Starting phenix.real_space_refine on Sun Dec 10 23:47:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y92_10732/12_2023/6y92_10732.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y92_10732/12_2023/6y92_10732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y92_10732/12_2023/6y92_10732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y92_10732/12_2023/6y92_10732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y92_10732/12_2023/6y92_10732.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y92_10732/12_2023/6y92_10732.pdb" } resolution = 4.73 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= 0.003 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6498 atoms to isotropic. 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 50 5.16 5 C 6105 2.51 5 N 1550 2.21 5 O 1792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D ARG 108": "NH1" <-> "NH2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 122": "OD1" <-> "OD2" Residue "D TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 167": "OD1" <-> "OD2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 110": "OD1" <-> "OD2" Residue "C PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 110": "OD1" <-> "OD2" Residue "H PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 153": "OD1" <-> "OD2" Residue "H TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "L ARG 103": "NH1" <-> "NH2" Residue "L ARG 108": "NH1" <-> "NH2" Residue "L PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 122": "OD1" <-> "OD2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 167": "OD1" <-> "OD2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 195": "OE1" <-> "OE2" Residue "L PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9497 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain: "D" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1632 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 198} Chain: "C" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1629 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain breaks: 1 Chain: "H" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1629 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain breaks: 1 Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1632 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 198} Chain: "B" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 121 Unusual residues: {'Y01': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 5.77, per 1000 atoms: 0.61 Number of scatterers: 9497 At special positions: 0 Unit cell: (91, 130, 147, 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 50 16.00 O 1792 8.00 N 1550 7.00 C 6105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 183 " distance=2.03 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.8 seconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 20 sheets defined 22.5% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 49 through 70 removed outlier: 3.924A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N MET A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 85 removed outlier: 4.138A pdb=" N THR A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP A 85 " --> pdb=" O CYS A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 85' Processing helix chain 'A' and resid 85 through 101 removed outlier: 3.559A pdb=" N TRP A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 140 removed outlier: 3.596A pdb=" N ASN A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 183 through 216 Processing helix chain 'D' and resid 121 through 128 removed outlier: 3.741A pdb=" N GLY D 128 " --> pdb=" O GLN D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 188 removed outlier: 3.566A pdb=" N LYS D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.741A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 188 removed outlier: 3.566A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 70 removed outlier: 3.617A pdb=" N GLY B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N MET B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 removed outlier: 4.174A pdb=" N THR B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 84' Processing helix chain 'B' and resid 85 through 101 removed outlier: 3.893A pdb=" N TRP B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 140 removed outlier: 4.254A pdb=" N ILE B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 177 through 216 removed outlier: 3.794A pdb=" N GLU B 215 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP B 216 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'D' and resid 20 through 21 removed outlier: 4.045A pdb=" N LEU D 21 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU D 73 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 45 through 49 removed outlier: 7.008A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA D 34 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN D 89 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR D 36 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR D 87 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN D 38 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 130 through 139 removed outlier: 3.966A pdb=" N VAL D 132 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU D 179 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 153 through 154 removed outlier: 4.161A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS D 194 " --> pdb=" O LYS D 207 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS D 207 " --> pdb=" O CYS D 194 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL D 196 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.708A pdb=" N VAL C 5 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR C 80 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.850A pdb=" N GLY C 59 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR C 50 " --> pdb=" O GLY C 59 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N THR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N MET C 34 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 111 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AA9, first strand: chain 'C' and resid 129 through 133 removed outlier: 3.529A pdb=" N LEU C 150 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 133 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY C 148 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 147 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 189 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL C 151 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU C 187 " --> pdb=" O VAL C 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 160 through 163 removed outlier: 3.728A pdb=" N THR C 160 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N CYS C 205 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS C 218 " --> pdb=" O CYS C 205 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 207 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL C 216 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.709A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TYR H 80 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 59 through 60 removed outlier: 3.851A pdb=" N GLY H 59 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR H 50 " --> pdb=" O GLY H 59 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL H 111 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 93 through 94 Processing sheet with id=AB5, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.529A pdb=" N LEU H 150 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU H 133 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU H 147 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER H 189 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL H 151 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU H 187 " --> pdb=" O VAL H 151 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 160 through 163 removed outlier: 3.729A pdb=" N THR H 160 " --> pdb=" O ASN H 208 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYS H 205 " --> pdb=" O LYS H 218 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS H 218 " --> pdb=" O CYS H 205 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL H 207 " --> pdb=" O VAL H 216 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL H 216 " --> pdb=" O VAL H 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'L' and resid 20 through 21 removed outlier: 4.044A pdb=" N LEU L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU L 73 " --> pdb=" O LEU L 21 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 45 through 49 removed outlier: 7.008A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN L 38 " --> pdb=" O VAL L 85 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 130 through 139 removed outlier: 3.966A pdb=" N VAL L 132 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU L 179 " --> pdb=" O VAL L 132 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 153 through 154 removed outlier: 4.161A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL L 196 " --> pdb=" O VAL L 205 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 768 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: 2.14 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2960 1.35 - 1.46: 2342 1.46 - 1.58: 4353 1.58 - 1.70: 0 1.70 - 1.81: 76 Bond restraints: 9731 Sorted by residual: bond pdb=" CAZ Y01 B 304 " pdb=" CBH Y01 B 304 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" CAZ Y01 B 302 " pdb=" CBH Y01 B 302 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" CAZ Y01 A 301 " pdb=" CBH Y01 A 301 " ideal model delta sigma weight residual 1.519 1.406 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" CAZ Y01 B 303 " pdb=" CBH Y01 B 303 " ideal model delta sigma weight residual 1.519 1.406 0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" CAZ Y01 B 301 " pdb=" CBH Y01 B 301 " ideal model delta sigma weight residual 1.519 1.407 0.112 2.00e-02 2.50e+03 3.16e+01 ... (remaining 9726 not shown) Histogram of bond angle deviations from ideal: 95.69 - 103.35: 126 103.35 - 111.00: 3522 111.00 - 118.66: 4233 118.66 - 126.32: 5214 126.32 - 133.98: 158 Bond angle restraints: 13253 Sorted by residual: angle pdb=" CB LYS L 190 " pdb=" CG LYS L 190 " pdb=" CD LYS L 190 " ideal model delta sigma weight residual 111.30 123.54 -12.24 2.30e+00 1.89e-01 2.83e+01 angle pdb=" CB LYS D 190 " pdb=" CG LYS D 190 " pdb=" CD LYS D 190 " ideal model delta sigma weight residual 111.30 123.53 -12.23 2.30e+00 1.89e-01 2.83e+01 angle pdb=" CG LYS L 190 " pdb=" CD LYS L 190 " pdb=" CE LYS L 190 " ideal model delta sigma weight residual 111.30 120.21 -8.91 2.30e+00 1.89e-01 1.50e+01 angle pdb=" CG LYS D 190 " pdb=" CD LYS D 190 " pdb=" CE LYS D 190 " ideal model delta sigma weight residual 111.30 120.21 -8.91 2.30e+00 1.89e-01 1.50e+01 angle pdb=" N VAL B 113 " pdb=" CA VAL B 113 " pdb=" C VAL B 113 " ideal model delta sigma weight residual 113.53 109.75 3.78 9.80e-01 1.04e+00 1.49e+01 ... (remaining 13248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.18: 5545 19.18 - 38.36: 441 38.36 - 57.54: 79 57.54 - 76.72: 30 76.72 - 95.91: 5 Dihedral angle restraints: 6100 sinusoidal: 2602 harmonic: 3498 Sorted by residual: dihedral pdb=" CB CYS B 167 " pdb=" SG CYS B 167 " pdb=" SG CYS B 183 " pdb=" CB CYS B 183 " ideal model delta sinusoidal sigma weight residual 93.00 159.74 -66.74 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CB CYS C 149 " pdb=" SG CYS C 149 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual 93.00 29.28 63.72 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CB CYS H 149 " pdb=" SG CYS H 149 " pdb=" SG CYS H 205 " pdb=" CB CYS H 205 " ideal model delta sinusoidal sigma weight residual 93.00 29.29 63.71 1 1.00e+01 1.00e-02 5.35e+01 ... (remaining 6097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1419 0.097 - 0.194: 63 0.194 - 0.292: 3 0.292 - 0.389: 12 0.389 - 0.486: 11 Chirality restraints: 1508 Sorted by residual: chirality pdb=" CBG Y01 A 302 " pdb=" CAQ Y01 A 302 " pdb=" CBD Y01 A 302 " pdb=" CBI Y01 A 302 " both_signs ideal model delta sigma weight residual False -2.33 -2.82 0.49 2.00e-01 2.50e+01 5.90e+00 chirality pdb=" CBH Y01 A 301 " pdb=" CAT Y01 A 301 " pdb=" CAZ Y01 A 301 " pdb=" CBF Y01 A 301 " both_signs ideal model delta sigma weight residual False -2.85 -2.40 -0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" CBH Y01 B 304 " pdb=" CAT Y01 B 304 " pdb=" CAZ Y01 B 304 " pdb=" CBF Y01 B 304 " both_signs ideal model delta sigma weight residual False -2.85 -2.40 -0.45 2.00e-01 2.50e+01 5.16e+00 ... (remaining 1505 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 182 " 0.022 2.00e-02 2.50e+03 2.05e-02 8.44e+00 pdb=" CG TYR A 182 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 182 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 182 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 182 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 182 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 182 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 182 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 159 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO A 160 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 160 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 160 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 157 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO C 158 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 158 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 158 " 0.017 5.00e-02 4.00e+02 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2227 2.79 - 3.32: 8536 3.32 - 3.85: 14163 3.85 - 4.37: 14742 4.37 - 4.90: 25309 Nonbonded interactions: 64977 Sorted by model distance: nonbonded pdb=" O PHE A 45 " pdb=" OG SER A 49 " model vdw 2.265 2.440 nonbonded pdb=" OE1 GLN D 124 " pdb=" OG SER D 131 " model vdw 2.276 2.440 nonbonded pdb=" OE1 GLN L 124 " pdb=" OG SER L 131 " model vdw 2.277 2.440 nonbonded pdb=" OE2 GLU H 6 " pdb=" OG1 THR H 116 " model vdw 2.303 2.440 nonbonded pdb=" OG1 THR H 125 " pdb=" O PHE H 155 " model vdw 2.303 2.440 ... (remaining 64972 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 41 through 218 or (resid 301 and (name CAA or name CAB or \ name CAC or name CAD or name CAE or name CAI or name CAJ or name CAK or name CAN \ or name CAO or name CAP or name CAQ or name CAR or name CAS or name CAT or name \ CAU or name CAV or name CAZ or name CBA or name CBB or name CBC or name CBD or \ name CBE or name CBF or name CBG or name CBH or name CBI or name OAW)) or (resid \ 302 and (name CAC or name CAD or name CAE or name CAI or name CAK or name CAL o \ r name CAM or name CAO or name CAP or name CAQ or name CAR or name CAS or name C \ AT or name CAU or name CAV or name CAX or name CAY or name CAZ or name CBB or na \ me CBC or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI o \ r name OAF or name OAG or name OAH or name OAW)))) selection = (chain 'B' and (resid 41 through 218 or resid 301 through 302)) } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 4.610 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 27.350 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 0.114 9731 Z= 0.366 Angle : 0.774 12.237 13253 Z= 0.355 Chirality : 0.064 0.486 1508 Planarity : 0.003 0.038 1646 Dihedral : 14.344 95.906 3830 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.77 % Allowed : 0.19 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.68 (0.24), residues: 1194 helix: 0.94 (0.33), residues: 232 sheet: 1.24 (0.36), residues: 224 loop : -1.57 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 216 HIS 0.001 0.000 HIS A 145 PHE 0.021 0.001 PHE C 29 TYR 0.049 0.001 TYR A 182 ARG 0.002 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 243 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 245 average time/residue: 0.1914 time to fit residues: 66.9461 Evaluate side-chains 174 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3469 time to fit residues: 1.8725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 107 optimal weight: 0.0030 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN A 214 ASN D 27 GLN D 100 GLN L 27 GLN L 100 GLN B 171 ASN B 181 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9731 Z= 0.271 Angle : 0.651 6.950 13253 Z= 0.336 Chirality : 0.043 0.171 1508 Planarity : 0.005 0.051 1646 Dihedral : 7.567 59.867 1708 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.10 % Allowed : 6.29 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 (0.24), residues: 1194 helix: 0.69 (0.33), residues: 234 sheet: 0.84 (0.36), residues: 226 loop : -1.61 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 36 HIS 0.007 0.002 HIS C 35 PHE 0.028 0.002 PHE B 200 TYR 0.054 0.002 TYR A 182 ARG 0.004 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.1881 time to fit residues: 57.9117 Evaluate side-chains 169 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 107 optimal weight: 0.0670 chunk 115 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN L 89 GLN B 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9731 Z= 0.140 Angle : 0.566 6.896 13253 Z= 0.281 Chirality : 0.040 0.149 1508 Planarity : 0.004 0.044 1646 Dihedral : 7.158 58.266 1708 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.76 (0.24), residues: 1194 helix: 0.92 (0.33), residues: 234 sheet: 0.64 (0.32), residues: 274 loop : -1.59 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 89 HIS 0.006 0.001 HIS B 63 PHE 0.014 0.001 PHE B 62 TYR 0.047 0.001 TYR A 182 ARG 0.002 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2009 time to fit residues: 63.7745 Evaluate side-chains 166 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 10.0000 chunk 80 optimal weight: 0.3980 chunk 55 optimal weight: 0.0370 chunk 11 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 30.0000 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN D 93 ASN L 89 GLN B 63 HIS B 181 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9731 Z= 0.180 Angle : 0.572 5.713 13253 Z= 0.290 Chirality : 0.041 0.153 1508 Planarity : 0.004 0.070 1646 Dihedral : 6.893 58.860 1708 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.10 % Allowed : 3.19 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.92 (0.24), residues: 1194 helix: 0.92 (0.33), residues: 234 sheet: 0.35 (0.34), residues: 252 loop : -1.59 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 36 HIS 0.004 0.001 HIS B 63 PHE 0.032 0.002 PHE A 62 TYR 0.049 0.001 TYR A 182 ARG 0.005 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 1.109 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.1920 time to fit residues: 59.8344 Evaluate side-chains 168 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN D 166 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN L 166 GLN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 9731 Z= 0.403 Angle : 0.814 8.370 13253 Z= 0.425 Chirality : 0.047 0.182 1508 Planarity : 0.006 0.075 1646 Dihedral : 7.655 58.790 1708 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.70 (0.23), residues: 1194 helix: 0.40 (0.32), residues: 230 sheet: -0.55 (0.32), residues: 248 loop : -1.95 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 36 HIS 0.006 0.002 HIS B 63 PHE 0.031 0.003 PHE A 62 TYR 0.060 0.003 TYR A 182 ARG 0.004 0.001 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2219 time to fit residues: 58.2280 Evaluate side-chains 146 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN D 166 GLN L 89 GLN L 166 GLN B 63 HIS B 181 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9731 Z= 0.163 Angle : 0.642 7.781 13253 Z= 0.320 Chirality : 0.043 0.150 1508 Planarity : 0.005 0.070 1646 Dihedral : 6.895 58.103 1708 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.10 % Allowed : 2.03 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.35 (0.24), residues: 1194 helix: 0.92 (0.34), residues: 232 sheet: -0.21 (0.32), residues: 262 loop : -1.90 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 89 HIS 0.006 0.001 HIS B 63 PHE 0.038 0.001 PHE A 62 TYR 0.040 0.002 TYR A 182 ARG 0.007 0.001 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 222 average time/residue: 0.2120 time to fit residues: 65.2429 Evaluate side-chains 161 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1167 time to fit residues: 1.6654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 64 optimal weight: 0.0470 chunk 96 optimal weight: 0.3980 chunk 63 optimal weight: 0.1980 chunk 113 optimal weight: 0.6980 chunk 71 optimal weight: 30.0000 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.4680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN H 39 GLN L 89 GLN L 93 ASN B 63 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9731 Z= 0.151 Angle : 0.633 11.436 13253 Z= 0.314 Chirality : 0.042 0.157 1508 Planarity : 0.004 0.067 1646 Dihedral : 6.505 56.209 1708 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.44 (0.24), residues: 1194 helix: 0.82 (0.33), residues: 246 sheet: -0.17 (0.35), residues: 222 loop : -1.96 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 89 HIS 0.007 0.001 HIS B 63 PHE 0.034 0.001 PHE A 62 TYR 0.033 0.001 TYR A 182 ARG 0.008 0.000 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2074 time to fit residues: 63.6540 Evaluate side-chains 163 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN D 93 ASN C 30 ASN H 30 ASN L 89 GLN B 63 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9731 Z= 0.171 Angle : 0.616 9.959 13253 Z= 0.309 Chirality : 0.042 0.184 1508 Planarity : 0.004 0.064 1646 Dihedral : 6.357 53.770 1708 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.19 % Allowed : 1.84 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.40 (0.24), residues: 1194 helix: 0.86 (0.33), residues: 244 sheet: -0.12 (0.33), residues: 246 loop : -2.00 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 47 HIS 0.006 0.001 HIS B 63 PHE 0.011 0.001 PHE L 71 TYR 0.033 0.001 TYR A 182 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 216 average time/residue: 0.1994 time to fit residues: 60.9663 Evaluate side-chains 155 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN C 30 ASN H 30 ASN L 89 GLN B 63 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9731 Z= 0.194 Angle : 0.659 7.649 13253 Z= 0.330 Chirality : 0.043 0.188 1508 Planarity : 0.005 0.064 1646 Dihedral : 6.316 53.308 1708 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.19 % Allowed : 1.26 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1194 helix: 0.86 (0.33), residues: 242 sheet: -0.27 (0.33), residues: 246 loop : -2.04 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 47 HIS 0.004 0.001 HIS B 63 PHE 0.037 0.002 PHE A 62 TYR 0.062 0.002 TYR A 182 ARG 0.005 0.000 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 215 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 217 average time/residue: 0.1971 time to fit residues: 60.6051 Evaluate side-chains 159 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 0.0060 chunk 57 optimal weight: 30.0000 chunk 74 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN D 93 ASN D 166 GLN C 30 ASN L 89 GLN L 93 ASN L 166 GLN B 63 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9731 Z= 0.326 Angle : 0.760 7.961 13253 Z= 0.391 Chirality : 0.046 0.242 1508 Planarity : 0.005 0.065 1646 Dihedral : 6.818 53.294 1708 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 0.10 % Allowed : 0.58 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.91 (0.23), residues: 1194 helix: 0.36 (0.32), residues: 242 sheet: -0.68 (0.34), residues: 236 loop : -2.17 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 36 HIS 0.004 0.001 HIS C 35 PHE 0.040 0.003 PHE B 190 TYR 0.086 0.003 TYR A 182 ARG 0.004 0.001 ARG A 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.2238 time to fit residues: 64.0812 Evaluate side-chains 152 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 30.0000 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 39 optimal weight: 0.0370 chunk 96 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN D 93 ASN D 166 GLN C 30 ASN H 30 ASN L 89 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.138376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111350 restraints weight = 23962.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110560 restraints weight = 21618.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111683 restraints weight = 17038.880| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9731 Z= 0.193 Angle : 0.684 8.160 13253 Z= 0.344 Chirality : 0.043 0.170 1508 Planarity : 0.005 0.067 1646 Dihedral : 6.493 51.866 1708 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.19 % Allowed : 0.39 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.76 (0.24), residues: 1194 helix: 0.64 (0.33), residues: 242 sheet: -0.59 (0.33), residues: 246 loop : -2.15 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 36 HIS 0.007 0.001 HIS B 63 PHE 0.022 0.001 PHE B 190 TYR 0.074 0.002 TYR A 182 ARG 0.006 0.000 ARG H 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2080.20 seconds wall clock time: 38 minutes 39.31 seconds (2319.31 seconds total)