Starting phenix.real_space_refine on Fri Nov 17 04:55:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/11_2023/6z5u_11082_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/11_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_11082/11_2023/6z5u_11082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/11_2023/6z5u_11082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/11_2023/6z5u_11082_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/11_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-1.21rc1-5144/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: 9.31, per 1000 atoms: 0.52 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: 6.97 Conformation dependent library (CDL) restraints added in 3.7 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: 3.29 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: 5.31 Time building geometry restraints manager: 7.54 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: 10357 18.13 - 36.27: 369 36.27 - 54.40: 120 54.40 - 72.53: 39 72.53 - 90.67: 11 Dihedral angle restraints: 10896 sinusoidal: 4266 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 10893 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: 0.010 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.500 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 49.470 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.120 ------------------------------------------------------------------------------- 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 : 11.905 90.668 6648 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 *********************** 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 : 1.927 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: 0.3191 time to fit residues: 134.5635 Evaluate side-chains 176 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 1.936 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1531 time to fit residues: 4.8851 ------------------------------------------------------------------------------- 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 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: 0.0746 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 18134 Z= 0.268 Angle : 0.788 10.111 24544 Z= 0.423 Chirality : 0.048 0.346 2947 Planarity : 0.006 0.041 3103 Dihedral : 6.160 57.590 2475 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.43 % Allowed : 5.32 % Favored : 93.25 % 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: -0.31 (0.16), residues: 2310 helix: 0.25 (0.15), residues: 1075 sheet: 0.30 (0.30), residues: 261 loop : -0.75 (0.19), residues: 974 *********************** 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 215 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 204 average time/residue: 0.2969 time to fit residues: 94.1347 Evaluate side-chains 177 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 162 time to evaluate : 2.005 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2250 time to fit residues: 8.5387 ------------------------------------------------------------------------------- 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: 0.0020 chunk 173 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 chunk 206 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- 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: 0.0941 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18134 Z= 0.211 Angle : 0.679 12.230 24544 Z= 0.359 Chirality : 0.044 0.179 2947 Planarity : 0.005 0.058 3103 Dihedral : 5.456 49.961 2475 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.23 % Allowed : 6.95 % Favored : 91.82 % 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: -0.40 (0.17), residues: 2310 helix: 0.33 (0.15), residues: 1086 sheet: 0.11 (0.29), residues: 269 loop : -0.98 (0.19), residues: 955 *********************** 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 204 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 195 average time/residue: 0.2999 time to fit residues: 91.9737 Evaluate side-chains 178 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 1.910 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1694 time to fit residues: 7.4678 ------------------------------------------------------------------------------- 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: 0.9980 chunk 156 optimal weight: 0.0770 chunk 108 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 139 optimal weight: 0.0970 chunk 209 optimal weight: 0.0170 chunk 221 optimal weight: 0.0770 chunk 109 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 59 optimal weight: 30.0000 overall best weight: 0.1932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN D 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0874 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18134 Z= 0.144 Angle : 0.592 12.143 24544 Z= 0.309 Chirality : 0.041 0.220 2947 Planarity : 0.004 0.039 3103 Dihedral : 5.055 47.007 2475 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.36 % Allowed : 8.95 % Favored : 90.70 % 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: -0.19 (0.17), residues: 2310 helix: 0.50 (0.16), residues: 1088 sheet: 0.13 (0.29), residues: 271 loop : -0.85 (0.19), residues: 951 *********************** 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 172 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 165 time to evaluate : 2.020 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 169 average time/residue: 0.2828 time to fit residues: 76.7165 Evaluate side-chains 157 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 2.010 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1691 time to fit residues: 4.4237 ------------------------------------------------------------------------------- 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: 2.9990 chunk 125 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 188 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 198 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 139 GLN B 189 ASN K 117 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1192 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18134 Z= 0.204 Angle : 0.665 13.004 24544 Z= 0.343 Chirality : 0.044 0.196 2947 Planarity : 0.005 0.038 3103 Dihedral : 5.047 41.856 2475 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.53 % Allowed : 9.51 % Favored : 88.96 % 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: -0.39 (0.17), residues: 2310 helix: 0.47 (0.16), residues: 1084 sheet: -0.25 (0.30), residues: 254 loop : -1.01 (0.19), residues: 972 *********************** 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 178 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 23 residues processed: 167 average time/residue: 0.2800 time to fit residues: 75.0045 Evaluate side-chains 165 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 1.891 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1907 time to fit residues: 10.4686 ------------------------------------------------------------------------------- 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: 0.9990 chunk 199 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 0.3980 chunk 54 optimal weight: 30.0000 chunk 221 optimal weight: 0.0020 chunk 183 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 116 optimal weight: 20.0000 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN L 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1235 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18134 Z= 0.168 Angle : 0.596 11.307 24544 Z= 0.309 Chirality : 0.042 0.205 2947 Planarity : 0.004 0.042 3103 Dihedral : 4.847 38.222 2475 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.72 % Allowed : 10.17 % Favored : 89.11 % 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: -0.33 (0.17), residues: 2310 helix: 0.58 (0.16), residues: 1077 sheet: -0.19 (0.29), residues: 285 loop : -1.09 (0.19), residues: 948 *********************** 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 168 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 165 average time/residue: 0.2674 time to fit residues: 70.4797 Evaluate side-chains 150 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 1.860 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1614 time to fit residues: 4.5484 ------------------------------------------------------------------------------- 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: 7.9990 chunk 24 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 186 optimal weight: 0.2980 chunk 123 optimal weight: 4.9990 chunk 220 optimal weight: 10.0000 chunk 138 optimal weight: 0.0470 chunk 134 optimal weight: 30.0000 chunk 101 optimal weight: 2.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN B 198 ASN H 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1291 moved from start: 0.6044 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= 0.155 Angle : 0.587 11.281 24544 Z= 0.304 Chirality : 0.041 0.198 2947 Planarity : 0.004 0.040 3103 Dihedral : 4.694 35.918 2475 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 0.51 % Allowed : 11.09 % 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: -0.27 (0.17), residues: 2310 helix: 0.69 (0.16), residues: 1080 sheet: -0.17 (0.30), residues: 270 loop : -1.13 (0.19), residues: 960 *********************** 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 160 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 158 average time/residue: 0.2850 time to fit residues: 71.8776 Evaluate side-chains 151 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1702 time to fit residues: 3.8803 ------------------------------------------------------------------------------- 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: 0.8980 chunk 88 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 0.0060 chunk 140 optimal weight: 0.3980 chunk 150 optimal weight: 4.9990 chunk 109 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 173 optimal weight: 0.0870 overall best weight: 0.3374 ------------------------------------------------------------------------------- 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: 0.1224 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 18134 Z= 0.132 Angle : 0.555 11.793 24544 Z= 0.287 Chirality : 0.041 0.380 2947 Planarity : 0.004 0.046 3103 Dihedral : 4.548 32.424 2475 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 0.46 % Allowed : 11.30 % Favored : 88.24 % 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: -0.11 (0.17), residues: 2310 helix: 0.85 (0.16), residues: 1080 sheet: -0.20 (0.30), residues: 276 loop : -1.06 (0.20), residues: 954 *********************** 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 162 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 159 average time/residue: 0.2914 time to fit residues: 73.3105 Evaluate side-chains 149 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 146 time to evaluate : 1.921 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1770 time to fit residues: 3.8758 ------------------------------------------------------------------------------- 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: 6.9990 chunk 211 optimal weight: 0.6980 chunk 192 optimal weight: 0.1980 chunk 205 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1361 moved from start: 0.6531 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= 0.158 Angle : 0.596 11.202 24544 Z= 0.306 Chirality : 0.042 0.364 2947 Planarity : 0.005 0.048 3103 Dihedral : 4.557 32.866 2475 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.06 % Rotamer: Outliers : 0.20 % Allowed : 11.66 % Favored : 88.14 % 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: 0.82 (0.16), residues: 1077 sheet: -0.37 (0.30), residues: 276 loop : -1.11 (0.20), residues: 957 *********************** 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 156 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 154 average time/residue: 0.2971 time to fit residues: 71.8749 Evaluate side-chains 148 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.908 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1669 time to fit residues: 3.0349 ------------------------------------------------------------------------------- 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: 9.9990 chunk 217 optimal weight: 0.0980 chunk 132 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 151 optimal weight: 50.0000 chunk 228 optimal weight: 0.8980 chunk 209 optimal weight: 8.9990 chunk 181 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 111 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 50 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1331 moved from start: 0.6670 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= 0.133 Angle : 0.565 11.414 24544 Z= 0.289 Chirality : 0.041 0.357 2947 Planarity : 0.004 0.066 3103 Dihedral : 4.441 31.057 2475 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 0.15 % Allowed : 11.76 % Favored : 88.09 % 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: -0.14 (0.17), residues: 2310 helix: 0.88 (0.16), residues: 1075 sheet: -0.40 (0.29), residues: 278 loop : -1.06 (0.20), residues: 957 ********************** 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 152 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 152 average time/residue: 0.3004 time to fit residues: 72.1949 Evaluate side-chains 148 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 1.852 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1651 time to fit residues: 3.3819 ------------------------------------------------------------------------------- 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: 0.9990 chunk 193 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 50.0000 chunk 181 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** G 45 GLN G 50 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5549 r_free = 0.5549 target = 0.347161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5414 r_free = 0.5414 target = 0.323366 restraints weight = 33369.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5458 r_free = 0.5458 target = 0.329568 restraints weight = 20174.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5468 r_free = 0.5468 target = 0.332480 restraints weight = 13706.828| |-----------------------------------------------------------------------------| r_work (final): 0.5500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1499 moved from start: 0.6988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18134 Z= 0.175 Angle : 0.598 10.786 24544 Z= 0.307 Chirality : 0.042 0.357 2947 Planarity : 0.005 0.061 3103 Dihedral : 4.525 32.367 2475 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 0.31 % Allowed : 11.91 % Favored : 87.78 % 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: -0.25 (0.17), residues: 2310 helix: 0.79 (0.16), residues: 1087 sheet: -0.51 (0.30), residues: 272 loop : -1.12 (0.20), residues: 951 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3113.82 seconds wall clock time: 58 minutes 2.22 seconds (3482.22 seconds total)