Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 01:00:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx5_21430/08_2023/6vx5_21430.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx5_21430/08_2023/6vx5_21430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx5_21430/08_2023/6vx5_21430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx5_21430/08_2023/6vx5_21430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx5_21430/08_2023/6vx5_21430.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx5_21430/08_2023/6vx5_21430.pdb" } resolution = 3.03 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= 0.002 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 90 5.16 5 Cl 1 4.86 5 C 8565 2.51 5 N 2140 2.21 5 O 2260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 34": "NH1" <-> "NH2" Residue "E PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 165": "NH1" <-> "NH2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E GLU 213": "OE1" <-> "OE2" Residue "E PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 259": "OD1" <-> "OD2" Residue "E ASP 268": "OD1" <-> "OD2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C ASP 70": "OD1" <-> "OD2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 259": "OD1" <-> "OD2" Residue "C ASP 268": "OD1" <-> "OD2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 259": "OD1" <-> "OD2" Residue "B ASP 268": "OD1" <-> "OD2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D ASP 268": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 13056 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2611 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain: "C" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2611 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2611 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain: "A" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2611 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain: "D" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2611 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.38, per 1000 atoms: 0.49 Number of scatterers: 13056 At special positions: 0 Unit cell: (92.96, 92.96, 109.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 90 16.00 O 2260 8.00 N 2140 7.00 C 8565 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: 5.10 Conformation dependent library (CDL) restraints added in 1.9 seconds 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2990 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 74.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'E' and resid 28 through 44 removed outlier: 3.879A pdb=" N TRP E 33 " --> pdb=" O TYR E 29 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 53 removed outlier: 3.514A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR E 50 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 64 removed outlier: 4.193A pdb=" N TYR E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS E 64 " --> pdb=" O ARG E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 4.297A pdb=" N VAL E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 88 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER E 99 " --> pdb=" O ASN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.907A pdb=" N CYS E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.516A pdb=" N ARG E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 149 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.560A pdb=" N LYS E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.656A pdb=" N CYS E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 230 removed outlier: 3.595A pdb=" N PHE E 217 " --> pdb=" O GLU E 213 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.707A pdb=" N VAL E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU E 249 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 252 " --> pdb=" O PHE E 248 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG E 255 " --> pdb=" O CYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.937A pdb=" N GLN E 262 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY E 263 " --> pdb=" O PRO E 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 259 through 263' Processing helix chain 'E' and resid 274 through 279 removed outlier: 3.593A pdb=" N LEU E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU E 279 " --> pdb=" O ILE E 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 274 through 279' Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.778A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 322 removed outlier: 3.519A pdb=" N SER E 318 " --> pdb=" O CYS E 314 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 44 removed outlier: 3.880A pdb=" N TRP C 33 " --> pdb=" O TYR C 29 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 53 removed outlier: 3.514A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 64 removed outlier: 4.193A pdb=" N TYR C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 99 removed outlier: 4.297A pdb=" N VAL C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 88 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.907A pdb=" N CYS C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.517A pdb=" N ARG C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.560A pdb=" N LYS C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.657A pdb=" N CYS C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 230 removed outlier: 3.596A pdb=" N PHE C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.708A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU C 249 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 252 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 255 " --> pdb=" O CYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.937A pdb=" N GLN C 262 " --> pdb=" O ASP C 259 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C 263 " --> pdb=" O PRO C 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 263' Processing helix chain 'C' and resid 274 through 279 removed outlier: 3.594A pdb=" N LEU C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C 279 " --> pdb=" O ILE C 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 274 through 279' Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.778A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 322 removed outlier: 3.519A pdb=" N SER C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.880A pdb=" N TRP B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 removed outlier: 3.515A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 64 removed outlier: 4.193A pdb=" N TYR B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 64 " --> pdb=" O ARG B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 4.297A pdb=" N VAL B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 88 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.907A pdb=" N CYS B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.516A pdb=" N ARG B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.560A pdb=" N LYS B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.657A pdb=" N CYS B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 230 removed outlier: 3.595A pdb=" N PHE B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.707A pdb=" N VAL B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU B 249 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 255 " --> pdb=" O CYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.936A pdb=" N GLN B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 263 " --> pdb=" O PRO B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 259 through 263' Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.594A pdb=" N LEU B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 279' Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.778A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.519A pdb=" N SER B 318 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 44 removed outlier: 3.879A pdb=" N TRP A 33 " --> pdb=" O TYR A 29 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.515A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 4.194A pdb=" N TYR A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 64 " --> pdb=" O ARG A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 4.297A pdb=" N VAL A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.907A pdb=" N CYS A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.517A pdb=" N ARG A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.559A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.657A pdb=" N CYS A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 230 removed outlier: 3.595A pdb=" N PHE A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.707A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 255 " --> pdb=" O CYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.937A pdb=" N GLN A 262 " --> pdb=" O ASP A 259 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A 263 " --> pdb=" O PRO A 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 263' Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.594A pdb=" N LEU A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 279 " --> pdb=" O ILE A 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 279' Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.778A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.520A pdb=" N SER A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 44 removed outlier: 3.880A pdb=" N TRP D 33 " --> pdb=" O TYR D 29 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 53 removed outlier: 3.516A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 64 removed outlier: 4.193A pdb=" N TYR D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS D 64 " --> pdb=" O ARG D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 removed outlier: 4.297A pdb=" N VAL D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 88 " --> pdb=" O PHE D 84 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER D 99 " --> pdb=" O ASN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.907A pdb=" N CYS D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.517A pdb=" N ARG D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE D 139 " --> pdb=" O SER D 135 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.560A pdb=" N LYS D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.657A pdb=" N CYS D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 230 removed outlier: 3.595A pdb=" N PHE D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.707A pdb=" N VAL D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU D 249 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 252 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 255 " --> pdb=" O CYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.937A pdb=" N GLN D 262 " --> pdb=" O ASP D 259 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY D 263 " --> pdb=" O PRO D 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 259 through 263' Processing helix chain 'D' and resid 274 through 279 removed outlier: 3.594A pdb=" N LEU D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 274 through 279' Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.778A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 322 removed outlier: 3.520A pdb=" N SER D 318 " --> pdb=" O CYS D 314 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 2040 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: 3.41 Time building geometry restraints manager: 5.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3510 1.33 - 1.45: 2822 1.45 - 1.57: 6948 1.57 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 13415 Sorted by residual: bond pdb=" N VAL E 183 " pdb=" CA VAL E 183 " ideal model delta sigma weight residual 1.463 1.497 -0.034 1.20e-02 6.94e+03 7.92e+00 bond pdb=" N VAL C 183 " pdb=" CA VAL C 183 " ideal model delta sigma weight residual 1.463 1.497 -0.034 1.20e-02 6.94e+03 7.83e+00 bond pdb=" N CYS A 272 " pdb=" CA CYS A 272 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.32e-02 5.74e+03 7.82e+00 bond pdb=" N VAL D 183 " pdb=" CA VAL D 183 " ideal model delta sigma weight residual 1.463 1.496 -0.033 1.20e-02 6.94e+03 7.77e+00 bond pdb=" N CYS E 272 " pdb=" CA CYS E 272 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.32e-02 5.74e+03 7.76e+00 ... (remaining 13410 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.18: 223 106.18 - 113.22: 6964 113.22 - 120.25: 5662 120.25 - 127.28: 5196 127.28 - 134.31: 145 Bond angle restraints: 18190 Sorted by residual: angle pdb=" CA VAL E 183 " pdb=" C VAL E 183 " pdb=" N PRO E 184 " ideal model delta sigma weight residual 120.83 122.81 -1.98 6.10e-01 2.69e+00 1.06e+01 angle pdb=" CA VAL D 183 " pdb=" C VAL D 183 " pdb=" N PRO D 184 " ideal model delta sigma weight residual 120.83 122.80 -1.97 6.10e-01 2.69e+00 1.05e+01 angle pdb=" CA VAL A 183 " pdb=" C VAL A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 120.83 122.79 -1.96 6.10e-01 2.69e+00 1.03e+01 angle pdb=" CA VAL B 183 " pdb=" C VAL B 183 " pdb=" N PRO B 184 " ideal model delta sigma weight residual 120.83 122.79 -1.96 6.10e-01 2.69e+00 1.03e+01 angle pdb=" CA VAL C 183 " pdb=" C VAL C 183 " pdb=" N PRO C 184 " ideal model delta sigma weight residual 120.83 122.77 -1.94 6.10e-01 2.69e+00 1.01e+01 ... (remaining 18185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7020 17.79 - 35.58: 655 35.58 - 53.37: 65 53.37 - 71.17: 25 71.17 - 88.96: 15 Dihedral angle restraints: 7780 sinusoidal: 3125 harmonic: 4655 Sorted by residual: dihedral pdb=" CA ARG B 200 " pdb=" C ARG B 200 " pdb=" N ILE B 201 " pdb=" CA ILE B 201 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ARG A 200 " pdb=" C ARG A 200 " pdb=" N ILE A 201 " pdb=" CA ILE A 201 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ARG E 200 " pdb=" C ARG E 200 " pdb=" N ILE E 201 " pdb=" CA ILE E 201 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 7777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1496 0.056 - 0.113: 403 0.113 - 0.169: 47 0.169 - 0.225: 9 0.225 - 0.281: 10 Chirality restraints: 1965 Sorted by residual: chirality pdb=" CA VAL E 273 " pdb=" N VAL E 273 " pdb=" C VAL E 273 " pdb=" CB VAL E 273 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA VAL C 273 " pdb=" N VAL C 273 " pdb=" C VAL C 273 " pdb=" CB VAL C 273 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ASP C 266 " pdb=" N ASP C 266 " pdb=" C ASP C 266 " pdb=" CB ASP C 266 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 1962 not shown) Planarity restraints: 2275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 80 " 0.017 2.00e-02 2.50e+03 1.30e-02 2.95e+00 pdb=" CG PHE A 80 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 80 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 80 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 80 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 80 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 80 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 80 " -0.017 2.00e-02 2.50e+03 1.29e-02 2.90e+00 pdb=" CG PHE C 80 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE C 80 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE C 80 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE C 80 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 80 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE C 80 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 80 " -0.017 2.00e-02 2.50e+03 1.27e-02 2.84e+00 pdb=" CG PHE D 80 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE D 80 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE D 80 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE D 80 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 80 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE D 80 " -0.004 2.00e-02 2.50e+03 ... (remaining 2272 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4696 2.86 - 3.37: 12172 3.37 - 3.88: 21364 3.88 - 4.39: 26898 4.39 - 4.90: 43584 Nonbonded interactions: 108714 Sorted by model distance: nonbonded pdb=" O THR D 237 " pdb=" OG1 THR D 241 " model vdw 2.348 2.440 nonbonded pdb=" O THR E 237 " pdb=" OG1 THR E 241 " model vdw 2.348 2.440 nonbonded pdb=" O THR B 237 " pdb=" OG1 THR B 241 " model vdw 2.348 2.440 nonbonded pdb=" O THR A 237 " pdb=" OG1 THR A 241 " model vdw 2.348 2.440 nonbonded pdb=" O THR C 237 " pdb=" OG1 THR C 241 " model vdw 2.348 2.440 ... (remaining 108709 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' and resid 26 through 340) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.000 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: 14.120 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 33.820 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.006 0.043 13415 Z= 0.407 Angle : 0.796 8.001 18190 Z= 0.437 Chirality : 0.054 0.281 1965 Planarity : 0.004 0.035 2275 Dihedral : 14.271 88.957 4790 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.15 (0.13), residues: 1565 helix: -4.43 (0.06), residues: 1085 sheet: None (None), residues: 0 loop : -2.51 (0.24), residues: 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.441 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.2671 time to fit residues: 103.9142 Evaluate side-chains 224 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.492 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN E 91 HIS E 194 GLN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN E 296 ASN E 316 GLN C 58 GLN C 194 GLN B 58 GLN B 91 HIS B 194 GLN B 238 GLN A 58 GLN A 91 HIS A 194 GLN A 293 GLN A 296 ASN D 58 GLN D 91 HIS D 194 GLN D 293 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 13415 Z= 0.221 Angle : 0.582 8.602 18190 Z= 0.304 Chirality : 0.040 0.149 1965 Planarity : 0.004 0.030 2275 Dihedral : 4.767 18.385 1770 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.16), residues: 1565 helix: -2.27 (0.12), residues: 1105 sheet: None (None), residues: 0 loop : -2.68 (0.24), residues: 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 267 time to evaluate : 1.457 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 278 average time/residue: 0.2399 time to fit residues: 98.0647 Evaluate side-chains 261 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 251 time to evaluate : 1.459 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1216 time to fit residues: 4.2274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 30.0000 chunk 95 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 139 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 GLN E 293 GLN E 296 ASN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN A 293 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 HIS ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 GLN D 296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 13415 Z= 0.212 Angle : 0.526 8.656 18190 Z= 0.274 Chirality : 0.039 0.149 1965 Planarity : 0.003 0.031 2275 Dihedral : 4.419 17.085 1770 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.19), residues: 1565 helix: -1.17 (0.14), residues: 1125 sheet: None (None), residues: 0 loop : -2.44 (0.26), residues: 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 263 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 268 average time/residue: 0.2449 time to fit residues: 94.9424 Evaluate side-chains 260 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 252 time to evaluate : 1.460 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1203 time to fit residues: 3.8246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 0.0000 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 15 optimal weight: 0.0270 chunk 67 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 GLN E 293 GLN C 96 GLN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN B 296 ASN A 96 GLN A 238 GLN A 293 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN D 293 GLN D 296 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 13415 Z= 0.165 Angle : 0.486 7.258 18190 Z= 0.252 Chirality : 0.038 0.149 1965 Planarity : 0.003 0.031 2275 Dihedral : 4.191 15.849 1770 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.20), residues: 1565 helix: -0.60 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : -2.35 (0.26), residues: 435 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 260 time to evaluate : 1.569 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 262 average time/residue: 0.2401 time to fit residues: 92.3836 Evaluate side-chains 260 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 250 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1275 time to fit residues: 4.1709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 0.0670 chunk 2 optimal weight: 0.3980 chunk 111 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 204 ASN E 293 GLN E 296 ASN C 204 ASN C 238 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 238 GLN B 296 ASN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN D 293 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 13415 Z= 0.174 Angle : 0.491 11.249 18190 Z= 0.253 Chirality : 0.039 0.155 1965 Planarity : 0.003 0.033 2275 Dihedral : 4.092 16.210 1770 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.20), residues: 1565 helix: -0.30 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.24 (0.26), residues: 445 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 254 time to evaluate : 1.466 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 255 average time/residue: 0.2351 time to fit residues: 89.0645 Evaluate side-chains 256 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 247 time to evaluate : 1.508 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1273 time to fit residues: 4.0663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.9980 chunk 29 optimal weight: 0.0060 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 149 optimal weight: 0.0980 chunk 124 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 293 GLN C 296 ASN B 91 HIS B 296 ASN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN D 293 GLN D 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 13415 Z= 0.147 Angle : 0.487 9.564 18190 Z= 0.247 Chirality : 0.038 0.150 1965 Planarity : 0.003 0.033 2275 Dihedral : 3.964 14.595 1770 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.20), residues: 1565 helix: -0.03 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -2.28 (0.26), residues: 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 252 time to evaluate : 1.391 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 255 average time/residue: 0.2349 time to fit residues: 88.5598 Evaluate side-chains 252 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 247 time to evaluate : 1.375 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1210 time to fit residues: 3.1905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 296 ASN C 238 GLN B 296 ASN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN D 293 GLN D 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 13415 Z= 0.226 Angle : 0.531 10.933 18190 Z= 0.268 Chirality : 0.040 0.148 1965 Planarity : 0.003 0.034 2275 Dihedral : 4.015 15.518 1770 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.21), residues: 1565 helix: 0.07 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.19 (0.27), residues: 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 251 time to evaluate : 1.399 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 252 average time/residue: 0.2364 time to fit residues: 87.9660 Evaluate side-chains 252 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 246 time to evaluate : 1.493 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1285 time to fit residues: 3.4875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 0.0030 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 ASN ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 13415 Z= 0.193 Angle : 0.542 11.457 18190 Z= 0.268 Chirality : 0.039 0.150 1965 Planarity : 0.003 0.031 2275 Dihedral : 3.985 15.028 1770 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.21), residues: 1565 helix: 0.19 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -2.20 (0.26), residues: 450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 253 time to evaluate : 1.506 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 253 average time/residue: 0.2402 time to fit residues: 89.7820 Evaluate side-chains 247 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 244 time to evaluate : 1.456 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1182 time to fit residues: 2.8144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 125 optimal weight: 0.3980 chunk 131 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN C 238 GLN C 296 ASN B 296 ASN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 13415 Z= 0.201 Angle : 0.552 11.607 18190 Z= 0.273 Chirality : 0.040 0.235 1965 Planarity : 0.003 0.033 2275 Dihedral : 3.999 15.472 1770 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.21), residues: 1565 helix: 0.25 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.10 (0.27), residues: 445 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 252 time to evaluate : 1.485 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 257 average time/residue: 0.2409 time to fit residues: 92.6382 Evaluate side-chains 248 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 242 time to evaluate : 1.394 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1465 time to fit residues: 3.5867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 154 optimal weight: 0.0470 chunk 142 optimal weight: 0.4980 chunk 122 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 97 optimal weight: 0.0270 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 ASN B 238 GLN B 296 ASN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 13415 Z= 0.156 Angle : 0.552 11.625 18190 Z= 0.271 Chirality : 0.040 0.258 1965 Planarity : 0.003 0.031 2275 Dihedral : 3.997 19.072 1770 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1565 helix: 0.40 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -2.16 (0.27), residues: 450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 254 time to evaluate : 1.559 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 257 average time/residue: 0.2335 time to fit residues: 90.2589 Evaluate side-chains 251 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 249 time to evaluate : 1.544 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1596 time to fit residues: 2.5997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 15 optimal weight: 0.0870 chunk 22 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 296 ASN C 238 GLN C 262 GLN C 296 ASN B 296 ASN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.162554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103160 restraints weight = 17813.145| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.89 r_work: 0.3184 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13415 Z= 0.171 Angle : 0.569 11.256 18190 Z= 0.278 Chirality : 0.040 0.233 1965 Planarity : 0.003 0.032 2275 Dihedral : 4.041 23.198 1770 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1565 helix: 0.51 (0.16), residues: 1115 sheet: None (None), residues: 0 loop : -2.11 (0.27), residues: 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2949.15 seconds wall clock time: 54 minutes 36.89 seconds (3276.89 seconds total)