Starting phenix.real_space_refine on Fri Mar 15 03:33:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka4_22758/03_2024/7ka4_22758.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka4_22758/03_2024/7ka4_22758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka4_22758/03_2024/7ka4_22758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka4_22758/03_2024/7ka4_22758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka4_22758/03_2024/7ka4_22758.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka4_22758/03_2024/7ka4_22758.pdb" } resolution = 2.8 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= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 1980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 33": "OD1" <-> "OD2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 33": "OD1" <-> "OD2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 195": "OD1" <-> "OD2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10472 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "D" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Time building chain proxies: 6.16, per 1000 atoms: 0.59 Number of scatterers: 10472 At special positions: 0 Unit cell: (97.37, 80.99, 104.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1980 8.00 N 1860 7.00 C 6588 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: 3.46 Conformation dependent library (CDL) restraints added in 1.8 seconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 55.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'B' and resid 8 through 23 removed outlier: 3.521A pdb=" N VAL B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 47 removed outlier: 3.658A pdb=" N ILE B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.544A pdb=" N VAL B 69 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.595A pdb=" N LEU B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 84' Processing helix chain 'B' and resid 92 through 99 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 removed outlier: 3.651A pdb=" N ASN B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 219 removed outlier: 3.509A pdb=" N CYS B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.556A pdb=" N THR B 226 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 258 Processing helix chain 'B' and resid 275 through 288 removed outlier: 3.503A pdb=" N ALA B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.778A pdb=" N GLN B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 319 through 338 Processing helix chain 'A' and resid 8 through 23 removed outlier: 3.522A pdb=" N VAL A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 47 removed outlier: 3.657A pdb=" N ILE A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.544A pdb=" N VAL A 69 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.596A pdb=" N LEU A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 84' Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 removed outlier: 3.651A pdb=" N ASN A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.510A pdb=" N CYS A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.556A pdb=" N THR A 226 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 258 Processing helix chain 'A' and resid 275 through 288 removed outlier: 3.503A pdb=" N ALA A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.777A pdb=" N GLN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 319 through 338 Processing helix chain 'C' and resid 8 through 23 removed outlier: 3.522A pdb=" N VAL C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 47 removed outlier: 3.658A pdb=" N ILE C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.544A pdb=" N VAL C 69 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.596A pdb=" N LEU C 83 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR C 84 " --> pdb=" O HIS C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 84' Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 removed outlier: 3.651A pdb=" N ASN C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 219 removed outlier: 3.509A pdb=" N CYS C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 removed outlier: 3.556A pdb=" N THR C 226 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 Processing helix chain 'C' and resid 275 through 288 removed outlier: 3.503A pdb=" N ALA C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.778A pdb=" N GLN C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 338 Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.522A pdb=" N VAL D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 47 removed outlier: 3.657A pdb=" N ILE D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.545A pdb=" N VAL D 69 " --> pdb=" O ASP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 removed outlier: 3.596A pdb=" N LEU D 83 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 84' Processing helix chain 'D' and resid 92 through 99 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 removed outlier: 3.651A pdb=" N ASN D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 219 removed outlier: 3.509A pdb=" N CYS D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 226 removed outlier: 3.555A pdb=" N THR D 226 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 258 Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.503A pdb=" N ALA D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.777A pdb=" N GLN D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 319 through 338 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.793A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL B 104 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ALA B 145 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE B 106 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TRP B 147 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE B 185 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA B 145 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLU B 187 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP B 147 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU B 189 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N CYS B 149 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU B 191 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU B 151 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.792A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLY A 105 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 76 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LYS A 107 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU A 78 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL A 104 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ALA A 145 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE A 106 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TRP A 147 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ILE A 185 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA A 145 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLU A 187 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N CYS A 149 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU A 191 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.793A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLY C 105 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL C 104 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ALA C 145 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE C 106 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TRP C 147 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE C 185 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA C 145 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLU C 187 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP C 147 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU C 189 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N CYS C 149 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU C 191 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU C 151 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.793A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY D 74 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLY D 105 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL D 76 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LYS D 107 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU D 78 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL D 104 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ALA D 145 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE D 106 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TRP D 147 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ILE D 185 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA D 145 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLU D 187 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP D 147 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU D 189 " --> pdb=" O TRP D 147 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N CYS D 149 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU D 191 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU D 151 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 512 hydrogen bonds defined for protein. 1512 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: 3.04 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3461 1.34 - 1.46: 1733 1.46 - 1.57: 5418 1.57 - 1.69: 4 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" C ASN B 70 " pdb=" N PRO B 71 " ideal model delta sigma weight residual 1.334 1.396 -0.063 2.34e-02 1.83e+03 7.15e+00 bond pdb=" C ASN D 70 " pdb=" N PRO D 71 " ideal model delta sigma weight residual 1.334 1.396 -0.063 2.34e-02 1.83e+03 7.14e+00 bond pdb=" C ASN A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 7.00e+00 bond pdb=" C ASN C 70 " pdb=" N PRO C 71 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 6.98e+00 bond pdb=" CB GLU D 318 " pdb=" CG GLU D 318 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.88e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.06: 356 107.06 - 113.81: 6049 113.81 - 120.55: 4220 120.55 - 127.29: 3726 127.29 - 134.04: 113 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA GLU B 318 " pdb=" CB GLU B 318 " pdb=" CG GLU B 318 " ideal model delta sigma weight residual 114.10 127.10 -13.00 2.00e+00 2.50e-01 4.22e+01 angle pdb=" CA GLU A 318 " pdb=" CB GLU A 318 " pdb=" CG GLU A 318 " ideal model delta sigma weight residual 114.10 127.10 -13.00 2.00e+00 2.50e-01 4.22e+01 angle pdb=" CA GLU C 318 " pdb=" CB GLU C 318 " pdb=" CG GLU C 318 " ideal model delta sigma weight residual 114.10 127.07 -12.97 2.00e+00 2.50e-01 4.21e+01 angle pdb=" CA GLU D 318 " pdb=" CB GLU D 318 " pdb=" CG GLU D 318 " ideal model delta sigma weight residual 114.10 127.07 -12.97 2.00e+00 2.50e-01 4.20e+01 angle pdb=" CB GLU C 318 " pdb=" CG GLU C 318 " pdb=" CD GLU C 318 " ideal model delta sigma weight residual 112.60 119.36 -6.76 1.70e+00 3.46e-01 1.58e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 5900 17.17 - 34.34: 460 34.34 - 51.52: 100 51.52 - 68.69: 36 68.69 - 85.86: 8 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CA LEU D 270 " pdb=" C LEU D 270 " pdb=" N SER D 271 " pdb=" CA SER D 271 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA LEU B 270 " pdb=" C LEU B 270 " pdb=" N SER B 271 " pdb=" CA SER B 271 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA LEU A 270 " pdb=" C LEU A 270 " pdb=" N SER A 271 " pdb=" CA SER A 271 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 876 0.030 - 0.060: 433 0.060 - 0.090: 197 0.090 - 0.119: 106 0.119 - 0.149: 32 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA ASN A 70 " pdb=" N ASN A 70 " pdb=" C ASN A 70 " pdb=" CB ASN A 70 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA ASN C 70 " pdb=" N ASN C 70 " pdb=" C ASN C 70 " pdb=" CB ASN C 70 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ASN D 70 " pdb=" N ASN D 70 " pdb=" C ASN D 70 " pdb=" CB ASN D 70 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 330 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C ARG C 330 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG C 330 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA C 331 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 330 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" C ARG B 330 " 0.051 2.00e-02 2.50e+03 pdb=" O ARG B 330 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA B 331 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 330 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C ARG A 330 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG A 330 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA A 331 " -0.017 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 3743 2.88 - 3.38: 9972 3.38 - 3.89: 18607 3.89 - 4.39: 20834 4.39 - 4.90: 35200 Nonbonded interactions: 88356 Sorted by model distance: nonbonded pdb=" O GLN C 60 " pdb=" OG1 THR C 64 " model vdw 2.372 2.440 nonbonded pdb=" O GLN A 60 " pdb=" OG1 THR A 64 " model vdw 2.372 2.440 nonbonded pdb=" O GLN D 60 " pdb=" OG1 THR D 64 " model vdw 2.372 2.440 nonbonded pdb=" O GLN B 60 " pdb=" OG1 THR B 64 " model vdw 2.373 2.440 nonbonded pdb=" ND2 ASN A 119 " pdb=" OE2 GLU A 155 " model vdw 2.394 2.520 ... (remaining 88351 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' selection = chain 'C' selection = chain 'D' } 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: 1.160 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: 6.240 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.330 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 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:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.005 0.066 10672 Z= 0.349 Angle : 0.885 12.997 14464 Z= 0.498 Chirality : 0.048 0.149 1644 Planarity : 0.008 0.061 1880 Dihedral : 14.056 85.859 3984 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.96 % Allowed : 4.41 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.20 (0.19), residues: 1364 helix: -1.27 (0.15), residues: 680 sheet: -2.08 (0.34), residues: 204 loop : -1.10 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 147 HIS 0.003 0.001 HIS D 156 PHE 0.017 0.003 PHE A 144 TYR 0.015 0.002 TYR C 213 ARG 0.006 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 247 time to evaluate : 1.207 Fit side-chains REVERT: B 124 THR cc_start: 0.8805 (t) cc_final: 0.8555 (m) REVERT: A 124 THR cc_start: 0.8954 (t) cc_final: 0.8744 (m) outliers start: 44 outliers final: 4 residues processed: 274 average time/residue: 1.4162 time to fit residues: 412.5821 Evaluate side-chains 141 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain D residue 175 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 123 optimal weight: 0.2980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 125 GLN B 231 ASN A 44 GLN A 125 GLN A 231 ASN C 44 GLN C 125 GLN C 168 ASN C 231 ASN D 44 GLN D 125 GLN D 231 ASN D 241 GLN D 334 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10672 Z= 0.182 Angle : 0.586 10.099 14464 Z= 0.296 Chirality : 0.042 0.121 1644 Planarity : 0.004 0.034 1880 Dihedral : 5.254 45.926 1476 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.24 % Allowed : 16.55 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.16 (0.22), residues: 1364 helix: 0.84 (0.19), residues: 684 sheet: -2.03 (0.35), residues: 200 loop : -0.41 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 147 HIS 0.001 0.000 HIS C 219 PHE 0.008 0.001 PHE C 144 TYR 0.013 0.001 TYR D 213 ARG 0.002 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 1.128 Fit side-chains REVERT: B 59 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7304 (mpp80) REVERT: A 41 LYS cc_start: 0.8046 (pptt) cc_final: 0.7730 (tmmt) REVERT: C 41 LYS cc_start: 0.8062 (pptt) cc_final: 0.7771 (tmmt) outliers start: 36 outliers final: 16 residues processed: 169 average time/residue: 1.4291 time to fit residues: 257.0277 Evaluate side-chains 139 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 175 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 GLN A 231 ASN ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 231 ASN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 231 ASN D 241 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10672 Z= 0.242 Angle : 0.565 7.692 14464 Z= 0.290 Chirality : 0.043 0.125 1644 Planarity : 0.004 0.034 1880 Dihedral : 4.620 25.025 1476 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.60 % Allowed : 16.55 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.57 (0.23), residues: 1364 helix: 1.55 (0.19), residues: 684 sheet: -1.94 (0.34), residues: 200 loop : -0.13 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 147 HIS 0.003 0.001 HIS A 156 PHE 0.008 0.001 PHE C 144 TYR 0.015 0.002 TYR D 213 ARG 0.003 0.001 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 1.227 Fit side-chains REVERT: B 59 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.6998 (mpp80) REVERT: A 41 LYS cc_start: 0.8142 (pptt) cc_final: 0.7546 (ptmm) REVERT: C 41 LYS cc_start: 0.8151 (pptt) cc_final: 0.7510 (ptmm) REVERT: D 41 LYS cc_start: 0.8075 (pptt) cc_final: 0.7751 (tmmt) outliers start: 40 outliers final: 20 residues processed: 154 average time/residue: 1.4008 time to fit residues: 230.6367 Evaluate side-chains 143 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 GLN A 231 ASN A 334 ASN C 44 GLN C 231 ASN C 334 ASN D 44 GLN D 231 ASN D 241 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10672 Z= 0.171 Angle : 0.510 7.043 14464 Z= 0.262 Chirality : 0.040 0.119 1644 Planarity : 0.003 0.032 1880 Dihedral : 4.163 15.599 1472 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.06 % Allowed : 16.91 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.05 (0.23), residues: 1364 helix: 2.04 (0.20), residues: 684 sheet: -1.85 (0.35), residues: 200 loop : -0.00 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 147 HIS 0.001 0.000 HIS D 196 PHE 0.008 0.001 PHE D 144 TYR 0.012 0.001 TYR A 213 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.256 Fit side-chains REVERT: B 329 LYS cc_start: 0.8010 (mtpt) cc_final: 0.7487 (ptmt) REVERT: A 41 LYS cc_start: 0.8062 (pptt) cc_final: 0.7418 (ptmm) REVERT: A 42 ARG cc_start: 0.7015 (mtt180) cc_final: 0.6423 (ptp-170) REVERT: C 41 LYS cc_start: 0.8055 (pptt) cc_final: 0.7441 (ptmm) REVERT: C 42 ARG cc_start: 0.7026 (mtt180) cc_final: 0.6432 (ptp-170) REVERT: D 41 LYS cc_start: 0.8094 (pptt) cc_final: 0.7746 (tmmt) outliers start: 34 outliers final: 17 residues processed: 157 average time/residue: 1.3672 time to fit residues: 229.6868 Evaluate side-chains 133 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 117 optimal weight: 0.0980 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 GLN A 231 ASN C 44 GLN C 168 ASN C 231 ASN D 44 GLN D 231 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10672 Z= 0.159 Angle : 0.505 6.878 14464 Z= 0.259 Chirality : 0.040 0.119 1644 Planarity : 0.003 0.031 1880 Dihedral : 3.974 13.741 1472 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.87 % Allowed : 17.54 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.24), residues: 1364 helix: 2.34 (0.20), residues: 684 sheet: -1.84 (0.35), residues: 200 loop : 0.13 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 147 HIS 0.001 0.000 HIS A 219 PHE 0.008 0.001 PHE D 144 TYR 0.013 0.001 TYR A 301 ARG 0.010 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 134 time to evaluate : 1.239 Fit side-chains REVERT: B 329 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7662 (ptmt) REVERT: A 41 LYS cc_start: 0.8037 (pptt) cc_final: 0.7432 (ptmm) REVERT: C 41 LYS cc_start: 0.8054 (pptt) cc_final: 0.7423 (ptmm) REVERT: D 41 LYS cc_start: 0.8068 (pptt) cc_final: 0.7771 (tmmt) REVERT: D 189 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6673 (tp30) outliers start: 43 outliers final: 19 residues processed: 163 average time/residue: 1.4207 time to fit residues: 247.1943 Evaluate side-chains 139 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 131 optimal weight: 0.0270 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.0050 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 overall best weight: 0.3052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN B 334 ASN A 44 GLN A 231 ASN A 334 ASN C 44 GLN C 231 ASN D 44 GLN D 231 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10672 Z= 0.141 Angle : 0.496 6.928 14464 Z= 0.253 Chirality : 0.040 0.129 1644 Planarity : 0.003 0.031 1880 Dihedral : 3.769 13.461 1472 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.78 % Allowed : 18.17 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.59 (0.24), residues: 1364 helix: 2.56 (0.20), residues: 684 sheet: -1.85 (0.35), residues: 200 loop : 0.26 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 295 HIS 0.002 0.000 HIS A 219 PHE 0.008 0.001 PHE B 144 TYR 0.013 0.001 TYR D 327 ARG 0.009 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 141 time to evaluate : 1.253 Fit side-chains REVERT: B 95 GLN cc_start: 0.7962 (tp-100) cc_final: 0.7714 (tp40) REVERT: B 189 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6638 (tp30) REVERT: B 329 LYS cc_start: 0.8026 (mtpt) cc_final: 0.7718 (ptmt) REVERT: A 41 LYS cc_start: 0.8006 (pptt) cc_final: 0.7390 (ptmm) REVERT: A 189 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6669 (tp30) REVERT: C 41 LYS cc_start: 0.8011 (pptt) cc_final: 0.7381 (ptmm) REVERT: C 189 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6634 (tp30) REVERT: D 41 LYS cc_start: 0.8025 (pptt) cc_final: 0.7766 (tmmt) REVERT: D 189 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6609 (tp30) outliers start: 42 outliers final: 16 residues processed: 173 average time/residue: 1.3890 time to fit residues: 257.4573 Evaluate side-chains 136 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 ASN B 231 ASN A 44 GLN A 168 ASN A 231 ASN C 44 GLN C 168 ASN C 231 ASN C 334 ASN D 44 GLN D 168 ASN D 231 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10672 Z= 0.178 Angle : 0.514 7.218 14464 Z= 0.261 Chirality : 0.041 0.188 1644 Planarity : 0.004 0.047 1880 Dihedral : 3.803 13.344 1472 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.15 % Allowed : 18.26 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.68 (0.24), residues: 1364 helix: 2.63 (0.20), residues: 684 sheet: -1.81 (0.35), residues: 200 loop : 0.31 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 147 HIS 0.001 0.000 HIS A 2 PHE 0.007 0.001 PHE D 144 TYR 0.015 0.001 TYR A 327 ARG 0.012 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 121 time to evaluate : 1.259 Fit side-chains REVERT: B 189 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6644 (tp30) REVERT: A 41 LYS cc_start: 0.8014 (pptt) cc_final: 0.7456 (ptmm) REVERT: A 329 LYS cc_start: 0.8135 (ptmt) cc_final: 0.7835 (ptmm) REVERT: C 41 LYS cc_start: 0.8008 (pptt) cc_final: 0.7454 (ptmm) REVERT: D 41 LYS cc_start: 0.8029 (pptt) cc_final: 0.7783 (tmmt) outliers start: 35 outliers final: 17 residues processed: 149 average time/residue: 1.2294 time to fit residues: 197.6700 Evaluate side-chains 136 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN A 44 GLN A 231 ASN C 44 GLN C 231 ASN D 44 GLN D 231 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10672 Z= 0.178 Angle : 0.517 7.288 14464 Z= 0.263 Chirality : 0.041 0.139 1644 Planarity : 0.003 0.031 1880 Dihedral : 3.808 13.598 1472 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.24 % Allowed : 18.62 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.67 (0.24), residues: 1364 helix: 2.61 (0.20), residues: 684 sheet: -1.82 (0.35), residues: 200 loop : 0.32 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 147 HIS 0.001 0.000 HIS A 2 PHE 0.007 0.001 PHE D 144 TYR 0.013 0.001 TYR A 213 ARG 0.006 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6721 (tp30) REVERT: A 329 LYS cc_start: 0.8142 (ptmt) cc_final: 0.7886 (ptmm) REVERT: C 189 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6695 (tp30) REVERT: D 41 LYS cc_start: 0.8056 (pptt) cc_final: 0.7804 (tmmt) REVERT: D 189 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6677 (tp30) outliers start: 36 outliers final: 20 residues processed: 158 average time/residue: 1.2762 time to fit residues: 216.9515 Evaluate side-chains 148 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 ASN B 231 ASN A 44 GLN A 231 ASN A 334 ASN C 44 GLN C 168 ASN C 231 ASN C 334 ASN D 44 GLN D 231 ASN D 241 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10672 Z= 0.235 Angle : 0.558 7.688 14464 Z= 0.283 Chirality : 0.042 0.144 1644 Planarity : 0.004 0.032 1880 Dihedral : 3.982 14.320 1472 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.88 % Allowed : 18.44 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.50 (0.24), residues: 1364 helix: 2.46 (0.20), residues: 684 sheet: -1.86 (0.34), residues: 200 loop : 0.23 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 147 HIS 0.002 0.001 HIS C 4 PHE 0.007 0.001 PHE C 144 TYR 0.016 0.002 TYR A 213 ARG 0.007 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 THR cc_start: 0.7862 (m) cc_final: 0.7632 (t) REVERT: A 189 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6704 (tp30) REVERT: A 329 LYS cc_start: 0.8116 (ptmt) cc_final: 0.7857 (ptmm) REVERT: C 189 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6673 (tp30) REVERT: D 41 LYS cc_start: 0.8061 (pptt) cc_final: 0.7413 (ptmm) REVERT: D 189 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6657 (tp30) outliers start: 32 outliers final: 18 residues processed: 157 average time/residue: 1.2500 time to fit residues: 211.3237 Evaluate side-chains 142 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN A 44 GLN A 231 ASN A 334 ASN C 44 GLN C 231 ASN C 334 ASN D 44 GLN D 231 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10672 Z= 0.206 Angle : 0.548 7.811 14464 Z= 0.279 Chirality : 0.042 0.139 1644 Planarity : 0.003 0.032 1880 Dihedral : 3.960 13.898 1472 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.79 % Allowed : 19.69 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.51 (0.24), residues: 1364 helix: 2.44 (0.20), residues: 688 sheet: -1.88 (0.34), residues: 200 loop : 0.29 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 147 HIS 0.002 0.001 HIS C 4 PHE 0.006 0.001 PHE C 144 TYR 0.015 0.001 TYR B 213 ARG 0.005 0.000 ARG B 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 THR cc_start: 0.7874 (m) cc_final: 0.7641 (t) REVERT: A 41 LYS cc_start: 0.8138 (tmmt) cc_final: 0.7648 (ptmm) REVERT: A 189 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6718 (tp30) REVERT: A 329 LYS cc_start: 0.8137 (ptmt) cc_final: 0.7914 (ptmm) REVERT: C 41 LYS cc_start: 0.8131 (tmmt) cc_final: 0.7507 (ptmm) REVERT: D 41 LYS cc_start: 0.8058 (pptt) cc_final: 0.7428 (ptmm) REVERT: D 189 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6648 (tp30) outliers start: 31 outliers final: 20 residues processed: 147 average time/residue: 1.2161 time to fit residues: 192.8657 Evaluate side-chains 140 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN A 44 GLN A 231 ASN ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 231 ASN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 231 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.140044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114040 restraints weight = 14438.290| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.97 r_work: 0.3386 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10672 Z= 0.225 Angle : 0.560 7.847 14464 Z= 0.285 Chirality : 0.042 0.139 1644 Planarity : 0.004 0.048 1880 Dihedral : 3.991 13.909 1472 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.97 % Allowed : 19.51 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.49 (0.24), residues: 1364 helix: 2.42 (0.20), residues: 688 sheet: -1.87 (0.34), residues: 200 loop : 0.27 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 147 HIS 0.002 0.001 HIS C 4 PHE 0.006 0.001 PHE D 144 TYR 0.016 0.002 TYR A 213 ARG 0.007 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4205.56 seconds wall clock time: 75 minutes 1.46 seconds (4501.46 seconds total)