Starting phenix.real_space_refine on Mon Dec 11 13:07:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/12_2023/6z5u_11082_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/12_2023/6z5u_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_11082/12_2023/6z5u_11082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/12_2023/6z5u_11082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/12_2023/6z5u_11082_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/12_2023/6z5u_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-1.21rc1-5172/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: 9.40, per 1000 atoms: 0.53 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: 6.91 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: 5.29 Time building geometry restraints manager: 7.50 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: 1.440 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: 4.530 Check model and map are aligned: 0.230 Set scattering table: 0.170 Process input model: 47.470 Find NCS groups from input model: 1.210 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.110 ------------------------------------------------------------------------------- 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 : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 8 residues processed: 280 average time/residue: 0.3159 time to fit residues: 132.7739 Evaluate side-chains 176 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 1.963 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1678 time to fit residues: 5.3925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 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: 1.5742 ------------------------------------------------------------------------------- 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 K 207 HIS ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0688 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 18134 Z= 0.268 Angle : 0.811 10.741 24544 Z= 0.436 Chirality : 0.048 0.395 2947 Planarity : 0.006 0.044 3103 Dihedral : 8.866 71.315 2531 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.43 % Allowed : 5.42 % Favored : 93.15 % 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: -0.27 (0.16), residues: 2310 helix: 0.25 (0.15), residues: 1078 sheet: 0.46 (0.30), residues: 259 loop : -0.73 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 146 HIS 0.003 0.001 HIS K 207 PHE 0.047 0.003 PHE J 22 TYR 0.026 0.003 TYR L 220 ARG 0.006 0.001 ARG J 78 *********************** 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 213 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 203 average time/residue: 0.2997 time to fit residues: 93.8403 Evaluate side-chains 177 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.837 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2175 time to fit residues: 8.5819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 173 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 208 optimal weight: 0.0370 chunk 225 optimal weight: 0.8980 chunk 185 optimal weight: 9.9990 chunk 206 optimal weight: 0.7980 chunk 71 optimal weight: 0.0470 chunk 167 optimal weight: 6.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 GLN L 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0692 moved from start: 0.3696 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= 0.180 Angle : 0.647 13.023 24544 Z= 0.341 Chirality : 0.043 0.186 2947 Planarity : 0.005 0.048 3103 Dihedral : 6.908 55.881 2531 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.97 % Allowed : 6.24 % Favored : 92.79 % 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: -0.18 (0.17), residues: 2310 helix: 0.42 (0.16), residues: 1082 sheet: 0.36 (0.29), residues: 265 loop : -0.77 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 183 HIS 0.002 0.000 HIS D 48 PHE 0.036 0.002 PHE J 22 TYR 0.018 0.001 TYR E 145 ARG 0.003 0.000 ARG F 172 *********************** 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 201 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 194 average time/residue: 0.2854 time to fit residues: 85.2652 Evaluate side-chains 173 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.719 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1573 time to fit residues: 6.2042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 209 optimal weight: 30.0000 chunk 221 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 198 optimal weight: 0.0020 chunk 59 optimal weight: 20.0000 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0828 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18134 Z= 0.159 Angle : 0.609 11.527 24544 Z= 0.317 Chirality : 0.042 0.205 2947 Planarity : 0.005 0.054 3103 Dihedral : 6.008 58.756 2531 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.72 % Allowed : 8.13 % Favored : 91.16 % 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: -0.12 (0.17), residues: 2310 helix: 0.56 (0.16), residues: 1086 sheet: 0.22 (0.30), residues: 265 loop : -0.83 (0.19), residues: 959 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 0.026 0.002 PHE J 22 TYR 0.013 0.001 TYR L 218 ARG 0.005 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 183 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 169 time to evaluate : 1.878 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 174 average time/residue: 0.2718 time to fit residues: 75.1384 Evaluate side-chains 161 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 1.929 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1722 time to fit residues: 5.5219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 184 optimal weight: 0.0040 chunk 125 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 198 optimal weight: 0.0020 chunk 55 optimal weight: 0.2980 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN D 63 GLN H 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0910 moved from start: 0.4707 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= 0.149 Angle : 0.585 12.286 24544 Z= 0.305 Chirality : 0.041 0.177 2947 Planarity : 0.004 0.042 3103 Dihedral : 5.653 60.645 2531 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.61 % Allowed : 9.41 % Favored : 89.98 % 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: -0.07 (0.17), residues: 2310 helix: 0.67 (0.16), residues: 1080 sheet: 0.07 (0.31), residues: 259 loop : -0.81 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 6 HIS 0.001 0.000 HIS L 117 PHE 0.021 0.002 PHE I 13 TYR 0.018 0.001 TYR E 158 ARG 0.005 0.000 ARG H 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 171 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 166 average time/residue: 0.2714 time to fit residues: 72.4406 Evaluate side-chains 156 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 1.710 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1538 time to fit residues: 4.9636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 74 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 30.0000 chunk 221 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 102 optimal weight: 0.0870 chunk 18 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 116 optimal weight: 20.0000 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.0994 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18134 Z= 0.143 Angle : 0.572 12.070 24544 Z= 0.296 Chirality : 0.041 0.208 2947 Planarity : 0.004 0.040 3103 Dihedral : 5.522 57.369 2531 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % Rotamer: Outliers : 0.66 % Allowed : 9.66 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2310 helix: 0.76 (0.16), residues: 1078 sheet: -0.01 (0.30), residues: 262 loop : -0.83 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 6 HIS 0.001 0.000 HIS C 71 PHE 0.022 0.002 PHE J 22 TYR 0.022 0.001 TYR L 218 ARG 0.009 0.000 ARG L 36 *********************** 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 164 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 158 average time/residue: 0.2654 time to fit residues: 68.1981 Evaluate side-chains 150 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 1.862 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2699 time to fit residues: 5.2141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 213 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 126 optimal weight: 0.0050 chunk 161 optimal weight: 0.2980 chunk 125 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 220 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 134 optimal weight: 30.0000 chunk 101 optimal weight: 5.9990 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1230 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18134 Z= 0.191 Angle : 0.635 11.350 24544 Z= 0.327 Chirality : 0.043 0.256 2947 Planarity : 0.005 0.042 3103 Dihedral : 5.787 62.703 2531 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 0.66 % Allowed : 10.69 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.17), residues: 2310 helix: 0.66 (0.16), residues: 1074 sheet: -0.18 (0.31), residues: 253 loop : -1.04 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 212 HIS 0.003 0.001 HIS L 207 PHE 0.020 0.002 PHE J 84 TYR 0.019 0.002 TYR J 158 ARG 0.007 0.001 ARG F 172 *********************** 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 168 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 161 average time/residue: 0.2853 time to fit residues: 72.7542 Evaluate side-chains 151 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 1.863 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1553 time to fit residues: 4.8588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 136 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 66 optimal weight: 0.0770 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 173 optimal weight: 0.9980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 ASN B 198 ASN G 45 GLN L 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1211 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18134 Z= 0.142 Angle : 0.573 11.697 24544 Z= 0.296 Chirality : 0.042 0.357 2947 Planarity : 0.004 0.045 3103 Dihedral : 5.642 65.680 2531 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 0.41 % Allowed : 10.89 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2310 helix: 0.75 (0.16), residues: 1083 sheet: -0.33 (0.30), residues: 270 loop : -1.02 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 6 HIS 0.002 0.000 HIS K 207 PHE 0.022 0.002 PHE J 84 TYR 0.015 0.001 TYR L 218 ARG 0.006 0.000 ARG F 172 *********************** 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 155 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 151 average time/residue: 0.2717 time to fit residues: 66.4291 Evaluate side-chains 142 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.870 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2713 time to fit residues: 4.3134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 123 optimal weight: 0.0670 chunk 89 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 204 optimal weight: 0.9990 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1269 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18134 Z= 0.154 Angle : 0.580 11.216 24544 Z= 0.301 Chirality : 0.042 0.296 2947 Planarity : 0.004 0.050 3103 Dihedral : 5.648 70.232 2531 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 0.46 % Allowed : 11.15 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2310 helix: 0.77 (0.16), residues: 1080 sheet: -0.33 (0.31), residues: 264 loop : -1.07 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 212 HIS 0.002 0.000 HIS L 117 PHE 0.024 0.002 PHE J 22 TYR 0.015 0.001 TYR J 158 ARG 0.006 0.000 ARG F 172 *********************** 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 150 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 146 average time/residue: 0.2701 time to fit residues: 63.6487 Evaluate side-chains 143 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 138 time to evaluate : 1.820 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2654 time to fit residues: 4.7761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 135 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 103 optimal weight: 0.4980 chunk 151 optimal weight: 50.0000 chunk 228 optimal weight: 0.0370 chunk 209 optimal weight: 0.3980 chunk 181 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 111 optimal weight: 0.3980 overall best weight: 0.4660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1234 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18134 Z= 0.137 Angle : 0.573 12.389 24544 Z= 0.294 Chirality : 0.042 0.262 2947 Planarity : 0.004 0.057 3103 Dihedral : 5.506 70.169 2531 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.84 % Rotamer: Outliers : 0.15 % Allowed : 11.25 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.17), residues: 2310 helix: 0.88 (0.16), residues: 1080 sheet: -0.47 (0.30), residues: 270 loop : -1.01 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 212 HIS 0.001 0.000 HIS L 117 PHE 0.025 0.001 PHE J 22 TYR 0.012 0.001 TYR L 218 ARG 0.005 0.000 ARG F 172 ********************** 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 144 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 142 average time/residue: 0.2801 time to fit residues: 64.1147 Evaluate side-chains 139 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1864 time to fit residues: 3.1035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 144 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 167 optimal weight: 0.0020 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 181 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 186 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5597 r_free = 0.5597 target = 0.349098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5462 r_free = 0.5462 target = 0.326558 restraints weight = 34864.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5510 r_free = 0.5510 target = 0.333143 restraints weight = 20814.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.5524 r_free = 0.5524 target = 0.337036 restraints weight = 13299.183| |-----------------------------------------------------------------------------| r_work (final): 0.5515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1282 moved from start: 0.6643 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= 0.135 Angle : 0.565 11.363 24544 Z= 0.291 Chirality : 0.041 0.229 2947 Planarity : 0.004 0.058 3103 Dihedral : 5.427 70.918 2531 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.41 % Rotamer: Outliers : 0.05 % Allowed : 11.50 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.18), residues: 2310 helix: 0.92 (0.16), residues: 1079 sheet: -0.47 (0.30), residues: 270 loop : -0.98 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 212 HIS 0.001 0.000 HIS L 117 PHE 0.024 0.001 PHE J 22 TYR 0.011 0.001 TYR L 218 ARG 0.005 0.000 ARG F 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3065.07 seconds wall clock time: 57 minutes 16.40 seconds (3436.40 seconds total)