Starting phenix.real_space_refine on Sun Mar 17 13:49:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/03_2024/6z5u_11082_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/03_2024/6z5u_11082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/03_2024/6z5u_11082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/03_2024/6z5u_11082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/03_2024/6z5u_11082_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/03_2024/6z5u_11082_updated.pdb" } resolution = 3.9 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= 0.007 sd= 0.089 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 P 6 5.49 5 Mg 2 5.21 5 S 92 5.16 5 C 11394 2.51 5 N 2967 2.21 5 O 3419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "E PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 141": "OD1" <-> "OD2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 156": "OE1" <-> "OE2" Residue "H TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 186": "OE1" <-> "OE2" Residue "I PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 87": "OD1" <-> "OD2" Residue "J PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 208": "OD1" <-> "OD2" Residue "K TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 174": "OE1" <-> "OE2" Residue "L TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 186": "OE1" <-> "OE2" Residue "F PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17880 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1886 Classifications: {'peptide': 254} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 244} Chain: "B" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1886 Classifications: {'peptide': 254} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 245} Chain: "C" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 696 Classifications: {'peptide': 87} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 82} Chain: "D" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 696 Classifications: {'peptide': 87} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 83} Chain: "E" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1450 Classifications: {'peptide': 190} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 184} Chain: "G" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1461 Classifications: {'peptide': 191} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 185} Chain: "H" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1443 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "I" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1476 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain: "J" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1450 Classifications: {'peptide': 190} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 183} Chain: "K" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1948 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "L" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1948 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "F" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1476 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.65, per 1000 atoms: 0.54 Number of scatterers: 17880 At special positions: 0 Unit cell: (135.89, 144.45, 145.52, 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) S 92 16.00 P 6 15.00 Mg 2 11.99 O 3419 8.00 N 2967 7.00 C 11394 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: 7.17 Conformation dependent library (CDL) restraints added in 3.5 seconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 15 sheets defined 49.1% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 5 through 29 Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 39 through 48 removed outlier: 3.720A pdb=" N HIS A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 78 removed outlier: 4.695A pdb=" N LEU A 54 " --> pdb=" O MET A 51 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 72 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 73 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL A 76 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 removed outlier: 3.592A pdb=" N MET A 87 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 88 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 89 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 94 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 122 removed outlier: 3.996A pdb=" N ALA A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLY A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 142 through 171 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 195 through 219 Processing helix chain 'A' and resid 225 through 254 removed outlier: 4.209A pdb=" N ILE A 228 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 229 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 239 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 252 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 254 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 30 Processing helix chain 'B' and resid 35 through 47 removed outlier: 4.048A pdb=" N GLY B 39 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 40 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL B 42 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET B 45 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.907A pdb=" N LEU B 54 " --> pdb=" O MET B 51 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 57 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 72 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B 76 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 removed outlier: 5.419A pdb=" N GLY B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 108 removed outlier: 4.138A pdb=" N ALA B 102 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.572A pdb=" N MET B 131 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 139 No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 142 through 171 Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 179 through 189 Processing helix chain 'B' and resid 192 through 218 removed outlier: 7.257A pdb=" N VAL B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 254 removed outlier: 3.506A pdb=" N ALA B 229 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 239 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 241 " --> pdb=" O TYR B 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 51 through 64 removed outlier: 4.225A pdb=" N THR C 64 " --> pdb=" O TRP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 85 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.687A pdb=" N ALA D 20 " --> pdb=" O PHE D 17 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU D 21 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 24 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 65 through 68 No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 77 through 85 Processing helix chain 'E' and resid 6 through 32 removed outlier: 5.188A pdb=" N ILE E 16 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE E 17 " --> pdb=" O PHE E 13 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE E 22 " --> pdb=" O GLY E 18 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL E 28 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 96 through 108 Processing helix chain 'E' and resid 113 through 116 No H-bonds generated for 'chain 'E' and resid 113 through 116' Processing helix chain 'E' and resid 120 through 136 removed outlier: 4.289A pdb=" N SER E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 190 Processing helix chain 'G' and resid 5 through 29 removed outlier: 5.060A pdb=" N VAL G 10 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE G 15 " --> pdb=" O GLY G 11 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE G 22 " --> pdb=" O GLY G 18 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 95 through 112 Processing helix chain 'G' and resid 115 through 118 No H-bonds generated for 'chain 'G' and resid 115 through 118' Processing helix chain 'G' and resid 121 through 136 removed outlier: 3.684A pdb=" N ASN G 135 " --> pdb=" O ILE G 131 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER G 136 " --> pdb=" O SER G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 190 Processing helix chain 'H' and resid 7 through 32 removed outlier: 3.948A pdb=" N ILE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU H 31 " --> pdb=" O LYS H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 92 through 111 removed outlier: 5.023A pdb=" N LEU H 98 " --> pdb=" O ALA H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 116 No H-bonds generated for 'chain 'H' and resid 113 through 116' Processing helix chain 'H' and resid 120 through 134 removed outlier: 4.845A pdb=" N THR H 125 " --> pdb=" O ALA H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 190 Processing helix chain 'I' and resid 3 through 30 removed outlier: 4.367A pdb=" N GLU I 7 " --> pdb=" O SER I 3 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU I 8 " --> pdb=" O ARG I 4 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER I 29 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY I 30 " --> pdb=" O MET I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 91 No H-bonds generated for 'chain 'I' and resid 88 through 91' Processing helix chain 'I' and resid 95 through 111 Processing helix chain 'I' and resid 115 through 117 No H-bonds generated for 'chain 'I' and resid 115 through 117' Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.877A pdb=" N MET I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN I 135 " --> pdb=" O ILE I 131 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER I 136 " --> pdb=" O SER I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 192 Processing helix chain 'J' and resid 6 through 30 removed outlier: 4.236A pdb=" N VAL J 14 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ILE J 15 " --> pdb=" O GLY J 11 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE J 16 " --> pdb=" O ILE J 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE J 17 " --> pdb=" O PHE J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 111 Processing helix chain 'J' and resid 113 through 115 No H-bonds generated for 'chain 'J' and resid 113 through 115' Processing helix chain 'J' and resid 120 through 136 removed outlier: 3.550A pdb=" N THR J 125 " --> pdb=" O GLN J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 192 Processing helix chain 'K' and resid 51 through 58 Processing helix chain 'K' and resid 76 through 78 No H-bonds generated for 'chain 'K' and resid 76 through 78' Processing helix chain 'K' and resid 81 through 90 removed outlier: 4.053A pdb=" N ALA K 89 " --> pdb=" O PHE K 85 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG K 90 " --> pdb=" O ALA K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 117 Proline residue: K 113 - end of helix removed outlier: 4.149A pdb=" N ALA K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS K 117 " --> pdb=" O PRO K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 136 removed outlier: 3.680A pdb=" N VAL K 136 " --> pdb=" O LYS K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 141 No H-bonds generated for 'chain 'K' and resid 139 through 141' Processing helix chain 'K' and resid 146 through 148 No H-bonds generated for 'chain 'K' and resid 146 through 148' Processing helix chain 'K' and resid 151 through 162 Processing helix chain 'K' and resid 175 through 177 No H-bonds generated for 'chain 'K' and resid 175 through 177' Processing helix chain 'K' and resid 181 through 197 Processing helix chain 'K' and resid 209 through 211 No H-bonds generated for 'chain 'K' and resid 209 through 211' Processing helix chain 'K' and resid 233 through 238 Processing helix chain 'K' and resid 242 through 249 Processing helix chain 'L' and resid 51 through 58 Processing helix chain 'L' and resid 81 through 90 removed outlier: 4.079A pdb=" N ALA L 89 " --> pdb=" O PHE L 85 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG L 90 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 117 Proline residue: L 113 - end of helix removed outlier: 4.065A pdb=" N ALA L 116 " --> pdb=" O PHE L 112 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS L 117 " --> pdb=" O PRO L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 136 removed outlier: 3.753A pdb=" N VAL L 136 " --> pdb=" O LYS L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 151 through 162 Processing helix chain 'L' and resid 181 through 197 removed outlier: 3.797A pdb=" N GLU L 196 " --> pdb=" O ARG L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 215 removed outlier: 4.141A pdb=" N SER L 214 " --> pdb=" O PRO L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 238 removed outlier: 3.717A pdb=" N ALA L 238 " --> pdb=" O GLU L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 242 through 249 Processing helix chain 'F' and resid 3 through 30 removed outlier: 4.367A pdb=" N GLU F 7 " --> pdb=" O SER F 3 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU F 8 " --> pdb=" O ARG F 4 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY F 30 " --> pdb=" O MET F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 91 No H-bonds generated for 'chain 'F' and resid 88 through 91' Processing helix chain 'F' and resid 95 through 111 Processing helix chain 'F' and resid 115 through 117 No H-bonds generated for 'chain 'F' and resid 115 through 117' Processing helix chain 'F' and resid 120 through 136 removed outlier: 3.877A pdb=" N MET F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN F 135 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER F 136 " --> pdb=" O SER F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 192 Processing sheet with id= A, first strand: chain 'D' and resid 40 through 42 removed outlier: 7.123A pdb=" N HIS D 71 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'E' and resid 39 through 46 removed outlier: 3.555A pdb=" N SER E 70 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ASP E 85 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL E 68 " --> pdb=" O ASP E 85 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP E 87 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY E 66 " --> pdb=" O ASP E 87 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET E 60 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL E 58 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS E 57 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 41 through 46 removed outlier: 6.350A pdb=" N ASP G 85 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL G 68 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET G 60 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL G 58 " --> pdb=" O ILE G 65 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 145 through 150 Processing sheet with id= E, first strand: chain 'H' and resid 40 through 46 removed outlier: 3.739A pdb=" N VAL H 63 " --> pdb=" O MET H 60 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET H 60 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL H 58 " --> pdb=" O ILE H 65 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 71 through 73 Processing sheet with id= G, first strand: chain 'I' and resid 40 through 46 removed outlier: 3.783A pdb=" N LEU I 79 " --> pdb=" O ASP I 74 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER I 70 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL I 68 " --> pdb=" O ASP I 85 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL I 58 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU I 159 " --> pdb=" O THR I 59 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 40 through 46 removed outlier: 3.505A pdb=" N LEU J 79 " --> pdb=" O ASP J 74 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASP J 85 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL J 68 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET J 60 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL J 58 " --> pdb=" O ILE J 65 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS J 57 " --> pdb=" O LYS J 157 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 33 through 35 Processing sheet with id= J, first strand: chain 'K' and resid 226 through 231 removed outlier: 6.456A pdb=" N VAL K 221 " --> pdb=" O GLN K 228 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU K 230 " --> pdb=" O ILE K 219 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE K 219 " --> pdb=" O GLU K 230 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR K 202 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE K 43 " --> pdb=" O THR K 202 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE K 204 " --> pdb=" O ILE K 43 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 18 through 20 removed outlier: 7.771A pdb=" N PHE K 20 " --> pdb=" O ASP K 29 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ASP K 29 " --> pdb=" O PHE K 20 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 33 through 35 Processing sheet with id= M, first strand: chain 'L' and resid 226 through 231 removed outlier: 6.581A pdb=" N VAL L 221 " --> pdb=" O GLN L 228 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU L 230 " --> pdb=" O ILE L 219 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE L 219 " --> pdb=" O GLU L 230 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR L 202 " --> pdb=" O THR L 41 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE L 43 " --> pdb=" O THR L 202 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE L 204 " --> pdb=" O ILE L 43 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 18 through 20 removed outlier: 7.745A pdb=" N PHE L 20 " --> pdb=" O ASP L 29 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASP L 29 " --> pdb=" O PHE L 20 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 40 through 46 removed outlier: 3.783A pdb=" N LEU F 79 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER F 70 " --> pdb=" O THR F 83 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP F 85 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL F 68 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL F 58 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU F 159 " --> pdb=" O THR F 59 " (cutoff:3.500A) 891 hydrogen bonds defined for protein. 2148 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.91 Time building geometry restraints manager: 7.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3092 1.30 - 1.44: 4705 1.44 - 1.58: 10101 1.58 - 1.71: 66 1.71 - 1.85: 170 Bond restraints: 18134 Sorted by residual: bond pdb=" N3B ANP K 301 " pdb=" PG ANP K 301 " ideal model delta sigma weight residual 1.795 1.566 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" N3B ANP L 302 " pdb=" PG ANP L 302 " ideal model delta sigma weight residual 1.795 1.568 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" O3A ANP L 302 " pdb=" PB ANP L 302 " ideal model delta sigma weight residual 1.700 1.487 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" O3A ANP K 301 " pdb=" PB ANP K 301 " ideal model delta sigma weight residual 1.700 1.517 0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" CB HIS L 207 " pdb=" CG HIS L 207 " ideal model delta sigma weight residual 1.497 1.379 0.118 1.40e-02 5.10e+03 7.06e+01 ... (remaining 18129 not shown) Histogram of bond angle deviations from ideal: 95.58 - 103.95: 261 103.95 - 112.31: 8606 112.31 - 120.68: 10215 120.68 - 129.04: 5405 129.04 - 137.40: 57 Bond angle restraints: 24544 Sorted by residual: angle pdb=" N SER K 206 " pdb=" CA SER K 206 " pdb=" C SER K 206 " ideal model delta sigma weight residual 108.19 122.23 -14.04 1.29e+00 6.01e-01 1.18e+02 angle pdb=" C ASP H 74 " pdb=" N PRO H 75 " pdb=" CA PRO H 75 " ideal model delta sigma weight residual 119.56 128.59 -9.03 1.02e+00 9.61e-01 7.84e+01 angle pdb=" N THR G 77 " pdb=" CA THR G 77 " pdb=" C THR G 77 " ideal model delta sigma weight residual 114.31 103.34 10.97 1.29e+00 6.01e-01 7.23e+01 angle pdb=" N ILE L 27 " pdb=" CA ILE L 27 " pdb=" C ILE L 27 " ideal model delta sigma weight residual 111.81 104.76 7.05 8.60e-01 1.35e+00 6.72e+01 angle pdb=" CA PHE H 22 " pdb=" CB PHE H 22 " pdb=" CG PHE H 22 " ideal model delta sigma weight residual 113.80 105.64 8.16 1.00e+00 1.00e+00 6.67e+01 ... (remaining 24539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 10369 18.13 - 36.27: 380 36.27 - 54.40: 135 54.40 - 72.53: 48 72.53 - 90.67: 20 Dihedral angle restraints: 10952 sinusoidal: 4322 harmonic: 6630 Sorted by residual: dihedral pdb=" CA MET L 79 " pdb=" C MET L 79 " pdb=" N SER L 80 " pdb=" CA SER L 80 " ideal model delta harmonic sigma weight residual -180.00 -89.33 -90.67 0 5.00e+00 4.00e-02 3.29e+02 dihedral pdb=" C GLU K 211 " pdb=" N GLU K 211 " pdb=" CA GLU K 211 " pdb=" CB GLU K 211 " ideal model delta harmonic sigma weight residual -122.60 -141.52 18.92 0 2.50e+00 1.60e-01 5.73e+01 dihedral pdb=" N GLU K 211 " pdb=" C GLU K 211 " pdb=" CA GLU K 211 " pdb=" CB GLU K 211 " ideal model delta harmonic sigma weight residual 122.80 140.13 -17.33 0 2.50e+00 1.60e-01 4.81e+01 ... (remaining 10949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 2505 0.148 - 0.297: 412 0.297 - 0.445: 22 0.445 - 0.593: 7 0.593 - 0.742: 1 Chirality restraints: 2947 Sorted by residual: chirality pdb=" CA GLU K 211 " pdb=" N GLU K 211 " pdb=" C GLU K 211 " pdb=" CB GLU K 211 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CA VAL K 209 " pdb=" N VAL K 209 " pdb=" C VAL K 209 " pdb=" CB VAL K 209 " both_signs ideal model delta sigma weight residual False 2.44 1.86 0.58 2.00e-01 2.50e+01 8.56e+00 chirality pdb=" CA LEU G 36 " pdb=" N LEU G 36 " pdb=" C LEU G 36 " pdb=" CB LEU G 36 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 2944 not shown) Planarity restraints: 3103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP L 302 " -0.629 2.00e-02 2.50e+03 2.45e-01 1.65e+03 pdb=" C2 ANP L 302 " 0.071 2.00e-02 2.50e+03 pdb=" C4 ANP L 302 " 0.180 2.00e-02 2.50e+03 pdb=" C5 ANP L 302 " 0.029 2.00e-02 2.50e+03 pdb=" C6 ANP L 302 " -0.095 2.00e-02 2.50e+03 pdb=" C8 ANP L 302 " 0.221 2.00e-02 2.50e+03 pdb=" N1 ANP L 302 " -0.074 2.00e-02 2.50e+03 pdb=" N3 ANP L 302 " 0.206 2.00e-02 2.50e+03 pdb=" N6 ANP L 302 " -0.228 2.00e-02 2.50e+03 pdb=" N7 ANP L 302 " 0.063 2.00e-02 2.50e+03 pdb=" N9 ANP L 302 " 0.256 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP K 301 " -0.550 2.00e-02 2.50e+03 2.15e-01 1.27e+03 pdb=" C2 ANP K 301 " 0.058 2.00e-02 2.50e+03 pdb=" C4 ANP K 301 " 0.157 2.00e-02 2.50e+03 pdb=" C5 ANP K 301 " 0.034 2.00e-02 2.50e+03 pdb=" C6 ANP K 301 " -0.080 2.00e-02 2.50e+03 pdb=" C8 ANP K 301 " 0.191 2.00e-02 2.50e+03 pdb=" N1 ANP K 301 " -0.068 2.00e-02 2.50e+03 pdb=" N3 ANP K 301 " 0.174 2.00e-02 2.50e+03 pdb=" N6 ANP K 301 " -0.208 2.00e-02 2.50e+03 pdb=" N7 ANP K 301 " 0.061 2.00e-02 2.50e+03 pdb=" N9 ANP K 301 " 0.231 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 158 " 0.226 2.00e-02 2.50e+03 1.16e-01 2.70e+02 pdb=" CG TYR H 158 " -0.113 2.00e-02 2.50e+03 pdb=" CD1 TYR H 158 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 TYR H 158 " -0.098 2.00e-02 2.50e+03 pdb=" CE1 TYR H 158 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR H 158 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR H 158 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 158 " 0.153 2.00e-02 2.50e+03 ... (remaining 3100 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.70: 20 1.70 - 2.50: 59 2.50 - 3.30: 22096 3.30 - 4.10: 42617 4.10 - 4.90: 74922 Warning: very small nonbonded interaction distances. Nonbonded interactions: 139714 Sorted by model distance: nonbonded pdb=" OG1 THR G 194 " pdb=" CD1 PHE F 192 " model vdw 0.901 3.340 nonbonded pdb=" CB THR G 194 " pdb=" CZ PHE F 192 " model vdw 0.902 3.770 nonbonded pdb=" CB THR G 194 " pdb=" CE1 PHE F 192 " model vdw 0.915 3.770 nonbonded pdb=" O THR G 194 " pdb=" CE LYS F 191 " model vdw 1.062 3.440 nonbonded pdb=" CE MET E 183 " pdb=" CD GLU F 186 " model vdw 1.065 3.690 ... (remaining 139709 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 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 6 through 194) selection = (chain 'F' and resid 6 through 194) selection = (chain 'G' and resid 6 through 194) selection = chain 'H' selection = (chain 'I' and resid 6 through 194) selection = (chain 'J' and resid 6 through 194) } ncs_group { reference = (chain 'K' and resid 11 through 263) selection = (chain 'L' and resid 11 through 263) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.690 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 48.700 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.100 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0301 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 : 0.021 0.229 18134 Z= 1.357 Angle : 1.881 15.582 24544 Z= 1.255 Chirality : 0.107 0.742 2947 Planarity : 0.012 0.245 3103 Dihedral : 12.689 90.668 6704 Min Nonbonded Distance : 0.901 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.03 % Favored : 97.66 % Rotamer: Outliers : 1.69 % Allowed : 1.99 % Favored : 96.32 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.47 (0.16), residues: 2310 helix: -0.27 (0.14), residues: 1070 sheet: 0.88 (0.33), residues: 259 loop : -0.53 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.006 TRP D 60 HIS 0.008 0.002 HIS A 194 PHE 0.172 0.010 PHE E 84 TYR 0.226 0.014 TYR H 158 ARG 0.008 0.001 ARG G 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 254 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 MET cc_start: 0.0251 (mtp) cc_final: -0.0243 (mpp) REVERT: E 16 ILE cc_start: 0.3016 (mm) cc_final: 0.2778 (mm) REVERT: E 141 ASP cc_start: 0.0007 (OUTLIER) cc_final: -0.2894 (m-30) REVERT: E 162 VAL cc_start: 0.2953 (OUTLIER) cc_final: 0.2599 (t) REVERT: G 160 LYS cc_start: -0.0016 (ttmt) cc_final: -0.0606 (ttpp) REVERT: G 162 VAL cc_start: 0.2803 (t) cc_final: 0.2035 (p) REVERT: H 183 MET cc_start: 0.0037 (mmm) cc_final: -0.0490 (pmm) REVERT: I 5 THR cc_start: -0.4658 (OUTLIER) cc_final: -0.5424 (m) REVERT: J 160 LYS cc_start: 0.1084 (ttpt) cc_final: 0.0089 (tttt) REVERT: K 202 THR cc_start: -0.0014 (p) cc_final: -0.1273 (m) REVERT: L 94 LEU cc_start: 0.0545 (mt) cc_final: -0.0686 (mp) REVERT: L 202 THR cc_start: -0.0385 (p) cc_final: -0.1414 (m) REVERT: F 5 THR cc_start: -0.4730 (OUTLIER) cc_final: -0.5562 (m) outliers start: 33 outliers final: 8 residues processed: 280 average time/residue: 0.2987 time to fit residues: 125.0362 Evaluate side-chains 185 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain H residue 60 MET Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain F residue 5 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 92 optimal weight: 0.0770 chunk 179 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 70 GLN B 77 ASN C 74 ASN D 84 GLN K 207 HIS L 96 GLN L 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0687 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 18134 Z= 0.255 Angle : 0.776 11.096 24544 Z= 0.412 Chirality : 0.046 0.228 2947 Planarity : 0.006 0.040 3103 Dihedral : 8.921 66.971 2550 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.58 % Allowed : 5.32 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.30 (0.16), residues: 2310 helix: 0.24 (0.15), residues: 1069 sheet: 0.41 (0.29), residues: 259 loop : -0.76 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 146 HIS 0.004 0.001 HIS L 207 PHE 0.043 0.003 PHE J 22 TYR 0.027 0.002 TYR L 220 ARG 0.006 0.001 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 26 MET cc_start: 0.3454 (ptm) cc_final: 0.3184 (mmm) REVERT: E 145 TYR cc_start: 0.2373 (OUTLIER) cc_final: 0.0411 (m-80) REVERT: E 162 VAL cc_start: 0.2958 (OUTLIER) cc_final: 0.2282 (t) REVERT: G 78 ARG cc_start: 0.2536 (mtt90) cc_final: 0.2212 (ttp80) REVERT: G 160 LYS cc_start: 0.0320 (ttmt) cc_final: -0.0618 (ttpt) REVERT: G 162 VAL cc_start: 0.2939 (t) cc_final: 0.2591 (p) REVERT: H 183 MET cc_start: 0.0106 (mmm) cc_final: -0.0349 (pmm) REVERT: I 172 ARG cc_start: 0.2367 (mmm-85) cc_final: 0.1791 (mmp80) REVERT: J 60 MET cc_start: 0.0452 (OUTLIER) cc_final: 0.0214 (ttm) REVERT: J 78 ARG cc_start: 0.3029 (mtt90) cc_final: 0.2452 (ttp80) REVERT: J 160 LYS cc_start: 0.1247 (ttpt) cc_final: -0.0090 (pttt) REVERT: K 153 MET cc_start: 0.1641 (tpp) cc_final: -0.0260 (mtp) REVERT: L 44 MET cc_start: 0.1441 (ptp) cc_final: 0.1240 (ptt) REVERT: F 172 ARG cc_start: 0.2401 (mmm-85) cc_final: 0.1821 (mmp80) outliers start: 31 outliers final: 17 residues processed: 208 average time/residue: 0.2766 time to fit residues: 88.7182 Evaluate side-chains 186 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 MET Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain F residue 42 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 115 optimal weight: 0.3980 chunk 64 optimal weight: 0.0030 chunk 173 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 208 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 206 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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: 0.0715 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18134 Z= 0.169 Angle : 0.624 12.527 24544 Z= 0.331 Chirality : 0.042 0.226 2947 Planarity : 0.005 0.043 3103 Dihedral : 7.083 56.890 2541 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.58 % Allowed : 6.39 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2310 helix: 0.41 (0.16), residues: 1087 sheet: 0.30 (0.30), residues: 267 loop : -0.79 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 183 HIS 0.002 0.000 HIS B 46 PHE 0.029 0.002 PHE J 22 TYR 0.016 0.001 TYR L 220 ARG 0.003 0.000 ARG B 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 60 MET cc_start: -0.2888 (ttt) cc_final: -0.4892 (mtt) REVERT: E 145 TYR cc_start: 0.2359 (OUTLIER) cc_final: 0.0480 (m-80) REVERT: E 162 VAL cc_start: 0.2718 (OUTLIER) cc_final: 0.2160 (t) REVERT: G 42 MET cc_start: 0.0948 (OUTLIER) cc_final: 0.0122 (mpp) REVERT: G 78 ARG cc_start: 0.2398 (mtt90) cc_final: 0.2184 (ttp80) REVERT: G 160 LYS cc_start: -0.0059 (ttmt) cc_final: -0.1028 (ttpp) REVERT: G 162 VAL cc_start: 0.3077 (t) cc_final: 0.2330 (p) REVERT: H 65 ILE cc_start: 0.1792 (pt) cc_final: 0.1582 (mm) REVERT: H 183 MET cc_start: 0.0375 (mmm) cc_final: -0.0340 (pmm) REVERT: J 78 ARG cc_start: 0.2568 (OUTLIER) cc_final: 0.2132 (ttp80) REVERT: J 160 LYS cc_start: 0.1024 (ttpt) cc_final: -0.0101 (pttt) REVERT: K 153 MET cc_start: 0.1638 (mpp) cc_final: -0.0015 (mtt) outliers start: 31 outliers final: 22 residues processed: 194 average time/residue: 0.2771 time to fit residues: 83.7860 Evaluate side-chains 189 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 22 PHE Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 150 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 0.1980 chunk 156 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 198 optimal weight: 0.0770 chunk 59 optimal weight: 20.0000 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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: 0.0827 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18134 Z= 0.150 Angle : 0.587 11.917 24544 Z= 0.305 Chirality : 0.042 0.176 2947 Planarity : 0.005 0.055 3103 Dihedral : 6.006 59.941 2537 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.64 % Allowed : 7.82 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2310 helix: 0.56 (0.16), residues: 1088 sheet: 0.12 (0.30), residues: 271 loop : -0.81 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 6 HIS 0.002 0.000 HIS B 46 PHE 0.031 0.002 PHE J 22 TYR 0.014 0.001 TYR L 220 ARG 0.004 0.000 ARG H 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 141 ASP cc_start: 0.0427 (OUTLIER) cc_final: -0.2013 (m-30) REVERT: E 162 VAL cc_start: 0.2971 (OUTLIER) cc_final: 0.2128 (t) REVERT: G 42 MET cc_start: 0.0173 (mpp) cc_final: -0.0116 (mpp) REVERT: G 60 MET cc_start: -0.0720 (ttt) cc_final: -0.1279 (mtp) REVERT: G 160 LYS cc_start: -0.0195 (ttmt) cc_final: -0.1579 (ttpt) REVERT: G 162 VAL cc_start: 0.2944 (t) cc_final: 0.2312 (p) REVERT: H 183 MET cc_start: 0.0336 (mmm) cc_final: -0.0465 (pmm) REVERT: J 160 LYS cc_start: 0.0771 (ttpt) cc_final: -0.0324 (pttt) REVERT: K 91 MET cc_start: 0.1026 (mtt) cc_final: 0.0559 (mtt) REVERT: K 153 MET cc_start: 0.2389 (tpp) cc_final: 0.0517 (mtp) outliers start: 32 outliers final: 25 residues processed: 190 average time/residue: 0.2876 time to fit residues: 86.2865 Evaluate side-chains 187 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 22 PHE Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 22 PHE Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 150 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 184 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 91 optimal weight: 0.2980 chunk 188 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 113 optimal weight: 30.0000 chunk 198 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN B 44 GLN B 189 ASN D 63 GLN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 HIS F 45 GLN ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1645 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 18134 Z= 0.372 Angle : 0.949 13.136 24544 Z= 0.491 Chirality : 0.053 0.240 2947 Planarity : 0.007 0.074 3103 Dihedral : 7.730 77.648 2537 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.91 % Allowed : 8.84 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.29 (0.16), residues: 2310 helix: -0.23 (0.15), residues: 1076 sheet: -0.82 (0.30), residues: 260 loop : -1.47 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.005 TRP B 212 HIS 0.007 0.001 HIS B 194 PHE 0.066 0.004 PHE H 84 TYR 0.046 0.003 TYR J 158 ARG 0.016 0.001 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 168 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.3240 (tmm) cc_final: 0.2965 (tmm) REVERT: A 234 ARG cc_start: 0.5826 (mtt-85) cc_final: 0.4452 (mmt90) REVERT: B 40 ARG cc_start: 0.3682 (OUTLIER) cc_final: 0.1572 (ptt-90) REVERT: B 54 LEU cc_start: 0.2528 (OUTLIER) cc_final: 0.1238 (tt) REVERT: E 141 ASP cc_start: 0.0501 (OUTLIER) cc_final: -0.1424 (p0) REVERT: G 42 MET cc_start: 0.0765 (OUTLIER) cc_final: 0.0554 (mpp) REVERT: G 60 MET cc_start: 0.0113 (ttt) cc_final: -0.0275 (mtt) REVERT: G 79 LEU cc_start: 0.2544 (OUTLIER) cc_final: 0.2084 (mt) REVERT: G 160 LYS cc_start: 0.0844 (ttmt) cc_final: -0.0714 (tttt) REVERT: H 78 ARG cc_start: 0.3483 (tmm160) cc_final: -0.0373 (ptp-170) REVERT: H 183 MET cc_start: 0.1328 (mmm) cc_final: 0.0008 (pmm) REVERT: I 26 MET cc_start: -0.1021 (tpt) cc_final: -0.1492 (mmt) REVERT: I 160 LYS cc_start: 0.2013 (ttmt) cc_final: 0.1725 (ttmt) REVERT: J 141 ASP cc_start: -0.0979 (OUTLIER) cc_final: -0.1495 (p0) REVERT: K 44 MET cc_start: 0.1472 (ptt) cc_final: 0.0875 (ptt) REVERT: K 91 MET cc_start: 0.0956 (mtt) cc_final: 0.0601 (mtt) REVERT: K 153 MET cc_start: 0.3116 (tpp) cc_final: 0.0496 (mtt) REVERT: F 26 MET cc_start: -0.0884 (tpt) cc_final: -0.1297 (mmt) outliers start: 57 outliers final: 41 residues processed: 211 average time/residue: 0.2774 time to fit residues: 90.1160 Evaluate side-chains 196 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 149 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 36 ARG Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 159 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 74 optimal weight: 0.6980 chunk 199 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 chunk 221 optimal weight: 10.0000 chunk 183 optimal weight: 0.0030 chunk 102 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN F 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1416 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18134 Z= 0.167 Angle : 0.625 12.945 24544 Z= 0.323 Chirality : 0.042 0.168 2947 Planarity : 0.005 0.047 3103 Dihedral : 6.804 74.431 2537 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 1.94 % Allowed : 10.53 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.84 (0.17), residues: 2310 helix: 0.21 (0.16), residues: 1083 sheet: -0.54 (0.30), residues: 255 loop : -1.38 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 6 HIS 0.002 0.000 HIS A 46 PHE 0.033 0.002 PHE E 13 TYR 0.014 0.001 TYR K 172 ARG 0.006 0.000 ARG K 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.5201 (mtt-85) cc_final: 0.4302 (mmp-170) REVERT: E 141 ASP cc_start: 0.1069 (OUTLIER) cc_final: -0.1368 (p0) REVERT: E 157 LYS cc_start: 0.1863 (ttmt) cc_final: 0.1105 (tptp) REVERT: E 183 MET cc_start: -0.0078 (mtt) cc_final: -0.0426 (mtt) REVERT: G 160 LYS cc_start: -0.0122 (ttmt) cc_final: -0.1420 (tttt) REVERT: G 183 MET cc_start: 0.0694 (ptt) cc_final: 0.0270 (mtm) REVERT: H 60 MET cc_start: 0.1050 (mmm) cc_final: -0.0122 (mmm) REVERT: H 65 ILE cc_start: 0.3546 (pt) cc_final: 0.1922 (mt) REVERT: H 183 MET cc_start: 0.0929 (mmm) cc_final: -0.0183 (pmm) REVERT: I 26 MET cc_start: -0.1171 (tpt) cc_final: -0.1576 (mmt) REVERT: I 160 LYS cc_start: 0.1274 (ttmt) cc_final: 0.0818 (ttmt) REVERT: J 134 MET cc_start: 0.3682 (OUTLIER) cc_final: 0.3427 (mtt) REVERT: J 183 MET cc_start: 0.1011 (pmm) cc_final: 0.0792 (pmm) REVERT: K 44 MET cc_start: 0.1057 (ptt) cc_final: 0.0768 (ptt) REVERT: K 153 MET cc_start: 0.2733 (tpp) cc_final: 0.0413 (mtt) REVERT: F 26 MET cc_start: -0.0862 (tpt) cc_final: -0.1195 (mmt) outliers start: 38 outliers final: 28 residues processed: 181 average time/residue: 0.2663 time to fit residues: 76.6148 Evaluate side-chains 178 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 42 MET Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 159 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 213 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 125 optimal weight: 0.0870 chunk 186 optimal weight: 0.2980 chunk 123 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN G 45 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1567 moved from start: 0.6658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 18134 Z= 0.204 Angle : 0.640 10.846 24544 Z= 0.331 Chirality : 0.043 0.194 2947 Planarity : 0.005 0.052 3103 Dihedral : 6.735 78.072 2537 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.41 % Favored : 94.55 % Rotamer: Outliers : 2.20 % Allowed : 11.20 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.17), residues: 2310 helix: 0.24 (0.16), residues: 1090 sheet: -0.78 (0.29), residues: 288 loop : -1.43 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 212 HIS 0.003 0.001 HIS L 207 PHE 0.020 0.002 PHE J 22 TYR 0.022 0.002 TYR H 145 ARG 0.011 0.001 ARG L 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 156 time to evaluate : 2.103 Fit side-chains revert: symmetry clash REVERT: A 234 ARG cc_start: 0.5301 (mtt-85) cc_final: 0.4350 (mmp-170) REVERT: E 141 ASP cc_start: 0.0838 (OUTLIER) cc_final: -0.1898 (p0) REVERT: E 157 LYS cc_start: 0.1362 (ttmt) cc_final: 0.0664 (tptp) REVERT: G 183 MET cc_start: 0.1278 (ptt) cc_final: 0.0795 (mtm) REVERT: H 60 MET cc_start: 0.1875 (mmm) cc_final: 0.0246 (mmm) REVERT: H 183 MET cc_start: 0.0880 (mmm) cc_final: 0.0050 (pmm) REVERT: I 160 LYS cc_start: 0.1557 (ttmt) cc_final: 0.1239 (ttmt) REVERT: J 134 MET cc_start: 0.3453 (OUTLIER) cc_final: 0.3122 (mtt) REVERT: J 183 MET cc_start: 0.1399 (pmm) cc_final: 0.1161 (pmm) REVERT: K 44 MET cc_start: 0.1275 (ptt) cc_final: 0.0982 (ptt) REVERT: K 153 MET cc_start: 0.2560 (tpp) cc_final: 0.0340 (mtt) REVERT: F 160 LYS cc_start: 0.0481 (ttmt) cc_final: 0.0117 (tppt) outliers start: 43 outliers final: 35 residues processed: 184 average time/residue: 0.2863 time to fit residues: 82.7250 Evaluate side-chains 187 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 42 MET Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 159 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 136 optimal weight: 0.0170 chunk 88 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 173 optimal weight: 0.0770 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1462 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18134 Z= 0.143 Angle : 0.585 12.393 24544 Z= 0.300 Chirality : 0.041 0.159 2947 Planarity : 0.004 0.048 3103 Dihedral : 6.305 74.762 2537 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.29 % Favored : 95.67 % Rotamer: Outliers : 2.10 % Allowed : 11.20 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.17), residues: 2310 helix: 0.46 (0.16), residues: 1091 sheet: -0.69 (0.29), residues: 271 loop : -1.30 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 6 HIS 0.002 0.000 HIS L 207 PHE 0.020 0.001 PHE I 13 TYR 0.021 0.001 TYR L 218 ARG 0.004 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 153 time to evaluate : 1.946 Fit side-chains REVERT: A 234 ARG cc_start: 0.5252 (mtt-85) cc_final: 0.4604 (mmp-170) REVERT: B 83 MET cc_start: 0.4539 (mmm) cc_final: 0.4281 (mmm) REVERT: E 134 MET cc_start: 0.2333 (mmt) cc_final: 0.1578 (mpp) REVERT: E 141 ASP cc_start: 0.0683 (OUTLIER) cc_final: -0.2273 (p0) REVERT: E 157 LYS cc_start: 0.1601 (ttmt) cc_final: 0.0868 (tptp) REVERT: E 183 MET cc_start: 0.1108 (mtt) cc_final: 0.0301 (mtt) REVERT: G 183 MET cc_start: 0.1233 (ptt) cc_final: 0.0816 (mtm) REVERT: H 60 MET cc_start: 0.1553 (mmm) cc_final: 0.0189 (mmm) REVERT: H 183 MET cc_start: 0.0705 (mmm) cc_final: -0.0112 (pmm) REVERT: I 160 LYS cc_start: 0.1536 (ttmt) cc_final: 0.1126 (ttmt) REVERT: J 134 MET cc_start: 0.3333 (OUTLIER) cc_final: 0.2858 (mtt) REVERT: J 183 MET cc_start: 0.1258 (pmm) cc_final: 0.0991 (pmm) REVERT: K 44 MET cc_start: 0.1226 (ptt) cc_final: 0.0951 (ptt) REVERT: K 153 MET cc_start: 0.2368 (tpp) cc_final: 0.0400 (mtt) REVERT: K 171 MET cc_start: -0.0843 (OUTLIER) cc_final: -0.1143 (pmm) REVERT: F 26 MET cc_start: -0.1110 (mmt) cc_final: -0.1631 (mmm) outliers start: 41 outliers final: 34 residues processed: 178 average time/residue: 0.2620 time to fit residues: 74.6078 Evaluate side-chains 185 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 42 MET Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 171 MET Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 159 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 200 optimal weight: 7.9990 chunk 211 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 chunk 205 optimal weight: 0.4980 chunk 123 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 161 optimal weight: 0.0270 chunk 63 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 overall best weight: 1.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN I 151 ASN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN F 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1743 moved from start: 0.7482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18134 Z= 0.233 Angle : 0.705 11.359 24544 Z= 0.361 Chirality : 0.045 0.188 2947 Planarity : 0.005 0.047 3103 Dihedral : 6.837 88.938 2537 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.36 % Favored : 93.59 % Rotamer: Outliers : 2.15 % Allowed : 11.55 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.98 (0.17), residues: 2310 helix: 0.19 (0.16), residues: 1085 sheet: -0.98 (0.30), residues: 277 loop : -1.45 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP A 212 HIS 0.004 0.001 HIS L 207 PHE 0.027 0.002 PHE B 182 TYR 0.033 0.002 TYR L 218 ARG 0.009 0.001 ARG K 195 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 149 time to evaluate : 2.042 Fit side-chains REVERT: A 234 ARG cc_start: 0.5525 (mtt-85) cc_final: 0.4305 (mmt180) REVERT: B 54 LEU cc_start: 0.1782 (OUTLIER) cc_final: 0.0997 (tt) REVERT: E 134 MET cc_start: 0.2455 (mmt) cc_final: 0.1623 (mpp) REVERT: E 141 ASP cc_start: 0.1298 (OUTLIER) cc_final: -0.1172 (m-30) REVERT: E 157 LYS cc_start: 0.1336 (ttmt) cc_final: 0.0543 (tptp) REVERT: E 183 MET cc_start: 0.1570 (mtt) cc_final: 0.1193 (mtt) REVERT: H 60 MET cc_start: 0.3237 (mmm) cc_final: 0.2562 (mmt) REVERT: H 183 MET cc_start: 0.1264 (mmm) cc_final: 0.0323 (pmm) REVERT: I 26 MET cc_start: -0.0858 (mmt) cc_final: -0.1110 (mmt) REVERT: J 134 MET cc_start: 0.3877 (OUTLIER) cc_final: 0.3379 (mtt) REVERT: J 183 MET cc_start: 0.1953 (pmm) cc_final: 0.1678 (pmm) REVERT: K 44 MET cc_start: 0.1546 (ptt) cc_final: 0.1236 (ptt) REVERT: K 153 MET cc_start: 0.2811 (tpp) cc_final: 0.0718 (mtt) REVERT: K 171 MET cc_start: -0.0494 (OUTLIER) cc_final: -0.1018 (pmm) REVERT: F 26 MET cc_start: -0.1075 (mmt) cc_final: -0.1519 (mmm) outliers start: 42 outliers final: 31 residues processed: 178 average time/residue: 0.2419 time to fit residues: 69.7987 Evaluate side-chains 178 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 171 MET Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 135 optimal weight: 8.9990 chunk 217 optimal weight: 0.5980 chunk 132 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 151 optimal weight: 40.0000 chunk 228 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1758 moved from start: 0.7874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18134 Z= 0.207 Angle : 0.668 11.992 24544 Z= 0.338 Chirality : 0.044 0.238 2947 Planarity : 0.005 0.048 3103 Dihedral : 6.654 79.533 2537 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.41 % Favored : 94.55 % Rotamer: Outliers : 1.84 % Allowed : 12.27 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.97 (0.17), residues: 2310 helix: 0.16 (0.16), residues: 1097 sheet: -0.90 (0.30), residues: 274 loop : -1.45 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 212 HIS 0.003 0.000 HIS A 46 PHE 0.022 0.002 PHE J 22 TYR 0.017 0.002 TYR F 158 ARG 0.008 0.001 ARG A 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 2.001 Fit side-chains REVERT: A 234 ARG cc_start: 0.5609 (mtt-85) cc_final: 0.4215 (mmt-90) REVERT: E 134 MET cc_start: 0.1868 (mmt) cc_final: 0.0827 (mpp) REVERT: E 141 ASP cc_start: 0.1769 (OUTLIER) cc_final: -0.0475 (m-30) REVERT: E 157 LYS cc_start: 0.1686 (ttmt) cc_final: 0.0833 (tptp) REVERT: E 183 MET cc_start: 0.1421 (mtt) cc_final: 0.0919 (mtt) REVERT: H 60 MET cc_start: 0.3248 (mmm) cc_final: 0.1781 (mmt) REVERT: H 141 ASP cc_start: 0.1260 (OUTLIER) cc_final: 0.0703 (m-30) REVERT: J 134 MET cc_start: 0.3957 (OUTLIER) cc_final: 0.3494 (mtt) REVERT: J 183 MET cc_start: 0.2008 (pmm) cc_final: 0.1771 (pmm) REVERT: K 44 MET cc_start: 0.2063 (ptt) cc_final: 0.1708 (ptt) REVERT: K 153 MET cc_start: 0.2774 (tpp) cc_final: 0.0759 (mtt) REVERT: K 171 MET cc_start: -0.0846 (OUTLIER) cc_final: -0.1281 (pmm) REVERT: L 31 ILE cc_start: 0.1970 (mm) cc_final: 0.1421 (mm) REVERT: L 79 MET cc_start: 0.3411 (mmm) cc_final: 0.3060 (tpp) REVERT: L 258 TYR cc_start: 0.4631 (OUTLIER) cc_final: 0.2416 (t80) outliers start: 36 outliers final: 29 residues processed: 176 average time/residue: 0.2712 time to fit residues: 76.0983 Evaluate side-chains 182 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain J residue 13 PHE Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 171 MET Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 258 TYR Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 144 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 30.0000 chunk 181 optimal weight: 0.9980 chunk 76 optimal weight: 20.0000 chunk 186 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5579 r_free = 0.5579 target = 0.344969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.5408 r_free = 0.5408 target = 0.319070 restraints weight = 35502.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.5452 r_free = 0.5452 target = 0.324974 restraints weight = 21570.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.5480 r_free = 0.5480 target = 0.329143 restraints weight = 14516.788| |-----------------------------------------------------------------------------| r_work (final): 0.5468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1911 moved from start: 0.8044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18134 Z= 0.168 Angle : 0.623 12.961 24544 Z= 0.316 Chirality : 0.042 0.166 2947 Planarity : 0.004 0.048 3103 Dihedral : 6.476 75.292 2537 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.58 % Favored : 94.37 % Rotamer: Outliers : 1.94 % Allowed : 12.42 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.84 (0.17), residues: 2310 helix: 0.29 (0.16), residues: 1092 sheet: -0.88 (0.30), residues: 275 loop : -1.38 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 212 HIS 0.002 0.000 HIS L 117 PHE 0.025 0.002 PHE A 255 TYR 0.018 0.001 TYR L 218 ARG 0.005 0.000 ARG K 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3250.95 seconds wall clock time: 59 minutes 51.42 seconds (3591.42 seconds total)