % Favored : 70.95 % 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: 1.40 (0.24), residues: 1259 helix: 2.30 (0.20), residues: 609 sheet: 0.30 (0.34), residues: 234 loop : -0.77 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 58 HIS 0.004 0.001 HIS K 170 PHE 0.009 0.001 PHE L 149 TYR 0.013 0.001 TYR K 72 ARG 0.007 0.001 ARG H 87 *********************** 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 264 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 79 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8743 (mtmm) REVERT: G 41 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7058 (tm-30) REVERT: G 92 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8187 (mt-10) REVERT: H 100 ARG cc_start: 0.8393 (mmt90) cc_final: 0.8156 (mtt-85) REVERT: A 56 LYS cc_start: 0.9144 (ptmm) cc_final: 0.8917 (ptpp) REVERT: A 99 TYR cc_start: 0.9082 (t80) cc_final: 0.8734 (t80) REVERT: A 133 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7442 (mt-10) REVERT: B 77 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8721 (mmtp) REVERT: B 92 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8219 (ttp80) REVERT: C 74 LYS cc_start: 0.8892 (mppt) cc_final: 0.8679 (mmtp) REVERT: K 103 MET cc_start: 0.8383 (ttt) cc_final: 0.7980 (ttt) REVERT: K 235 ASN cc_start: 0.8165 (p0) cc_final: 0.7835 (p0) outliers start: 33 outliers final: 11 residues processed: 251 average time/residue: 1.7122 time to fit residues: 464.1162 Evaluate side-chains 221 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 115 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 62 ILE 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 D residue 56 SER Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 247 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 164 GLN K 27 GLN K 164 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17096 Z= 0.289 Angle : 0.605 12.271 24387 Z= 0.343 Chirality : 0.037 0.174 2757 Planarity : 0.004 0.057 2046 Dihedral : 29.664 171.362 4685 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.63 % Allowed : 26.54 % Favored : 69.83 % 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: 1.69 (0.24), residues: 1259 helix: 2.50 (0.21), residues: 610 sheet: 0.66 (0.35), residues: 238 loop : -0.75 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 69 HIS 0.004 0.001 HIS H 50 PHE 0.009 0.001 PHE L 149 TYR 0.013 0.001 TYR K 72 ARG 0.007 0.001 ARG H 87 *********************** 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 255 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: F 79 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8721 (mtmm) REVERT: F 91 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8739 (ttmt) REVERT: G 91 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: G 92 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8164 (mt-10) REVERT: H 93 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7642 (mtp85) REVERT: H 100 ARG cc_start: 0.8383 (mmt90) cc_final: 0.8110 (mtt180) REVERT: A 133 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7480 (mt-10) REVERT: B 77 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8745 (mmtp) REVERT: B 92 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8110 (ttp80) REVERT: C 35 ARG cc_start: 0.8110 (mtm110) cc_final: 0.7893 (mtm110) REVERT: C 74 LYS cc_start: 0.8931 (mppt) cc_final: 0.8717 (mmtp) REVERT: C 91 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: C 104 GLN cc_start: 0.8633 (mm110) cc_final: 0.8374 (mm110) REVERT: N 130 ASP cc_start: 0.8528 (p0) cc_final: 0.8278 (p0) REVERT: N 237 GLU cc_start: 0.7548 (mp0) cc_final: 0.7346 (mp0) REVERT: N 262 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8765 (tm) REVERT: K 103 MET cc_start: 0.8310 (ttt) cc_final: 0.8081 (ttt) outliers start: 39 outliers final: 17 residues processed: 241 average time/residue: 1.7462 time to fit residues: 453.7309 Evaluate side-chains 231 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 79 LYS 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 62 ILE Chi-restraints excluded: chain H residue 93 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 47 LYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 262 LEU 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 120 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 17096 Z= 0.353 Angle : 0.626 12.103 24387 Z= 0.354 Chirality : 0.039 0.175 2757 Planarity : 0.004 0.051 2046 Dihedral : 29.747 171.203 4685 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.19 % Allowed : 25.88 % 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: 1.65 (0.24), residues: 1259 helix: 2.48 (0.21), residues: 610 sheet: 0.60 (0.35), residues: 238 loop : -0.75 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 69 HIS 0.004 0.001 HIS D 50 PHE 0.010 0.001 PHE L 149 TYR 0.014 0.001 TYR K 72 ARG 0.009 0.001 ARG H 87 *********************** 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 258 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 213 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: F 79 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8720 (mtmm) REVERT: F 91 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8792 (ttmt) REVERT: G 91 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: G 92 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8148 (mt-10) REVERT: H 93 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7700 (mtp85) REVERT: H 100 ARG cc_start: 0.8423 (mmt90) cc_final: 0.8140 (mtt180) REVERT: A 56 LYS cc_start: 0.9207 (ptmm) cc_final: 0.8982 (ptpp) REVERT: A 133 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7749 (mt-10) REVERT: B 77 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8757 (mmtp) REVERT: B 92 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7996 (ttp80) REVERT: C 74 LYS cc_start: 0.8961 (mppt) cc_final: 0.8729 (mmtp) REVERT: C 91 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: N 64 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7521 (tmm-80) REVERT: N 65 GLN cc_start: 0.8304 (mp10) cc_final: 0.8101 (mm-40) REVERT: N 162 MET cc_start: 0.8694 (mmm) cc_final: 0.8388 (mmm) REVERT: N 169 MET cc_start: 0.8607 (pmt) cc_final: 0.8025 (pmt) REVERT: N 237 GLU cc_start: 0.7742 (mp0) cc_final: 0.7478 (mp0) REVERT: K 45 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8757 (tmtm) REVERT: K 103 MET cc_start: 0.8464 (ttt) cc_final: 0.8223 (ttt) outliers start: 45 outliers final: 19 residues processed: 245 average time/residue: 1.8504 time to fit residues: 486.9874 Evaluate side-chains 232 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 79 LYS 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 52 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 93 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 62 ILE 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 45 LYS 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 48 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 28 optimal weight: 40.0000 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 145 optimal weight: 0.0010 chunk 120 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17096 Z= 0.165 Angle : 0.571 11.945 24387 Z= 0.327 Chirality : 0.035 0.170 2757 Planarity : 0.004 0.046 2046 Dihedral : 29.292 172.461 4685 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.89 % Allowed : 26.63 % Favored : 70.48 % 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: 1.95 (0.24), residues: 1259 helix: 2.78 (0.20), residues: 613 sheet: 0.58 (0.35), residues: 238 loop : -0.62 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 199 HIS 0.003 0.001 HIS H 50 PHE 0.010 0.001 PHE L 149 TYR 0.010 0.001 TYR K 72 ARG 0.009 0.000 ARG H 87 *********************** 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 262 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 1.430 Fit side-chains revert: symmetry clash REVERT: F 79 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8739 (mtmm) REVERT: F 91 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8696 (ttmt) REVERT: G 19 SER cc_start: 0.8966 (t) cc_final: 0.8709 (m) REVERT: G 91 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: G 92 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8095 (mt-10) REVERT: A 99 TYR cc_start: 0.8976 (t80) cc_final: 0.8710 (t80) REVERT: B 24 ASP cc_start: 0.7859 (p0) cc_final: 0.7519 (p0) REVERT: B 92 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8202 (ttp80) REVERT: C 35 ARG cc_start: 0.8189 (mtm110) cc_final: 0.7935 (mtm110) REVERT: C 74 LYS cc_start: 0.8913 (mppt) cc_final: 0.8686 (mmtp) REVERT: C 91 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: N 64 ARG cc_start: 0.7870 (ttp80) cc_final: 0.7576 (ttp-110) REVERT: N 130 ASP cc_start: 0.8545 (p0) cc_final: 0.8282 (p0) REVERT: K 103 MET cc_start: 0.8371 (ttt) cc_final: 0.8131 (ttt) REVERT: K 176 ARG cc_start: 0.8732 (mtm-85) cc_final: 0.8476 (mtp85) REVERT: K 235 ASN cc_start: 0.8231 (p0) cc_final: 0.8030 (p0) outliers start: 31 outliers final: 13 residues processed: 249 average time/residue: 1.7363 time to fit residues: 466.3048 Evaluate side-chains 237 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 219 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain A residue 71 VAL 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 91 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 122 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 90 optimal weight: 0.0670 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 25 ASN G 73 ASN A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 ASN K 65 GLN K 164 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17096 Z= 0.173 Angle : 0.585 11.832 24387 Z= 0.332 Chirality : 0.035 0.209 2757 Planarity : 0.004 0.044 2046 Dihedral : 29.295 173.523 4685 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.70 % Allowed : 27.75 % Favored : 69.55 % 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: 2.06 (0.24), residues: 1259 helix: 2.86 (0.20), residues: 613 sheet: 0.63 (0.35), residues: 238 loop : -0.56 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 199 HIS 0.002 0.001 HIS D 50 PHE 0.009 0.001 PHE L 149 TYR 0.010 0.001 TYR K 72 ARG 0.010 0.000 ARG H 87 *********************** 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 247 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 1.311 Fit side-chains revert: symmetry clash REVERT: G 19 SER cc_start: 0.8985 (t) cc_final: 0.8739 (m) REVERT: G 91 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: A 133 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7581 (mt-10) REVERT: B 92 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8284 (ttp80) REVERT: B 93 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: C 74 LYS cc_start: 0.8924 (mppt) cc_final: 0.8688 (mmtp) REVERT: C 91 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: N 130 ASP cc_start: 0.8507 (p0) cc_final: 0.8265 (p0) REVERT: K 45 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8664 (tmtm) REVERT: K 103 MET cc_start: 0.8350 (ttt) cc_final: 0.8107 (ttt) outliers start: 29 outliers final: 14 residues processed: 239 average time/residue: 1.6986 time to fit residues: 438.7404 Evaluate side-chains 227 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 53 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN 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 95 ASP Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 65 GLN 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 86 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 40.0000 chunk 91 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 71 optimal weight: 0.0980 chunk 13 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 ASN K 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17096 Z= 0.171 Angle : 0.593 11.769 24387 Z= 0.335 Chirality : 0.035 0.239 2757 Planarity : 0.004 0.051 2046 Dihedral : 29.196 173.482 4685 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.42 % Allowed : 28.58 % Favored : 68.99 % 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: 2.08 (0.24), residues: 1259 helix: 2.91 (0.20), residues: 613 sheet: 0.77 (0.37), residues: 214 loop : -0.61 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 69 HIS 0.003 0.001 HIS C 31 PHE 0.008 0.001 PHE L 149 TYR 0.010 0.001 TYR K 72 ARG 0.013 0.001 ARG N 64 *********************** 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 238 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 1.352 Fit side-chains revert: symmetry clash REVERT: G 91 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: B 92 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8263 (ttp80) REVERT: C 91 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: N 239 ASP cc_start: 0.8628 (p0) cc_final: 0.8112 (p0) REVERT: K 103 MET cc_start: 0.8386 (ttt) cc_final: 0.8152 (ttt) outliers start: 26 outliers final: 19 residues processed: 229 average time/residue: 1.6779 time to fit residues: 415.3610 Evaluate side-chains 227 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain A residue 71 VAL 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 D residue 56 SER Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 45 LYS 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 134 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** C 38 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 ASN K 164 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17096 Z= 0.359 Angle : 0.651 11.699 24387 Z= 0.364 Chirality : 0.039 0.298 2757 Planarity : 0.005 0.052 2046 Dihedral : 29.595 172.390 4685 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.51 % Allowed : 28.03 % 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: 1.84 (0.24), residues: 1259 helix: 2.63 (0.21), residues: 612 sheet: 0.67 (0.35), residues: 238 loop : -0.68 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 58 HIS 0.006 0.001 HIS D 50 PHE 0.008 0.002 PHE B 61 TYR 0.019 0.002 TYR H 41 ARG 0.013 0.001 ARG C 20 *********************** 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 228 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 1.287 Fit side-chains REVERT: F 91 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8758 (ttmt) REVERT: G 91 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: B 92 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8094 (ttp80) REVERT: C 91 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: N 239 ASP cc_start: 0.8628 (p0) cc_final: 0.8149 (p0) outliers start: 27 outliers final: 17 residues processed: 221 average time/residue: 1.6743 time to fit residues: 400.3420 Evaluate side-chains 218 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 91 GLU Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain A residue 71 VAL 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 D residue 56 SER Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 95 ASP 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 67 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17096 Z= 0.197 Angle : 0.610 11.659 24387 Z= 0.343 Chirality : 0.036 0.272 2757 Planarity : 0.004 0.055 2046 Dihedral : 29.264 172.602 4685 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.96 % Allowed : 28.86 % Favored : 69.18 % 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: 0.72 (0.37), residues: 214 loop : -0.73 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 199 HIS 0.003 0.001 HIS C 31 PHE 0.008 0.001 PHE L 187 TYR 0.016 0.001 TYR H 41 ARG 0.013 0.001 ARG N 64 ********************** 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 227 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 1.447 Fit side-chains revert: symmetry clash REVERT: G 91 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: B 92 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8172 (ttp80) REVERT: C 91 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: D 94 GLU cc_start: 0.8559 (mp0) cc_final: 0.8276 (mp0) REVERT: N 239 ASP cc_start: 0.8676 (p0) cc_final: 0.8185 (p0) outliers start: 21 outliers final: 17 residues processed: 222 average time/residue: 1.7676 time to fit residues: 424.1296 Evaluate side-chains 224 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain A residue 71 VAL 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 D residue 56 SER 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 N residue 234 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN N 196 GLN N 234 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.103359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.059905 restraints weight = 32969.409| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.61 r_work: 0.2677 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 17096 Z= 0.471 Angle : 0.701 11.617 24387 Z= 0.390 Chirality : 0.042 0.324 2757 Planarity : 0.005 0.059 2046 Dihedral : 29.764 171.846 4685 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.70 % Allowed : 27.84 % 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: 1.54 (0.24), residues: 1259 helix: 2.45 (0.21), residues: 608 sheet: 0.64 (0.37), residues: 214 loop : -0.87 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 58 HIS 0.006 0.002 HIS D 110 PHE 0.009 0.002 PHE E 84 TYR 0.023 0.002 TYR C 50 ARG 0.015 0.001 ARG C 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7131.94 seconds wall clock time: 127 minutes 40.82 seconds (7660.82 seconds total)