Starting phenix.real_space_refine on Mon Nov 18 10:38:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sps_40683/11_2024/8sps_40683.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sps_40683/11_2024/8sps_40683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sps_40683/11_2024/8sps_40683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sps_40683/11_2024/8sps_40683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sps_40683/11_2024/8sps_40683.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sps_40683/11_2024/8sps_40683.cif" } resolution = 3.0 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= 0.051 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 294 5.49 5 S 37 5.16 5 C 9478 2.51 5 N 2996 2.21 5 O 3710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16515 Number of models: 1 Model: "" Number of chains: 14 Chain: "I" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3055 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2972 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" 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: "B" 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: "C" 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: "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: "E" 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: "F" 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: "G" 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: "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: "K" 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: "N" 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 Chain: "M" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 373 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 46} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 10.20, per 1000 atoms: 0.62 Number of scatterers: 16515 At special positions: 0 Unit cell: (139.392, 145.728, 157.344, 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 37 16.00 P 294 15.00 O 3710 8.00 N 2996 7.00 C 9478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 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 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 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: 4.69 Conformation dependent library (CDL) restraints added in 1.5 seconds 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2484 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 21 sheets defined 50.6% alpha, 17.9% beta 139 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 8.98 Creating SS restraints... Processing helix chain 'L' and resid 140 through 161 removed outlier: 4.105A pdb=" N LYS L 144 " --> pdb=" O LYS L 140 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU L 145 " --> pdb=" O ALA L 141 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS L 151 " --> pdb=" O GLU L 147 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU L 152 " --> pdb=" O GLN L 148 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY L 161 " --> pdb=" O ARG L 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 176 Processing helix chain 'L' and resid 180 through 189 removed outlier: 3.520A pdb=" N GLU L 188 " --> pdb=" O ILE L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 193 through 214 Proline residue: L 202 - end of helix Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.592A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.803A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.645A pdb=" N LEU C 55 " --> pdb=" O MET C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.548A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.609A pdb=" N TYR D 43 " --> pdb=" O SER D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.530A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.746A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.511A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.620A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 removed outlier: 3.548A pdb=" N ASN H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 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 109 through 113 removed outlier: 4.114A pdb=" N SER K 113 " --> pdb=" O SER K 110 " (cutoff:3.500A) 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 84 through 87 removed outlier: 3.828A pdb=" N LYS N 87 " --> pdb=" O GLU N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 87' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.673A pdb=" N ASP N 112 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 109 through 113' Processing helix chain 'N' and resid 237 through 241 removed outlier: 3.709A pdb=" N ASP N 240 " --> pdb=" O GLU N 237 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR N 241 " --> pdb=" O SER N 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 237 through 241' Processing helix chain 'M' and resid 240 through 247 Processing helix chain 'M' and resid 255 through 268 removed outlier: 3.586A pdb=" N HIS M 262 " --> pdb=" O GLN M 258 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN M 265 " --> pdb=" O SER M 261 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN M 266 " --> pdb=" O HIS M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 287 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.970A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.573A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.154A pdb=" N ARG C 42 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.501A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.139A pdb=" N ARG G 42 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 25 through 28 removed outlier: 3.564A pdb=" N VAL K 101 " --> pdb=" O CYS K 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 32 through 34 removed outlier: 7.998A pdb=" N TYR K 54 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR K 74 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE K 56 " --> pdb=" O TYR K 72 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR K 72 " --> pdb=" O ILE K 56 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP K 58 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.502A pdb=" N MET K 169 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU K 191 " --> pdb=" O TYR K 207 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR K 207 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TRP K 193 " --> pdb=" O LEU K 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.502A pdb=" N MET K 169 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR K 255 " --> pdb=" O GLN K 248 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 177 through 180 Processing sheet with id=AB7, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AB8, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.274A pdb=" N LYS N 60 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP N 69 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR N 62 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU N 67 " --> pdb=" O THR N 62 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 4.029A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 39 through 43 Processing sheet with id=AC2, first strand: chain 'N' and resid 162 through 164 removed outlier: 3.955A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.817A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 7.33 Time building geometry restraints manager: 5.28 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: 4862 1.36 - 1.51: 7352 1.51 - 1.67: 5139 1.67 - 1.83: 57 Bond restraints: 17425 Sorted by residual: bond pdb=" C LEU B 90 " pdb=" O LEU B 90 " ideal model delta sigma weight residual 1.237 1.052 0.184 1.19e-02 7.06e+03 2.40e+02 bond pdb=" C MET C 51 " pdb=" O MET C 51 " ideal model delta sigma weight residual 1.236 1.045 0.191 1.29e-02 6.01e+03 2.20e+02 bond pdb=" C LEU C 93 " pdb=" O LEU C 93 " ideal model delta sigma weight residual 1.237 1.069 0.168 1.17e-02 7.31e+03 2.06e+02 bond pdb=" C ASN C 94 " pdb=" O ASN C 94 " ideal model delta sigma weight residual 1.237 1.087 0.150 1.17e-02 7.31e+03 1.65e+02 bond pdb=" CA MET C 51 " pdb=" C MET C 51 " ideal model delta sigma weight residual 1.523 1.362 0.161 1.37e-02 5.33e+03 1.38e+02 ... (remaining 17420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.95: 24738 5.95 - 11.91: 56 11.91 - 17.86: 9 17.86 - 23.82: 1 23.82 - 29.77: 1 Bond angle restraints: 24805 Sorted by residual: angle pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" C SER H 33 " ideal model delta sigma weight residual 110.61 126.90 -16.29 1.25e+00 6.40e-01 1.70e+02 angle pdb=" CB MET C 51 " pdb=" CG MET C 51 " pdb=" SD MET C 51 " ideal model delta sigma weight residual 112.70 82.93 29.77 3.00e+00 1.11e-01 9.85e+01 angle pdb=" N LYS C 13 " pdb=" CA LYS C 13 " pdb=" C LYS C 13 " ideal model delta sigma weight residual 110.80 128.73 -17.93 2.13e+00 2.20e-01 7.09e+01 angle pdb=" C LYS C 13 " pdb=" N ALA C 14 " pdb=" CA ALA C 14 " ideal model delta sigma weight residual 121.54 134.08 -12.54 1.91e+00 2.74e-01 4.31e+01 angle pdb=" CA GLN B 93 " pdb=" CB GLN B 93 " pdb=" CG GLN B 93 " ideal model delta sigma weight residual 114.10 101.79 12.31 2.00e+00 2.50e-01 3.79e+01 ... (remaining 24800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 8097 35.44 - 70.87: 1595 70.87 - 106.31: 36 106.31 - 141.74: 0 141.74 - 177.18: 2 Dihedral angle restraints: 9730 sinusoidal: 5861 harmonic: 3869 Sorted by residual: dihedral pdb=" C LEU E 82 " pdb=" N LEU E 82 " pdb=" CA LEU E 82 " pdb=" CB LEU E 82 " ideal model delta harmonic sigma weight residual -122.60 -108.50 -14.10 0 2.50e+00 1.60e-01 3.18e+01 dihedral pdb=" C SER H 33 " pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" CB SER H 33 " ideal model delta harmonic sigma weight residual -122.60 -134.44 11.84 0 2.50e+00 1.60e-01 2.24e+01 dihedral pdb=" CA PRO D 104 " pdb=" C PRO D 104 " pdb=" N GLY D 105 " pdb=" CA GLY D 105 " ideal model delta harmonic sigma weight residual -180.00 -156.78 -23.22 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 9727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2763 0.137 - 0.273: 26 0.273 - 0.410: 6 0.410 - 0.547: 2 0.547 - 0.684: 2 Chirality restraints: 2799 Sorted by residual: chirality pdb=" CA SER H 33 " pdb=" N SER H 33 " pdb=" C SER H 33 " pdb=" CB SER H 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 C 93 " pdb=" CB LEU C 93 " pdb=" CD1 LEU C 93 " pdb=" CD2 LEU C 93 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CA LYS C 13 " pdb=" N LYS C 13 " pdb=" C LYS C 13 " pdb=" CB LYS C 13 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 2796 not shown) Planarity restraints: 2116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 92 " 0.035 2.00e-02 2.50e+03 7.34e-02 5.39e+01 pdb=" C GLU C 92 " -0.127 2.00e-02 2.50e+03 pdb=" O GLU C 92 " 0.049 2.00e-02 2.50e+03 pdb=" N LEU C 93 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 51 " -0.026 2.00e-02 2.50e+03 5.34e-02 2.85e+01 pdb=" C MET C 51 " 0.092 2.00e-02 2.50e+03 pdb=" O MET C 51 " -0.035 2.00e-02 2.50e+03 pdb=" N ALA C 52 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 62 " 0.084 5.00e-02 4.00e+02 1.27e-01 2.56e+01 pdb=" N PRO N 63 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO N 63 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO N 63 " 0.067 5.00e-02 4.00e+02 ... (remaining 2113 not shown) Histogram of nonbonded interaction distances: 0.57 - 1.44: 3 1.44 - 2.30: 8 2.30 - 3.17: 12600 3.17 - 4.03: 48048 4.03 - 4.90: 81529 Warning: very small nonbonded interaction distances. Nonbonded interactions: 142188 Sorted by model distance: nonbonded pdb=" O TYR L 162 " pdb=" NZ LYS G 13 " model vdw 0.574 3.120 nonbonded pdb=" C TYR L 162 " pdb=" NZ LYS G 13 " model vdw 0.937 3.350 nonbonded pdb=" O TYR L 162 " pdb=" CE LYS G 13 " model vdw 1.305 3.440 nonbonded pdb=" N THR L 163 " pdb=" NZ LYS G 13 " model vdw 1.818 3.200 nonbonded pdb=" O SER H 33 " pdb=" OG SER H 33 " model vdw 2.088 3.040 ... (remaining 142183 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' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 32 through 125) selection = (chain 'H' and resid 32 through 125) } ncs_group { reference = chain 'K' selection = (chain 'N' 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 )))) } 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 46.540 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 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 0.191 17425 Z= 0.504 Angle : 0.882 29.772 24805 Z= 0.494 Chirality : 0.049 0.684 2799 Planarity : 0.007 0.127 2116 Dihedral : 27.009 177.177 7234 Min Nonbonded Distance : 0.574 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.59 % Favored : 95.33 % Rotamer: Outliers : 0.53 % Allowed : 21.53 % Favored : 77.94 % Cbeta Deviations : 0.24 % 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: -0.87 (0.21), residues: 1306 helix: -0.09 (0.18), residues: 634 sheet: -0.23 (0.34), residues: 234 loop : -1.31 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 58 HIS 0.006 0.002 HIS C 31 PHE 0.029 0.002 PHE A 78 TYR 0.045 0.002 TYR H 41 ARG 0.012 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 360 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 ASN cc_start: 0.8364 (m110) cc_final: 0.7835 (m-40) REVERT: H 84 TYR cc_start: 0.8585 (m-10) cc_final: 0.8108 (m-10) outliers start: 6 outliers final: 2 residues processed: 362 average time/residue: 1.5724 time to fit residues: 620.7947 Evaluate side-chains 224 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain K residue 264 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 31 HIS C 38 ASN C 73 ASN D 85 ASN F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 50 HIS K 196 GLN K 234 ASN N 61 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17425 Z= 0.196 Angle : 0.606 8.277 24805 Z= 0.342 Chirality : 0.036 0.175 2799 Planarity : 0.005 0.082 2116 Dihedral : 29.526 175.758 4697 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.11 % Allowed : 26.78 % 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: 0.62 (0.23), residues: 1306 helix: 1.52 (0.20), residues: 647 sheet: -0.02 (0.34), residues: 234 loop : -1.02 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 207 HIS 0.004 0.001 HIS B 75 PHE 0.012 0.001 PHE N 256 TYR 0.020 0.001 TYR B 88 ARG 0.008 0.001 ARG K 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6439 (mt-10) REVERT: C 76 THR cc_start: 0.8931 (p) cc_final: 0.8629 (t) REVERT: D 94 GLU cc_start: 0.8014 (mp0) cc_final: 0.7787 (mp0) REVERT: E 73 GLU cc_start: 0.7934 (tt0) cc_final: 0.7543 (tt0) REVERT: E 83 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.6610 (ptm-80) REVERT: F 25 ASN cc_start: 0.8239 (m110) cc_final: 0.8037 (m-40) REVERT: H 84 TYR cc_start: 0.8653 (m-10) cc_final: 0.8061 (m-10) REVERT: K 32 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7526 (mm-30) REVERT: K 84 GLU cc_start: 0.8451 (tp30) cc_final: 0.8109 (tp30) REVERT: K 176 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.7805 (tpt-90) REVERT: K 239 ASP cc_start: 0.7929 (t70) cc_final: 0.7378 (t0) outliers start: 35 outliers final: 9 residues processed: 274 average time/residue: 1.5146 time to fit residues: 455.0421 Evaluate side-chains 218 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 235 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN E 39 HIS E 76 GLN G 31 HIS N 57 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17425 Z= 0.383 Angle : 0.673 9.615 24805 Z= 0.376 Chirality : 0.039 0.156 2799 Planarity : 0.005 0.068 2116 Dihedral : 29.765 176.788 4693 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.63 % Allowed : 24.56 % Favored : 70.82 % 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: 1.09 (0.23), residues: 1306 helix: 2.03 (0.20), residues: 640 sheet: 0.39 (0.36), residues: 214 loop : -1.05 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 199 HIS 0.007 0.002 HIS F 75 PHE 0.012 0.001 PHE A 104 TYR 0.032 0.002 TYR D 84 ARG 0.008 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6943 (mt-10) REVERT: C 61 GLU cc_start: 0.8084 (tp30) cc_final: 0.7868 (tp30) REVERT: E 73 GLU cc_start: 0.8104 (tt0) cc_final: 0.7624 (tt0) REVERT: E 83 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.6587 (ptm-80) REVERT: E 123 ASP cc_start: 0.8352 (m-30) cc_final: 0.8058 (m-30) REVERT: F 23 ARG cc_start: 0.7836 (ttp80) cc_final: 0.7585 (ttp-110) REVERT: F 25 ASN cc_start: 0.8209 (m110) cc_final: 0.7848 (m-40) REVERT: K 103 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7667 (tmm) REVERT: K 109 THR cc_start: 0.8305 (m) cc_final: 0.8078 (t) REVERT: K 239 ASP cc_start: 0.8238 (t70) cc_final: 0.7960 (t0) outliers start: 52 outliers final: 19 residues processed: 255 average time/residue: 1.5890 time to fit residues: 443.1281 Evaluate side-chains 206 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 137 SER Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 170 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 72 optimal weight: 0.0060 chunk 15 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 148 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS C 38 ASN C 73 ASN D 96 GLN G 38 ASN K 164 GLN K 196 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17425 Z= 0.187 Angle : 0.602 9.358 24805 Z= 0.338 Chirality : 0.036 0.150 2799 Planarity : 0.004 0.058 2116 Dihedral : 29.425 175.239 4693 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.76 % Allowed : 27.49 % Favored : 69.75 % 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: 1.44 (0.24), residues: 1306 helix: 2.39 (0.20), residues: 645 sheet: 0.53 (0.37), residues: 214 loop : -1.03 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 69 HIS 0.004 0.001 HIS A 39 PHE 0.012 0.001 PHE N 256 TYR 0.039 0.001 TYR D 84 ARG 0.009 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7002 (mt-10) REVERT: D 44 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8835 (mtmm) REVERT: E 73 GLU cc_start: 0.8118 (tt0) cc_final: 0.7679 (tt0) REVERT: E 83 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.6475 (ptm-80) REVERT: F 23 ARG cc_start: 0.7781 (ttp80) cc_final: 0.7545 (ptp-110) REVERT: F 25 ASN cc_start: 0.8182 (m110) cc_final: 0.7883 (m-40) REVERT: K 239 ASP cc_start: 0.8324 (t70) cc_final: 0.8022 (t0) outliers start: 31 outliers final: 11 residues processed: 249 average time/residue: 1.5246 time to fit residues: 416.1203 Evaluate side-chains 213 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 170 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 76 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN B 75 HIS C 38 ASN C 73 ASN D 64 ASN E 76 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17425 Z= 0.298 Angle : 0.644 10.542 24805 Z= 0.359 Chirality : 0.038 0.162 2799 Planarity : 0.005 0.054 2116 Dihedral : 29.507 176.532 4693 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.45 % Allowed : 27.76 % Favored : 67.79 % 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: 1.42 (0.24), residues: 1306 helix: 2.44 (0.20), residues: 641 sheet: 0.72 (0.37), residues: 198 loop : -1.17 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 69 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE N 256 TYR 0.036 0.002 TYR D 84 ARG 0.010 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 203 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: D 44 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8982 (mtmm) REVERT: E 63 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7670 (mmp80) REVERT: E 73 GLU cc_start: 0.8144 (tt0) cc_final: 0.7622 (tt0) REVERT: E 83 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.6605 (ptm-80) REVERT: F 25 ASN cc_start: 0.8184 (m110) cc_final: 0.7850 (m-40) REVERT: K 103 MET cc_start: 0.8295 (ttt) cc_final: 0.7937 (ttp) REVERT: K 237 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7207 (tm-30) REVERT: K 239 ASP cc_start: 0.8453 (t70) cc_final: 0.8079 (t0) outliers start: 50 outliers final: 19 residues processed: 234 average time/residue: 1.5723 time to fit residues: 402.6177 Evaluate side-chains 211 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 0.0870 chunk 29 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 68 optimal weight: 0.0670 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN C 73 ASN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17425 Z= 0.170 Angle : 0.612 10.659 24805 Z= 0.340 Chirality : 0.036 0.165 2799 Planarity : 0.004 0.067 2116 Dihedral : 29.181 176.618 4693 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.47 % Allowed : 28.83 % Favored : 67.70 % 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: 1.62 (0.24), residues: 1306 helix: 2.67 (0.20), residues: 641 sheet: 0.23 (0.36), residues: 234 loop : -0.96 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 199 HIS 0.003 0.001 HIS H 50 PHE 0.010 0.001 PHE N 256 TYR 0.043 0.001 TYR D 84 ARG 0.011 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 192 LEU cc_start: 0.6036 (pt) cc_final: 0.5616 (pt) REVERT: D 44 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8891 (mtmm) REVERT: D 94 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7086 (mt-10) REVERT: E 73 GLU cc_start: 0.8171 (tt0) cc_final: 0.7649 (tt0) REVERT: F 25 ASN cc_start: 0.8150 (m110) cc_final: 0.7873 (m-40) REVERT: H 50 HIS cc_start: 0.8551 (OUTLIER) cc_final: 0.8104 (m170) REVERT: K 239 ASP cc_start: 0.8344 (t70) cc_final: 0.8063 (t0) outliers start: 39 outliers final: 17 residues processed: 255 average time/residue: 1.4535 time to fit residues: 408.5938 Evaluate side-chains 226 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN C 38 ASN C 73 ASN D 64 ASN E 76 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17425 Z= 0.200 Angle : 0.631 9.941 24805 Z= 0.347 Chirality : 0.036 0.141 2799 Planarity : 0.004 0.049 2116 Dihedral : 29.198 177.838 4693 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.29 % Allowed : 30.60 % Favored : 66.10 % 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: 1.57 (0.24), residues: 1306 helix: 2.61 (0.20), residues: 645 sheet: 0.23 (0.36), residues: 234 loop : -0.99 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 199 HIS 0.003 0.001 HIS K 249 PHE 0.009 0.001 PHE N 256 TYR 0.054 0.002 TYR D 84 ARG 0.012 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 192 LEU cc_start: 0.5853 (pt) cc_final: 0.5434 (pt) REVERT: D 94 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: E 73 GLU cc_start: 0.8178 (tt0) cc_final: 0.7607 (tt0) REVERT: F 25 ASN cc_start: 0.8163 (m110) cc_final: 0.7853 (m-40) REVERT: H 50 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.8243 (m170) REVERT: K 64 ARG cc_start: 0.7904 (ttp-110) cc_final: 0.7685 (ttp-110) REVERT: K 214 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: K 239 ASP cc_start: 0.8389 (t70) cc_final: 0.8128 (t0) outliers start: 37 outliers final: 20 residues processed: 240 average time/residue: 1.4812 time to fit residues: 393.0023 Evaluate side-chains 227 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 44 optimal weight: 0.0870 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 116 optimal weight: 0.0270 chunk 135 optimal weight: 4.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN C 38 ASN C 73 ASN D 64 ASN D 68 ASN E 76 GLN G 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17425 Z= 0.176 Angle : 0.624 10.294 24805 Z= 0.343 Chirality : 0.036 0.157 2799 Planarity : 0.005 0.052 2116 Dihedral : 29.060 178.991 4693 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.85 % Allowed : 31.23 % Favored : 65.93 % 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: 1306 helix: 2.59 (0.20), residues: 648 sheet: 0.34 (0.37), residues: 228 loop : -0.85 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 199 HIS 0.003 0.001 HIS H 50 PHE 0.009 0.001 PHE N 256 TYR 0.028 0.001 TYR B 88 ARG 0.013 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 192 LEU cc_start: 0.5851 (pt) cc_final: 0.5072 (pt) REVERT: L 197 MET cc_start: 0.2911 (mpt) cc_final: 0.2426 (mpp) REVERT: B 88 TYR cc_start: 0.8110 (m-80) cc_final: 0.7562 (m-80) REVERT: E 73 GLU cc_start: 0.8155 (tt0) cc_final: 0.7685 (tt0) REVERT: E 83 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.6503 (ptm-80) REVERT: F 25 ASN cc_start: 0.8142 (m110) cc_final: 0.7894 (m-40) REVERT: H 50 HIS cc_start: 0.8596 (OUTLIER) cc_final: 0.8173 (m170) REVERT: K 64 ARG cc_start: 0.7892 (ttp-110) cc_final: 0.7664 (ttp-110) REVERT: K 176 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.7786 (tpt-90) REVERT: K 239 ASP cc_start: 0.8319 (t70) cc_final: 0.8089 (t0) outliers start: 32 outliers final: 18 residues processed: 239 average time/residue: 1.4343 time to fit residues: 377.5236 Evaluate side-chains 229 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 138 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN C 38 ASN C 73 ASN D 64 ASN E 76 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17425 Z= 0.199 Angle : 0.643 11.215 24805 Z= 0.350 Chirality : 0.036 0.152 2799 Planarity : 0.005 0.056 2116 Dihedral : 29.082 179.762 4693 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.67 % Allowed : 32.21 % Favored : 65.12 % 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: 1.63 (0.24), residues: 1306 helix: 2.58 (0.20), residues: 648 sheet: 0.29 (0.37), residues: 228 loop : -0.86 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 199 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE N 256 TYR 0.037 0.002 TYR D 84 ARG 0.015 0.001 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 192 LEU cc_start: 0.5928 (pt) cc_final: 0.5528 (pt) REVERT: B 88 TYR cc_start: 0.8319 (m-80) cc_final: 0.7985 (m-80) REVERT: E 73 GLU cc_start: 0.8181 (tt0) cc_final: 0.7682 (tt0) REVERT: E 83 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.6495 (ptm-80) REVERT: F 25 ASN cc_start: 0.8160 (m110) cc_final: 0.7896 (m-40) REVERT: H 50 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.8211 (m170) REVERT: K 176 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7808 (tpt-90) outliers start: 30 outliers final: 21 residues processed: 232 average time/residue: 1.4131 time to fit residues: 360.9448 Evaluate side-chains 228 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 153 optimal weight: 30.0000 chunk 141 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 73 ASN C 104 GLN D 64 ASN D 85 ASN E 76 GLN K 164 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17425 Z= 0.257 Angle : 0.677 12.762 24805 Z= 0.366 Chirality : 0.037 0.180 2799 Planarity : 0.005 0.065 2116 Dihedral : 29.139 179.842 4693 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.94 % Allowed : 31.94 % Favored : 65.12 % 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: 1.45 (0.24), residues: 1306 helix: 2.50 (0.20), residues: 647 sheet: 0.43 (0.37), residues: 216 loop : -1.17 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 199 HIS 0.004 0.001 HIS F 75 PHE 0.007 0.001 PHE L 149 TYR 0.044 0.002 TYR D 84 ARG 0.014 0.001 ARG G 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 192 LEU cc_start: 0.5802 (pt) cc_final: 0.5486 (pt) REVERT: B 88 TYR cc_start: 0.8453 (m-80) cc_final: 0.8243 (m-80) REVERT: D 94 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: E 73 GLU cc_start: 0.8178 (tt0) cc_final: 0.7599 (tt0) REVERT: E 83 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.6500 (ptm-80) REVERT: F 25 ASN cc_start: 0.8159 (m110) cc_final: 0.7818 (m-40) REVERT: F 93 GLN cc_start: 0.8286 (mt0) cc_final: 0.7987 (mp10) REVERT: H 50 HIS cc_start: 0.8684 (OUTLIER) cc_final: 0.8471 (m170) REVERT: K 176 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.7760 (tpt-90) REVERT: K 214 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7701 (m-30) outliers start: 33 outliers final: 22 residues processed: 227 average time/residue: 1.4541 time to fit residues: 363.9107 Evaluate side-chains 231 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 251 GLU Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 73 ASN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.123196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.076616 restraints weight = 38528.492| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.64 r_work: 0.2951 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17425 Z= 0.275 Angle : 0.687 12.127 24805 Z= 0.372 Chirality : 0.038 0.181 2799 Planarity : 0.005 0.068 2116 Dihedral : 29.217 179.896 4693 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.76 % Allowed : 31.85 % Favored : 65.39 % 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: 1.33 (0.24), residues: 1306 helix: 2.37 (0.20), residues: 649 sheet: 0.42 (0.37), residues: 216 loop : -1.21 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 199 HIS 0.007 0.001 HIS K 249 PHE 0.007 0.001 PHE F 61 TYR 0.043 0.002 TYR G 57 ARG 0.015 0.001 ARG F 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6852.23 seconds wall clock time: 123 minutes 4.22 seconds (7384.22 seconds total)