Starting phenix.real_space_refine on Mon Apr 8 17:36:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8of4_16845/04_2024/8of4_16845.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8of4_16845/04_2024/8of4_16845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8of4_16845/04_2024/8of4_16845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8of4_16845/04_2024/8of4_16845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8of4_16845/04_2024/8of4_16845.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8of4_16845/04_2024/8of4_16845.pdb" } resolution = 2.94 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= 0.010 sd= 0.087 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 288 5.49 5 S 21 5.16 5 C 7933 2.51 5 N 2664 2.21 5 O 3180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "F ARG 17": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G ARG 29": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H ARG 30": "NH1" <-> "NH2" Residue "H ARG 69": "NH1" <-> "NH2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H ARG 89": "NH1" <-> "NH2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L ARG 39": "NH1" <-> "NH2" Residue "L ARG 90": "NH1" <-> "NH2" Residue "L ARG 103": "NH1" <-> "NH2" Residue "L ARG 108": "NH1" <-> "NH2" Residue "L ARG 121": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "L ARG 150": "NH1" <-> "NH2" Residue "L ARG 164": "NH1" <-> "NH2" Residue "L ARG 172": "NH1" <-> "NH2" Residue "L ARG 175": "NH1" <-> "NH2" Residue "L ARG 178": "NH1" <-> "NH2" Residue "L ARG 182": "NH1" <-> "NH2" Residue "L ARG 195": "NH1" <-> "NH2" Residue "L ARG 205": "NH1" <-> "NH2" Residue "L ARG 220": "NH1" <-> "NH2" Residue "L ARG 231": "NH1" <-> "NH2" Residue "L ARG 232": "NH1" <-> "NH2" Residue "L ARG 235": "NH1" <-> "NH2" Residue "L ARG 248": "NH1" <-> "NH2" Residue "L ARG 253": "NH1" <-> "NH2" Residue "L ARG 264": "NH1" <-> "NH2" Residue "L ARG 280": "NH1" <-> "NH2" Residue "L ARG 284": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14087 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 916 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "D" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 785 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 785 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "L" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1850 Classifications: {'peptide': 237} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12968 SG CYS L 141 43.940 64.998 46.759 1.00 66.29 S ATOM 12988 SG CYS L 144 43.083 62.071 45.610 1.00 61.78 S ATOM 13153 SG CYS L 166 41.246 63.788 49.455 1.00 72.90 S ATOM 13231 SG CYS L 177 44.562 61.755 48.746 1.00 71.13 S Time building chain proxies: 7.41, per 1000 atoms: 0.53 Number of scatterers: 14087 At special positions: 0 Unit cell: (110.836, 118.164, 121.828, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 21 16.00 P 288 15.00 O 3180 8.00 N 2664 7.00 C 7933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 7.08 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 144 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 177 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 141 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 166 " Number of angles added : 6 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 63.1% alpha, 4.2% beta 141 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 6.94 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.521A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.786A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 5 through 11 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.293A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.663A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.595A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.588A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N THR D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.985A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.578A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.509A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.535A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.311A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.637A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.738A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 44 Processing helix chain 'L' and resid 52 through 58 removed outlier: 4.444A pdb=" N SER L 56 " --> pdb=" O GLY L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 104 Processing helix chain 'L' and resid 117 through 122 Processing helix chain 'L' and resid 125 through 127 No H-bonds generated for 'chain 'L' and resid 125 through 127' Processing helix chain 'L' and resid 193 through 206 Processing helix chain 'L' and resid 221 through 223 No H-bonds generated for 'chain 'L' and resid 221 through 223' Processing helix chain 'L' and resid 224 through 232 removed outlier: 3.745A pdb=" N ALA L 228 " --> pdb=" O ASN L 224 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR L 229 " --> pdb=" O LEU L 225 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS L 230 " --> pdb=" O PRO L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 250 removed outlier: 4.150A pdb=" N ALA L 250 " --> pdb=" O ASP L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 269 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.840A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.733A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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 101 through 102 removed outlier: 6.737A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.898A 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: 7.060A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 'L' and resid 129 through 131 removed outlier: 6.728A pdb=" N VAL L 47 " --> pdb=" O PHE L 109 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL L 111 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N PHE L 49 " --> pdb=" O VAL L 111 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL L 48 " --> pdb=" O ILE L 211 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU L 213 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS L 50 " --> pdb=" O LEU L 213 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER L 210 " --> pdb=" O VAL L 237 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL L 239 " --> pdb=" O SER L 210 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR L 212 " --> pdb=" O VAL L 239 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU L 236 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE L 254 " --> pdb=" O LEU L 236 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE L 238 " --> pdb=" O ILE L 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 139 through 141 455 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 6.22 Time building geometry restraints manager: 7.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3203 1.33 - 1.46: 4238 1.46 - 1.58: 6863 1.58 - 1.70: 580 1.70 - 1.82: 37 Bond restraints: 14921 Sorted by residual: bond pdb=" C5 DT I -65 " pdb=" C7 DT I -65 " ideal model delta sigma weight residual 1.500 1.817 -0.317 2.00e-02 2.50e+03 2.52e+02 bond pdb=" C5 DT I -59 " pdb=" C7 DT I -59 " ideal model delta sigma weight residual 1.500 1.662 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" N LYS C 119 " pdb=" CA LYS C 119 " ideal model delta sigma weight residual 1.454 1.517 -0.063 1.27e-02 6.20e+03 2.45e+01 bond pdb=" CZ ARG H 96 " pdb=" NH2 ARG H 96 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.30e-02 5.92e+03 1.29e+01 bond pdb=" CZ ARG A 72 " pdb=" NH2 ARG A 72 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+01 ... (remaining 14916 not shown) Histogram of bond angle deviations from ideal: 60.44 - 75.44: 1 75.44 - 90.44: 0 90.44 - 105.44: 1435 105.44 - 120.43: 14541 120.43 - 135.43: 5402 Bond angle restraints: 21379 Sorted by residual: angle pdb=" O LYS C 118 " pdb=" C LYS C 118 " pdb=" N LYS C 119 " ideal model delta sigma weight residual 122.96 60.44 62.52 1.26e+00 6.30e-01 2.46e+03 angle pdb=" O SER C 122 " pdb=" C SER C 122 " pdb=" N ALA C 123 " ideal model delta sigma weight residual 122.04 95.03 27.01 1.35e+00 5.49e-01 4.00e+02 angle pdb=" CA PRO E 38 " pdb=" N PRO E 38 " pdb=" CD PRO E 38 " ideal model delta sigma weight residual 112.00 100.79 11.21 1.40e+00 5.10e-01 6.41e+01 angle pdb=" CA LYS C 118 " pdb=" C LYS C 118 " pdb=" O LYS C 118 " ideal model delta sigma weight residual 121.51 112.88 8.63 1.12e+00 7.97e-01 5.94e+01 angle pdb=" C SER C 122 " pdb=" N ALA C 123 " pdb=" CA ALA C 123 " ideal model delta sigma weight residual 121.70 134.68 -12.98 1.80e+00 3.09e-01 5.20e+01 ... (remaining 21374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 6991 33.84 - 67.68: 1230 67.68 - 101.51: 49 101.51 - 135.35: 1 135.35 - 169.19: 3 Dihedral angle restraints: 8274 sinusoidal: 5309 harmonic: 2965 Sorted by residual: dihedral pdb=" CA LYS C 118 " pdb=" C LYS C 118 " pdb=" N LYS C 119 " pdb=" CA LYS C 119 " ideal model delta harmonic sigma weight residual -180.00 -151.20 -28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA THR L 215 " pdb=" C THR L 215 " pdb=" N SER L 216 " pdb=" CA SER L 216 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA LEU L 186 " pdb=" C LEU L 186 " pdb=" N ASP L 187 " pdb=" CA ASP L 187 " ideal model delta harmonic sigma weight residual -180.00 -151.26 -28.74 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 8271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1880 0.101 - 0.202: 457 0.202 - 0.303: 62 0.303 - 0.404: 28 0.404 - 0.505: 2 Chirality restraints: 2429 Sorted by residual: chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.66 -2.16 -0.50 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" C3' DG J 20 " pdb=" C4' DG J 20 " pdb=" O3' DG J 20 " pdb=" C2' DG J 20 " both_signs ideal model delta sigma weight residual False -2.66 -2.22 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.78e+00 ... (remaining 2426 not shown) Planarity restraints: 1708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 70 " -0.449 2.00e-02 2.50e+03 1.88e-01 1.05e+03 pdb=" N9 DG J 70 " 0.082 2.00e-02 2.50e+03 pdb=" C8 DG J 70 " 0.228 2.00e-02 2.50e+03 pdb=" N7 DG J 70 " 0.178 2.00e-02 2.50e+03 pdb=" C5 DG J 70 " 0.064 2.00e-02 2.50e+03 pdb=" C6 DG J 70 " -0.085 2.00e-02 2.50e+03 pdb=" O6 DG J 70 " -0.276 2.00e-02 2.50e+03 pdb=" N1 DG J 70 " -0.052 2.00e-02 2.50e+03 pdb=" C2 DG J 70 " 0.013 2.00e-02 2.50e+03 pdb=" N2 DG J 70 " 0.178 2.00e-02 2.50e+03 pdb=" N3 DG J 70 " 0.039 2.00e-02 2.50e+03 pdb=" C4 DG J 70 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 118 " 0.193 2.00e-02 2.50e+03 2.79e-01 7.76e+02 pdb=" C LYS C 118 " -0.481 2.00e-02 2.50e+03 pdb=" O LYS C 118 " 0.136 2.00e-02 2.50e+03 pdb=" N LYS C 119 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -6 " 0.314 2.00e-02 2.50e+03 1.54e-01 5.93e+02 pdb=" N1 DT I -6 " -0.033 2.00e-02 2.50e+03 pdb=" C2 DT I -6 " -0.089 2.00e-02 2.50e+03 pdb=" O2 DT I -6 " -0.187 2.00e-02 2.50e+03 pdb=" N3 DT I -6 " -0.025 2.00e-02 2.50e+03 pdb=" C4 DT I -6 " 0.059 2.00e-02 2.50e+03 pdb=" O4 DT I -6 " 0.246 2.00e-02 2.50e+03 pdb=" C5 DT I -6 " -0.063 2.00e-02 2.50e+03 pdb=" C7 DT I -6 " -0.133 2.00e-02 2.50e+03 pdb=" C6 DT I -6 " -0.089 2.00e-02 2.50e+03 ... (remaining 1705 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 5401 2.97 - 3.45: 14075 3.45 - 3.93: 26652 3.93 - 4.42: 29933 4.42 - 4.90: 41949 Nonbonded interactions: 118010 Sorted by model distance: nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 75 " model vdw 2.486 2.440 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 75 " model vdw 2.490 2.440 nonbonded pdb=" O LYS C 118 " pdb=" CA LYS C 119 " model vdw 2.511 2.776 nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.550 2.440 nonbonded pdb=" OG SER B 47 " pdb=" OP1 DC J 7 " model vdw 2.572 2.440 ... (remaining 118005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 102) } ncs_group { reference = (chain 'C' and resid 12 through 119) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.500 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: 3.060 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 49.160 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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 : 0.014 0.317 14921 Z= 0.767 Angle : 1.972 62.518 21379 Z= 1.325 Chirality : 0.093 0.505 2429 Planarity : 0.031 0.279 1708 Dihedral : 25.752 169.188 6360 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.58 % Allowed : 2.80 % Favored : 96.62 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: -0.35 (0.24), residues: 1009 helix: 0.25 (0.19), residues: 610 sheet: -1.00 (0.95), residues: 35 loop : -0.79 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.250 0.042 TRP L 276 HIS 0.013 0.003 HIS H 46 PHE 0.048 0.013 PHE D 67 TYR 0.143 0.017 TYR C 57 ARG 0.016 0.002 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 269 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7937 (tt0) cc_final: 0.7675 (tt0) REVERT: A 90 MET cc_start: 0.7478 (mmp) cc_final: 0.7257 (mmp) REVERT: A 105 GLU cc_start: 0.7502 (tt0) cc_final: 0.7300 (mt-10) REVERT: B 84 MET cc_start: 0.8093 (mmp) cc_final: 0.7850 (mmp) REVERT: D 59 MET cc_start: 0.8475 (mmm) cc_final: 0.8210 (mmp) REVERT: F 35 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7307 (mtp85) REVERT: H 75 SER cc_start: 0.8778 (t) cc_final: 0.8545 (t) REVERT: H 96 ARG cc_start: 0.8472 (tpp80) cc_final: 0.7954 (ttt-90) REVERT: H 112 THR cc_start: 0.8798 (t) cc_final: 0.8454 (p) REVERT: L 49 PHE cc_start: 0.6716 (m-80) cc_final: 0.6323 (m-80) REVERT: L 55 ILE cc_start: 0.3933 (OUTLIER) cc_final: 0.3582 (pt) REVERT: L 129 LEU cc_start: 0.7845 (tp) cc_final: 0.7430 (tm) REVERT: L 185 ILE cc_start: 0.7343 (mm) cc_final: 0.6997 (mt) REVERT: L 194 ASP cc_start: 0.7764 (p0) cc_final: 0.7270 (p0) REVERT: L 205 ARG cc_start: 0.7761 (tpt170) cc_final: 0.7487 (mmm160) REVERT: L 262 MET cc_start: 0.6270 (mmm) cc_final: 0.5697 (mmm) outliers start: 5 outliers final: 1 residues processed: 272 average time/residue: 1.6538 time to fit residues: 481.4782 Evaluate side-chains 225 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain L residue 55 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN D 106 HIS F 93 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS L 113 GLN ** L 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14921 Z= 0.210 Angle : 0.666 9.103 21379 Z= 0.394 Chirality : 0.039 0.143 2429 Planarity : 0.005 0.041 1708 Dihedral : 30.600 178.940 4323 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.92 % Allowed : 13.07 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.39 (0.26), residues: 1009 helix: 1.97 (0.21), residues: 633 sheet: -0.40 (0.90), residues: 30 loop : -0.96 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP L 276 HIS 0.008 0.001 HIS L 268 PHE 0.008 0.001 PHE L 49 TYR 0.009 0.001 TYR E 41 ARG 0.008 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 234 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.7537 (mmp) cc_final: 0.7270 (mmp) REVERT: C 73 ASN cc_start: 0.8024 (t0) cc_final: 0.7814 (t0) REVERT: F 35 ARG cc_start: 0.7559 (mtp85) cc_final: 0.7200 (mtp85) REVERT: F 85 ASP cc_start: 0.7763 (m-30) cc_final: 0.7557 (m-30) REVERT: F 92 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8580 (ttp80) REVERT: G 73 ASN cc_start: 0.8150 (t0) cc_final: 0.7918 (t0) REVERT: H 76 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7324 (mtp85) REVERT: L 100 GLN cc_start: 0.7374 (tp-100) cc_final: 0.6884 (tp-100) REVERT: L 109 PHE cc_start: 0.5613 (t80) cc_final: 0.5221 (t80) REVERT: L 205 ARG cc_start: 0.7745 (tpt170) cc_final: 0.7530 (mmm160) REVERT: L 262 MET cc_start: 0.6353 (mmm) cc_final: 0.5751 (mmm) outliers start: 25 outliers final: 12 residues processed: 244 average time/residue: 1.6200 time to fit residues: 424.3677 Evaluate side-chains 223 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 209 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 212 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS E 76 GLN ** L 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 14921 Z= 0.497 Angle : 0.768 7.781 21379 Z= 0.445 Chirality : 0.046 0.165 2429 Planarity : 0.006 0.057 1708 Dihedral : 30.300 174.282 4320 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.20 % Allowed : 15.52 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 0.70 (0.26), residues: 1009 helix: 1.51 (0.20), residues: 633 sheet: -0.97 (0.81), residues: 40 loop : -1.40 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP L 276 HIS 0.005 0.001 HIS L 268 PHE 0.021 0.002 PHE L 49 TYR 0.013 0.002 TYR F 51 ARG 0.008 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7897 (m-30) cc_final: 0.7594 (m-30) REVERT: A 90 MET cc_start: 0.7878 (mmp) cc_final: 0.7607 (mmp) REVERT: B 93 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: C 29 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8001 (ttm-80) REVERT: C 73 ASN cc_start: 0.8418 (t0) cc_final: 0.7942 (t0) REVERT: D 32 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8102 (mt-10) REVERT: E 105 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7085 (tm-30) REVERT: F 35 ARG cc_start: 0.7763 (mtp85) cc_final: 0.7449 (mtp85) REVERT: G 73 ASN cc_start: 0.8575 (t0) cc_final: 0.8145 (t0) REVERT: H 76 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7427 (mtp85) REVERT: L 49 PHE cc_start: 0.7144 (m-80) cc_final: 0.6763 (t80) REVERT: L 189 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8039 (tp30) REVERT: L 205 ARG cc_start: 0.8059 (tpt170) cc_final: 0.7642 (mmm160) REVERT: L 262 MET cc_start: 0.6674 (mmm) cc_final: 0.6143 (mmm) outliers start: 36 outliers final: 21 residues processed: 230 average time/residue: 1.6915 time to fit residues: 417.0463 Evaluate side-chains 228 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 211 ILE Chi-restraints excluded: chain L residue 271 LEU Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.3980 chunk 85 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN E 39 HIS E 76 GLN G 89 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 246 HIS ** L 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14921 Z= 0.226 Angle : 0.625 13.803 21379 Z= 0.368 Chirality : 0.038 0.179 2429 Planarity : 0.005 0.057 1708 Dihedral : 29.663 174.172 4320 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.38 % Allowed : 20.19 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.21 (0.27), residues: 1009 helix: 1.99 (0.21), residues: 630 sheet: -1.59 (0.72), residues: 45 loop : -1.21 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 42 HIS 0.008 0.001 HIS L 246 PHE 0.011 0.001 PHE L 49 TYR 0.008 0.001 TYR H 37 ARG 0.007 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 213 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7603 (mmp) cc_final: 0.7349 (mmp) REVERT: B 93 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: C 73 ASN cc_start: 0.8389 (t0) cc_final: 0.7962 (t0) REVERT: F 35 ARG cc_start: 0.7455 (mtp85) cc_final: 0.7178 (mtp85) REVERT: F 77 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8685 (mtmp) REVERT: F 85 ASP cc_start: 0.7683 (m-30) cc_final: 0.7453 (m-30) REVERT: G 73 ASN cc_start: 0.8566 (t0) cc_final: 0.8068 (t0) REVERT: H 76 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7318 (mtp85) REVERT: L 49 PHE cc_start: 0.6790 (m-80) cc_final: 0.6397 (t80) REVERT: L 100 GLN cc_start: 0.7144 (tt0) cc_final: 0.6759 (tp-100) REVERT: L 180 GLU cc_start: 0.5657 (tt0) cc_final: 0.4998 (tt0) REVERT: L 182 ARG cc_start: 0.5081 (tpp80) cc_final: 0.4668 (tpp80) REVERT: L 189 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7824 (tp30) REVERT: L 205 ARG cc_start: 0.7871 (tpt170) cc_final: 0.7553 (mmm160) REVERT: L 269 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5850 (mm) outliers start: 29 outliers final: 17 residues processed: 222 average time/residue: 1.5617 time to fit residues: 373.2201 Evaluate side-chains 225 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 203 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 211 ILE Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 40 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 E 76 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14921 Z= 0.318 Angle : 0.655 10.820 21379 Z= 0.383 Chirality : 0.039 0.172 2429 Planarity : 0.005 0.052 1708 Dihedral : 29.517 173.976 4320 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.60 % Allowed : 19.84 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.10 (0.27), residues: 1009 helix: 1.94 (0.21), residues: 626 sheet: -1.89 (0.70), residues: 47 loop : -1.24 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 42 HIS 0.005 0.001 HIS L 268 PHE 0.010 0.001 PHE L 49 TYR 0.013 0.002 TYR H 80 ARG 0.008 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 209 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7754 (mmp) cc_final: 0.7466 (mmp) REVERT: B 93 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: C 29 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8420 (ttm170) REVERT: C 56 GLU cc_start: 0.8292 (tt0) cc_final: 0.7987 (tt0) REVERT: C 73 ASN cc_start: 0.8488 (t0) cc_final: 0.8053 (t0) REVERT: E 56 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8899 (ttmp) REVERT: E 96 SER cc_start: 0.8696 (p) cc_final: 0.8481 (m) REVERT: F 35 ARG cc_start: 0.7544 (mtp85) cc_final: 0.7303 (mtp85) REVERT: F 77 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8706 (mtmp) REVERT: F 85 ASP cc_start: 0.7705 (m-30) cc_final: 0.7472 (m-30) REVERT: G 73 ASN cc_start: 0.8609 (t0) cc_final: 0.8101 (t0) REVERT: H 76 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7350 (mtp85) REVERT: L 49 PHE cc_start: 0.6954 (m-80) cc_final: 0.6645 (t80) REVERT: L 153 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8060 (p) REVERT: L 180 GLU cc_start: 0.5554 (tt0) cc_final: 0.5005 (tt0) REVERT: L 182 ARG cc_start: 0.5051 (tpp80) cc_final: 0.4679 (tpp80) REVERT: L 189 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7863 (tp30) REVERT: L 205 ARG cc_start: 0.7956 (tpt170) cc_final: 0.7563 (mmm160) REVERT: L 282 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7510 (tp) outliers start: 48 outliers final: 26 residues processed: 232 average time/residue: 1.5932 time to fit residues: 396.8242 Evaluate side-chains 241 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 207 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 141 CYS Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 211 ILE Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14921 Z= 0.194 Angle : 0.611 9.901 21379 Z= 0.355 Chirality : 0.036 0.131 2429 Planarity : 0.004 0.053 1708 Dihedral : 29.254 174.223 4320 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.62 % Allowed : 22.29 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.47 (0.27), residues: 1009 helix: 2.23 (0.21), residues: 628 sheet: -1.58 (0.78), residues: 43 loop : -1.15 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 42 HIS 0.003 0.001 HIS L 268 PHE 0.009 0.001 PHE L 49 TYR 0.010 0.001 TYR H 80 ARG 0.012 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 220 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7576 (mmp) cc_final: 0.7265 (mmp) REVERT: B 93 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: C 73 ASN cc_start: 0.8441 (t0) cc_final: 0.8084 (t0) REVERT: E 56 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8888 (ttmp) REVERT: F 77 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8698 (mtmp) REVERT: F 85 ASP cc_start: 0.7596 (m-30) cc_final: 0.7339 (m-30) REVERT: G 73 ASN cc_start: 0.8605 (t0) cc_final: 0.8094 (t0) REVERT: H 75 SER cc_start: 0.8784 (t) cc_final: 0.8509 (t) REVERT: H 76 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7280 (mtp85) REVERT: L 109 PHE cc_start: 0.5826 (t80) cc_final: 0.5502 (t80) REVERT: L 153 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7870 (p) REVERT: L 174 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8659 (mp) REVERT: L 205 ARG cc_start: 0.7817 (tpt170) cc_final: 0.7482 (mmm160) REVERT: L 282 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7481 (tp) outliers start: 31 outliers final: 21 residues processed: 231 average time/residue: 1.6302 time to fit residues: 406.7441 Evaluate side-chains 239 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 211 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 114 ASN Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14921 Z= 0.281 Angle : 0.646 10.076 21379 Z= 0.375 Chirality : 0.038 0.138 2429 Planarity : 0.005 0.055 1708 Dihedral : 29.325 173.844 4320 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.97 % Allowed : 23.10 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.27), residues: 1009 helix: 2.09 (0.21), residues: 625 sheet: -0.98 (0.84), residues: 40 loop : -1.26 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 42 HIS 0.004 0.001 HIS L 95 PHE 0.015 0.001 PHE L 49 TYR 0.017 0.002 TYR H 80 ARG 0.014 0.001 ARG L 195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 214 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7744 (mmp) cc_final: 0.7435 (mmp) REVERT: B 93 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7824 (mp10) REVERT: C 73 ASN cc_start: 0.8532 (t0) cc_final: 0.8142 (t0) REVERT: E 56 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8911 (ttmp) REVERT: F 77 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8697 (mtmp) REVERT: F 85 ASP cc_start: 0.7698 (m-30) cc_final: 0.7434 (m-30) REVERT: G 73 ASN cc_start: 0.8619 (t0) cc_final: 0.8095 (t0) REVERT: H 75 SER cc_start: 0.8782 (t) cc_final: 0.8510 (t) REVERT: H 76 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7329 (mtp85) REVERT: L 51 THR cc_start: 0.7528 (m) cc_final: 0.7213 (p) REVERT: L 109 PHE cc_start: 0.6148 (t80) cc_final: 0.5838 (t80) REVERT: L 153 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.7885 (t) REVERT: L 174 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8866 (mp) REVERT: L 205 ARG cc_start: 0.7913 (tpt170) cc_final: 0.7519 (mmm160) REVERT: L 282 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7723 (tp) outliers start: 34 outliers final: 23 residues processed: 228 average time/residue: 1.5681 time to fit residues: 384.3238 Evaluate side-chains 238 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 208 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 114 ASN Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14921 Z= 0.213 Angle : 0.616 10.337 21379 Z= 0.358 Chirality : 0.036 0.167 2429 Planarity : 0.005 0.058 1708 Dihedral : 29.194 173.884 4320 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.20 % Allowed : 22.99 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.46 (0.27), residues: 1009 helix: 2.21 (0.21), residues: 628 sheet: -0.67 (0.86), residues: 38 loop : -1.27 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 42 HIS 0.004 0.001 HIS L 95 PHE 0.013 0.001 PHE L 49 TYR 0.017 0.001 TYR H 80 ARG 0.016 0.001 ARG L 195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7616 (mmp) cc_final: 0.7299 (mmp) REVERT: A 105 GLU cc_start: 0.7477 (tt0) cc_final: 0.7263 (mt-10) REVERT: B 93 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7824 (mp10) REVERT: C 73 ASN cc_start: 0.8541 (t0) cc_final: 0.8184 (t0) REVERT: C 110 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.8093 (p0) REVERT: E 56 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8915 (ttmp) REVERT: F 77 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8705 (mtmp) REVERT: F 85 ASP cc_start: 0.7527 (m-30) cc_final: 0.7278 (m-30) REVERT: G 73 ASN cc_start: 0.8633 (t0) cc_final: 0.8133 (t0) REVERT: H 75 SER cc_start: 0.8788 (t) cc_final: 0.8516 (t) REVERT: H 76 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7289 (mtp85) REVERT: L 51 THR cc_start: 0.7552 (m) cc_final: 0.7283 (p) REVERT: L 109 PHE cc_start: 0.5958 (t80) cc_final: 0.5722 (t80) REVERT: L 153 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7839 (p) REVERT: L 174 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8673 (mp) REVERT: L 205 ARG cc_start: 0.7869 (tpt170) cc_final: 0.7478 (mmm160) outliers start: 36 outliers final: 23 residues processed: 216 average time/residue: 1.5612 time to fit residues: 363.0804 Evaluate side-chains 229 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 199 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 114 ASN Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 141 CYS Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain L residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.0050 chunk 115 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14921 Z= 0.214 Angle : 0.621 11.888 21379 Z= 0.358 Chirality : 0.036 0.174 2429 Planarity : 0.005 0.054 1708 Dihedral : 29.177 173.628 4320 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.08 % Allowed : 23.10 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.43 (0.27), residues: 1009 helix: 2.20 (0.21), residues: 628 sheet: -1.87 (0.77), residues: 46 loop : -1.12 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 42 HIS 0.004 0.001 HIS L 95 PHE 0.013 0.001 PHE L 49 TYR 0.020 0.001 TYR H 80 ARG 0.014 0.001 ARG L 195 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7649 (mmp) cc_final: 0.7328 (mmp) REVERT: A 105 GLU cc_start: 0.7461 (tt0) cc_final: 0.7249 (mt-10) REVERT: B 93 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: C 73 ASN cc_start: 0.8548 (t0) cc_final: 0.8212 (t0) REVERT: C 76 THR cc_start: 0.8779 (p) cc_final: 0.8492 (t) REVERT: C 110 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.8099 (p0) REVERT: E 56 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8921 (ttmp) REVERT: F 77 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8710 (mtmp) REVERT: F 85 ASP cc_start: 0.7544 (m-30) cc_final: 0.7299 (m-30) REVERT: G 73 ASN cc_start: 0.8632 (t0) cc_final: 0.8166 (t0) REVERT: H 75 SER cc_start: 0.8806 (t) cc_final: 0.8538 (t) REVERT: H 76 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7294 (mtp85) REVERT: L 109 PHE cc_start: 0.6032 (t80) cc_final: 0.5825 (t80) REVERT: L 153 VAL cc_start: 0.8095 (OUTLIER) cc_final: 0.7824 (p) REVERT: L 205 ARG cc_start: 0.7851 (tpt170) cc_final: 0.7474 (mmm160) REVERT: L 266 MET cc_start: 0.3276 (tpt) cc_final: 0.2755 (tpt) outliers start: 35 outliers final: 23 residues processed: 218 average time/residue: 1.5978 time to fit residues: 374.6289 Evaluate side-chains 226 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 114 ASN Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 124 optimal weight: 0.0060 chunk 114 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14921 Z= 0.306 Angle : 0.665 13.065 21379 Z= 0.381 Chirality : 0.039 0.193 2429 Planarity : 0.005 0.052 1708 Dihedral : 29.274 173.130 4320 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.85 % Allowed : 23.34 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.22 (0.27), residues: 1009 helix: 2.05 (0.21), residues: 625 sheet: -1.97 (0.77), residues: 46 loop : -1.19 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP L 42 HIS 0.004 0.001 HIS L 95 PHE 0.016 0.001 PHE L 49 TYR 0.026 0.002 TYR H 80 ARG 0.011 0.001 ARG L 195 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7736 (mmp) cc_final: 0.7416 (mmp) REVERT: A 105 GLU cc_start: 0.7527 (tt0) cc_final: 0.7318 (mt-10) REVERT: B 93 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: B 97 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8584 (tp) REVERT: C 73 ASN cc_start: 0.8618 (t0) cc_final: 0.8263 (t0) REVERT: C 76 THR cc_start: 0.8718 (p) cc_final: 0.8501 (t) REVERT: C 110 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.8145 (p0) REVERT: D 83 ARG cc_start: 0.8460 (mmt90) cc_final: 0.8130 (mpt180) REVERT: F 77 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8710 (mtmp) REVERT: F 85 ASP cc_start: 0.7660 (m-30) cc_final: 0.7442 (m-30) REVERT: G 73 ASN cc_start: 0.8656 (t0) cc_final: 0.8131 (t0) REVERT: H 75 SER cc_start: 0.8803 (t) cc_final: 0.8523 (t) REVERT: H 76 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7319 (mtp85) REVERT: H 96 ARG cc_start: 0.8616 (tpp80) cc_final: 0.8287 (mtt-85) REVERT: L 109 PHE cc_start: 0.6251 (t80) cc_final: 0.5988 (t80) REVERT: L 153 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7810 (t) REVERT: L 205 ARG cc_start: 0.7935 (tpt170) cc_final: 0.7466 (mmm160) REVERT: L 254 ILE cc_start: 0.8749 (mp) cc_final: 0.8463 (tp) outliers start: 33 outliers final: 26 residues processed: 213 average time/residue: 1.6983 time to fit residues: 388.6131 Evaluate side-chains 227 residues out of total 857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 114 ASN Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 141 CYS Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 211 ILE Chi-restraints excluded: chain L residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.136634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.110817 restraints weight = 28679.390| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.33 r_work: 0.3365 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14921 Z= 0.223 Angle : 0.640 12.536 21379 Z= 0.367 Chirality : 0.037 0.174 2429 Planarity : 0.005 0.048 1708 Dihedral : 29.196 173.627 4320 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.50 % Allowed : 24.04 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.39 (0.27), residues: 1009 helix: 2.16 (0.21), residues: 629 sheet: -1.40 (0.79), residues: 44 loop : -1.21 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP L 42 HIS 0.006 0.001 HIS L 95 PHE 0.012 0.001 PHE L 49 TYR 0.024 0.002 TYR H 80 ARG 0.010 0.001 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5800.85 seconds wall clock time: 105 minutes 35.79 seconds (6335.79 seconds total)