Starting phenix.real_space_refine on Thu Mar 14 21:22:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y90_10731/03_2024/6y90_10731.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y90_10731/03_2024/6y90_10731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y90_10731/03_2024/6y90_10731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y90_10731/03_2024/6y90_10731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y90_10731/03_2024/6y90_10731.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y90_10731/03_2024/6y90_10731.pdb" } resolution = 3.69 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= 0.004 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 56 5.16 5 C 6368 2.51 5 N 1520 2.21 5 O 1832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 121": "OD1" <-> "OD2" Residue "D ASP 166": "OD1" <-> "OD2" Residue "D TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 194": "OE1" <-> "OE2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 121": "OD1" <-> "OD2" Residue "L ASP 166": "OD1" <-> "OD2" Residue "L TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 194": "OE1" <-> "OE2" Residue "L PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 210": "NH1" <-> "NH2" Residue "L GLU 212": "OE1" <-> "OE2" 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: 9778 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1341 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "B" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1341 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "C" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1669 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 210} Chain: "D" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1623 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 199} Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1669 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 210} Chain: "L" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1623 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 199} Chain: "A" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 256 Unusual residues: {'MYS': 5, 'PC1': 1, 'Y01': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 256 Unusual residues: {'MYS': 5, 'PC1': 1, 'Y01': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.74, per 1000 atoms: 0.59 Number of scatterers: 9778 At special positions: 0 Unit cell: (103.378, 142.45, 134.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 2 15.00 O 1832 8.00 N 1520 7.00 C 6368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 224 " - pdb=" SG CYS D 213 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 224 " - pdb=" SG CYS L 213 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 1.7 seconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2252 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 20 sheets defined 24.7% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 48 through 70 Processing helix chain 'A' and resid 79 through 84 removed outlier: 4.004A pdb=" N VAL A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 102 removed outlier: 3.805A pdb=" N TRP A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 143 removed outlier: 4.010A pdb=" N MET A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 177 through 215 removed outlier: 3.859A pdb=" N CYS A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 71 removed outlier: 3.567A pdb=" N LEU B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.707A pdb=" N VAL B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 102 removed outlier: 3.889A pdb=" N TRP B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 143 removed outlier: 4.054A pdb=" N MET B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 177 through 215 removed outlier: 3.729A pdb=" N CYS B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 Processing helix chain 'D' and resid 120 through 127 removed outlier: 3.540A pdb=" N LEU D 124 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY D 127 " --> pdb=" O GLN D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 188 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'L' and resid 120 through 127 removed outlier: 3.539A pdb=" N LEU L 124 " --> pdb=" O SER L 120 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY L 127 " --> pdb=" O GLN L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 188 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.752A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 59 removed outlier: 3.620A pdb=" N ILE C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.817A pdb=" N ASP C 105 " --> pdb=" O TYR C 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.881A pdb=" N SER C 128 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY C 147 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER C 188 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N SER C 185 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA C 176 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER C 187 " --> pdb=" O PHE C 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 159 through 160 removed outlier: 3.537A pdb=" N THR C 159 " --> pdb=" O ASN C 207 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.668A pdb=" N THR D 22 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 19 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.558A pdb=" N LEU D 11 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR D 84 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N GLN D 36 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR D 48 " --> pdb=" O ASN D 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 113 through 117 removed outlier: 3.516A pdb=" N SER D 113 " --> pdb=" O ASN D 136 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN D 136 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 132 " --> pdb=" O PHE D 117 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA D 129 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 180 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER D 176 " --> pdb=" O CYS D 133 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 135 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D 174 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 161 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR D 177 " --> pdb=" O GLN D 159 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN D 159 " --> pdb=" O THR D 177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.953A pdb=" N TRP D 147 " --> pdb=" O GLN D 154 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS D 144 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU D 194 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR D 191 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE D 208 " --> pdb=" O TYR D 191 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS D 193 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS D 206 " --> pdb=" O CYS D 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.753A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.620A pdb=" N ILE H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 100 through 102 removed outlier: 3.819A pdb=" N ASP H 105 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 128 through 132 removed outlier: 3.881A pdb=" N SER H 128 " --> pdb=" O LYS H 151 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER H 188 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N SER H 185 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA H 176 " --> pdb=" O SER H 185 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER H 187 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 159 through 160 removed outlier: 3.537A pdb=" N THR H 159 " --> pdb=" O ASN H 207 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.668A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.558A pdb=" N LEU L 11 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR L 84 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N GLN L 36 " --> pdb=" O PRO L 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR L 48 " --> pdb=" O ASN L 52 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 113 through 117 removed outlier: 3.516A pdb=" N SER L 113 " --> pdb=" O ASN L 136 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN L 136 " --> pdb=" O SER L 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL L 132 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA L 129 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU L 180 " --> pdb=" O ALA L 129 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER L 176 " --> pdb=" O CYS L 133 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU L 135 " --> pdb=" O LEU L 174 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU L 174 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER L 161 " --> pdb=" O SER L 175 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR L 177 " --> pdb=" O GLN L 159 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN L 159 " --> pdb=" O THR L 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 152 through 154 removed outlier: 3.954A pdb=" N TRP L 147 " --> pdb=" O GLN L 154 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS L 144 " --> pdb=" O THR L 196 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU L 194 " --> pdb=" O GLN L 146 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR L 191 " --> pdb=" O PHE L 208 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE L 208 " --> pdb=" O TYR L 191 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS L 193 " --> pdb=" O LYS L 206 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS L 206 " --> pdb=" O CYS L 193 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1077 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: 2.54 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1498 1.31 - 1.44: 2686 1.44 - 1.56: 5745 1.56 - 1.69: 5 1.69 - 1.81: 84 Bond restraints: 10018 Sorted by residual: bond pdb=" CAZ Y01 A 303 " pdb=" CBH Y01 A 303 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.26e+01 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 3.24e+01 bond pdb=" CAZ Y01 A 302 " pdb=" CBH Y01 A 302 " 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 301 " pdb=" CBH Y01 B 301 " 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 302 " pdb=" CBH Y01 B 302 " ideal model delta sigma weight residual 1.519 1.406 0.113 2.00e-02 2.50e+03 3.17e+01 ... (remaining 10013 not shown) Histogram of bond angle deviations from ideal: 96.53 - 104.03: 194 104.03 - 111.53: 4916 111.53 - 119.04: 3287 119.04 - 126.54: 5021 126.54 - 134.04: 172 Bond angle restraints: 13590 Sorted by residual: angle pdb=" O12 PC1 A 304 " pdb=" P PC1 A 304 " pdb=" O14 PC1 A 304 " ideal model delta sigma weight residual 123.67 109.51 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" O12 PC1 B 305 " pdb=" P PC1 B 305 " pdb=" O14 PC1 B 305 " ideal model delta sigma weight residual 123.67 109.53 14.14 3.00e+00 1.11e-01 2.22e+01 angle pdb=" CAY Y01 A 303 " pdb=" OAW Y01 A 303 " pdb=" CBC Y01 A 303 " ideal model delta sigma weight residual 119.39 109.59 9.80 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CAY Y01 B 304 " pdb=" OAW Y01 B 304 " pdb=" CBC Y01 B 304 " ideal model delta sigma weight residual 119.39 109.65 9.74 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C22 PC1 B 305 " pdb=" C21 PC1 B 305 " pdb=" O21 PC1 B 305 " ideal model delta sigma weight residual 111.12 119.88 -8.76 3.00e+00 1.11e-01 8.52e+00 ... (remaining 13585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.87: 5891 20.87 - 41.75: 441 41.75 - 62.62: 74 62.62 - 83.49: 16 83.49 - 104.36: 6 Dihedral angle restraints: 6428 sinusoidal: 2906 harmonic: 3522 Sorted by residual: dihedral pdb=" CA PHE B 146 " pdb=" C PHE B 146 " pdb=" N LEU B 147 " pdb=" CA LEU B 147 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CAR Y01 A 303 " pdb=" CAV Y01 A 303 " pdb=" CBC Y01 A 303 " pdb=" CAZ Y01 A 303 " ideal model delta sinusoidal sigma weight residual 55.40 -48.96 104.36 1 3.00e+01 1.11e-03 1.33e+01 dihedral pdb=" CAR Y01 B 304 " pdb=" CAV Y01 B 304 " pdb=" CBC Y01 B 304 " pdb=" CAZ Y01 B 304 " ideal model delta sinusoidal sigma weight residual 55.40 -48.94 104.34 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 6425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1428 0.096 - 0.192: 62 0.192 - 0.288: 5 0.288 - 0.384: 15 0.384 - 0.480: 14 Chirality restraints: 1524 Sorted by residual: chirality pdb=" CBH Y01 B 301 " pdb=" CAT Y01 B 301 " pdb=" CAZ Y01 B 301 " pdb=" CBF Y01 B 301 " both_signs ideal model delta sigma weight residual False -2.85 -2.37 -0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CBH Y01 A 310 " pdb=" CAT Y01 A 310 " pdb=" CAZ Y01 A 310 " pdb=" CBF Y01 A 310 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CBG Y01 B 301 " pdb=" CAQ Y01 B 301 " pdb=" CBD Y01 B 301 " pdb=" CBI Y01 B 301 " both_signs ideal model delta sigma weight residual False -2.33 -2.81 0.47 2.00e-01 2.50e+01 5.62e+00 ... (remaining 1521 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 94 " -0.007 2.00e-02 2.50e+03 1.03e-02 2.11e+00 pdb=" CG TYR A 94 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 94 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 94 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 94 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 94 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 94 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 94 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 57 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO L 58 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO L 58 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 58 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 57 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO D 58 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO D 58 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 58 " 0.018 5.00e-02 4.00e+02 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2180 2.79 - 3.32: 8677 3.32 - 3.85: 15209 3.85 - 4.37: 16780 4.37 - 4.90: 29883 Nonbonded interactions: 72729 Sorted by model distance: nonbonded pdb=" O ASN A 163 " pdb=" OH TYR B 182 " model vdw 2.268 2.440 nonbonded pdb=" OD1 ASP C 90 " pdb=" OH TYR C 94 " model vdw 2.279 2.440 nonbonded pdb=" OD1 ASP H 90 " pdb=" OH TYR H 94 " model vdw 2.279 2.440 nonbonded pdb=" OD1 ASN L 136 " pdb=" OG SER L 173 " model vdw 2.287 2.440 nonbonded pdb=" OD1 ASN D 136 " pdb=" OG SER D 173 " model vdw 2.287 2.440 ... (remaining 72724 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 45 through 216 or resid 301 through 303 or resid 306 throu \ gh 309)) selection = (chain 'B' and (resid 45 through 216 or resid 301 through 302 or (resid 303 and \ (name CAA or name CAB or name CAD or name CAE or name CAI or name CAJ or name CA \ K or name CAL or name CAM or name CAN or name CAO or name CAP or name CAQ or nam \ e CAR or name CAS or name CAT or name CAU or name CAV or name CAX or name CAY or \ name CAZ or name CBA or name CBB or name CBC or name CBD or name CBE or name CB \ F or name CBG or name CBH or name CBI or name OAF or name OAG or name OAH or nam \ e OAW)) or resid 306 through 309)) } 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: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 6.000 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.090 Find NCS groups from input model: 0.550 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 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 : 0.007 0.114 10018 Z= 0.431 Angle : 0.903 14.163 13590 Z= 0.356 Chirality : 0.068 0.480 1524 Planarity : 0.003 0.032 1642 Dihedral : 14.795 104.364 4140 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: 0.18 (0.25), residues: 1206 helix: 2.02 (0.35), residues: 234 sheet: 0.31 (0.28), residues: 352 loop : -0.72 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 89 HIS 0.002 0.000 HIS B 145 PHE 0.018 0.001 PHE A 62 TYR 0.024 0.001 TYR A 94 ARG 0.001 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 1.005 Fit side-chains REVERT: B 106 LYS cc_start: 0.8472 (mmmt) cc_final: 0.7933 (pttm) REVERT: B 142 LYS cc_start: 0.8655 (tppt) cc_final: 0.8315 (tptt) REVERT: D 89 GLN cc_start: 0.8320 (pp30) cc_final: 0.8114 (pp30) REVERT: H 62 GLN cc_start: 0.7764 (mt0) cc_final: 0.7519 (mt0) REVERT: L 89 GLN cc_start: 0.8291 (pp30) cc_final: 0.8079 (pp30) outliers start: 2 outliers final: 2 residues processed: 191 average time/residue: 0.2078 time to fit residues: 56.2714 Evaluate side-chains 153 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain H residue 34 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 30.0000 chunk 50 optimal weight: 0.0570 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 40.0000 chunk 94 optimal weight: 20.0000 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 181 GLN A 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS B 166 ASN B 181 GLN B 214 ASN C 207 ASN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 207 ASN ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10018 Z= 0.247 Angle : 0.642 8.992 13590 Z= 0.303 Chirality : 0.044 0.282 1524 Planarity : 0.004 0.034 1642 Dihedral : 11.087 73.399 2056 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.06 % Allowed : 9.54 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: 0.01 (0.25), residues: 1206 helix: 1.58 (0.33), residues: 254 sheet: 0.36 (0.28), residues: 374 loop : -0.94 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 89 HIS 0.004 0.001 HIS C 172 PHE 0.018 0.002 PHE B 146 TYR 0.019 0.001 TYR A 94 ARG 0.006 0.001 ARG L 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 162 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.5980 (pmm) cc_final: 0.5668 (ptp) REVERT: A 50 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7076 (pttp) REVERT: B 50 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7499 (ttmm) REVERT: B 106 LYS cc_start: 0.8498 (mmmt) cc_final: 0.7918 (pttm) REVERT: B 109 ARG cc_start: 0.6181 (tmt-80) cc_final: 0.5828 (tpm170) REVERT: B 142 LYS cc_start: 0.8709 (tppt) cc_final: 0.8465 (tptt) REVERT: C 48 ILE cc_start: 0.8543 (tp) cc_final: 0.8274 (tp) REVERT: D 21 MET cc_start: 0.7912 (ptp) cc_final: 0.7685 (ptp) REVERT: D 168 LYS cc_start: 0.7826 (tttm) cc_final: 0.7175 (tppt) REVERT: H 48 ILE cc_start: 0.8600 (tp) cc_final: 0.8310 (tp) REVERT: H 62 GLN cc_start: 0.7896 (mt0) cc_final: 0.7687 (mt0) outliers start: 11 outliers final: 6 residues processed: 167 average time/residue: 0.1900 time to fit residues: 45.8551 Evaluate side-chains 156 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 40.0000 chunk 74 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 140 ASN A 181 GLN A 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN C 33 ASN ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10018 Z= 0.264 Angle : 0.618 8.635 13590 Z= 0.295 Chirality : 0.045 0.264 1524 Planarity : 0.004 0.035 1642 Dihedral : 10.179 58.920 2050 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.93 % Allowed : 13.87 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.02 (0.25), residues: 1206 helix: 1.44 (0.33), residues: 254 sheet: 0.17 (0.26), residues: 418 loop : -0.83 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 89 HIS 0.004 0.001 HIS H 172 PHE 0.015 0.002 PHE B 203 TYR 0.018 0.002 TYR D 31 ARG 0.003 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.003 Fit side-chains REVERT: A 50 LYS cc_start: 0.8391 (ttmt) cc_final: 0.7096 (pttp) REVERT: A 150 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8000 (mt-10) REVERT: B 106 LYS cc_start: 0.8581 (mmmt) cc_final: 0.7818 (pttm) REVERT: B 109 ARG cc_start: 0.6321 (tmt-80) cc_final: 0.6041 (tpm170) REVERT: B 142 LYS cc_start: 0.8664 (tppt) cc_final: 0.8442 (tptt) REVERT: C 64 PHE cc_start: 0.6453 (m-10) cc_final: 0.6102 (m-10) REVERT: D 89 GLN cc_start: 0.8436 (pp30) cc_final: 0.8091 (pp30) REVERT: H 64 PHE cc_start: 0.6640 (m-10) cc_final: 0.6267 (m-10) REVERT: L 89 GLN cc_start: 0.8391 (pp30) cc_final: 0.8065 (pp30) outliers start: 20 outliers final: 10 residues processed: 170 average time/residue: 0.1890 time to fit residues: 46.7582 Evaluate side-chains 154 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 120 ASN A 181 GLN A 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 HIS ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10018 Z= 0.359 Angle : 0.665 9.442 13590 Z= 0.323 Chirality : 0.046 0.269 1524 Planarity : 0.004 0.036 1642 Dihedral : 10.488 59.987 2050 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.70 % Allowed : 17.34 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.30 (0.25), residues: 1206 helix: 1.11 (0.32), residues: 254 sheet: -0.00 (0.25), residues: 444 loop : -0.98 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 89 HIS 0.004 0.001 HIS H 208 PHE 0.016 0.002 PHE B 45 TYR 0.022 0.002 TYR C 107 ARG 0.006 0.001 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.085 Fit side-chains REVERT: A 50 LYS cc_start: 0.8412 (ttmt) cc_final: 0.7081 (pttp) REVERT: A 150 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7906 (mt-10) REVERT: B 109 ARG cc_start: 0.6324 (tmt-80) cc_final: 0.6059 (tpm170) outliers start: 28 outliers final: 19 residues processed: 173 average time/residue: 0.1875 time to fit residues: 47.1139 Evaluate side-chains 158 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 40.0000 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 104 optimal weight: 0.0060 chunk 29 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 137 ASN ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10018 Z= 0.164 Angle : 0.584 9.397 13590 Z= 0.278 Chirality : 0.043 0.223 1524 Planarity : 0.003 0.029 1642 Dihedral : 9.872 59.924 2050 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.22 % Allowed : 20.13 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.17 (0.25), residues: 1206 helix: 1.34 (0.33), residues: 248 sheet: 0.10 (0.26), residues: 418 loop : -0.93 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 89 HIS 0.001 0.000 HIS H 208 PHE 0.014 0.001 PHE B 203 TYR 0.012 0.001 TYR C 107 ARG 0.002 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 0.796 Fit side-chains REVERT: A 50 LYS cc_start: 0.8341 (ttmt) cc_final: 0.6990 (pttp) REVERT: A 71 MET cc_start: 0.7433 (mtt) cc_final: 0.7174 (mtt) REVERT: A 72 ILE cc_start: 0.9185 (mm) cc_final: 0.8985 (mm) REVERT: A 150 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7881 (mt-10) REVERT: B 109 ARG cc_start: 0.6371 (tmt-80) cc_final: 0.6144 (tpm170) outliers start: 23 outliers final: 17 residues processed: 177 average time/residue: 0.1827 time to fit residues: 46.7890 Evaluate side-chains 165 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 96 optimal weight: 30.0000 chunk 53 optimal weight: 30.0000 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10018 Z= 0.245 Angle : 0.596 8.999 13590 Z= 0.287 Chirality : 0.044 0.218 1524 Planarity : 0.003 0.030 1642 Dihedral : 9.803 59.060 2050 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.70 % Allowed : 20.62 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.12 (0.25), residues: 1206 helix: 1.27 (0.33), residues: 248 sheet: 0.12 (0.25), residues: 444 loop : -0.87 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 85 HIS 0.002 0.001 HIS H 208 PHE 0.012 0.001 PHE B 203 TYR 0.017 0.001 TYR H 107 ARG 0.002 0.000 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8402 (ttmt) cc_final: 0.7023 (pttp) REVERT: A 72 ILE cc_start: 0.9260 (mm) cc_final: 0.9024 (mm) REVERT: B 109 ARG cc_start: 0.6357 (tmt-80) cc_final: 0.6136 (tpm170) REVERT: B 193 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8664 (mt) REVERT: D 32 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7993 (tp) outliers start: 28 outliers final: 22 residues processed: 173 average time/residue: 0.1870 time to fit residues: 47.3534 Evaluate side-chains 170 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 5.9990 chunk 13 optimal weight: 0.0070 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 97 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 115 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- 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 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10018 Z= 0.186 Angle : 0.585 9.516 13590 Z= 0.279 Chirality : 0.044 0.202 1524 Planarity : 0.003 0.029 1642 Dihedral : 9.577 57.512 2050 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.70 % Allowed : 21.19 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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 (0.25), residues: 1206 helix: 1.29 (0.33), residues: 248 sheet: 0.07 (0.26), residues: 416 loop : -0.85 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 89 HIS 0.001 0.001 HIS H 208 PHE 0.012 0.001 PHE B 203 TYR 0.014 0.001 TYR A 94 ARG 0.002 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8379 (ttmt) cc_final: 0.7016 (pttp) REVERT: A 72 ILE cc_start: 0.9205 (mm) cc_final: 0.8977 (mm) REVERT: A 106 LYS cc_start: 0.8574 (mmmt) cc_final: 0.7926 (pttm) REVERT: B 109 ARG cc_start: 0.6350 (tmt-80) cc_final: 0.6125 (tpm170) REVERT: D 32 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7898 (tp) outliers start: 28 outliers final: 21 residues processed: 170 average time/residue: 0.2063 time to fit residues: 51.1601 Evaluate side-chains 169 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 0.0980 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 90 optimal weight: 0.0270 chunk 105 optimal weight: 0.6980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 120 ASN A 145 HIS A 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10018 Z= 0.154 Angle : 0.561 8.755 13590 Z= 0.270 Chirality : 0.043 0.199 1524 Planarity : 0.003 0.028 1642 Dihedral : 9.266 58.507 2050 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.31 % Allowed : 22.06 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.07 (0.25), residues: 1206 helix: 1.40 (0.33), residues: 248 sheet: 0.12 (0.26), residues: 416 loop : -0.82 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 85 HIS 0.003 0.000 HIS A 145 PHE 0.013 0.001 PHE B 203 TYR 0.013 0.001 TYR B 94 ARG 0.001 0.000 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8396 (ttmt) cc_final: 0.6976 (pttp) REVERT: A 72 ILE cc_start: 0.9180 (mm) cc_final: 0.8969 (mm) REVERT: A 106 LYS cc_start: 0.8535 (mmmt) cc_final: 0.7939 (pttm) REVERT: B 109 ARG cc_start: 0.6327 (tmt-80) cc_final: 0.6089 (tpm170) outliers start: 24 outliers final: 18 residues processed: 166 average time/residue: 0.1937 time to fit residues: 46.7399 Evaluate side-chains 165 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 120 ASN A 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN H 179 GLN ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10018 Z= 0.337 Angle : 0.651 9.743 13590 Z= 0.320 Chirality : 0.046 0.215 1524 Planarity : 0.004 0.032 1642 Dihedral : 9.711 58.828 2050 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.70 % Allowed : 21.68 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.25 (0.25), residues: 1206 helix: 1.06 (0.32), residues: 254 sheet: 0.07 (0.27), residues: 406 loop : -0.87 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 89 HIS 0.003 0.001 HIS H 208 PHE 0.012 0.002 PHE C 154 TYR 0.024 0.002 TYR C 107 ARG 0.002 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 1.027 Fit side-chains REVERT: A 50 LYS cc_start: 0.8465 (ttmt) cc_final: 0.7077 (pttp) REVERT: A 106 LYS cc_start: 0.8642 (mmmt) cc_final: 0.7871 (pttm) REVERT: B 109 ARG cc_start: 0.6361 (tmt-80) cc_final: 0.6157 (tpm170) REVERT: D 32 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8072 (tp) outliers start: 28 outliers final: 23 residues processed: 169 average time/residue: 0.1835 time to fit residues: 45.3441 Evaluate side-chains 168 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 29 optimal weight: 0.0670 overall best weight: 3.0124 ------------------------------------------------------------------------------- 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 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10018 Z= 0.366 Angle : 0.688 12.925 13590 Z= 0.334 Chirality : 0.047 0.222 1524 Planarity : 0.004 0.033 1642 Dihedral : 9.887 59.984 2050 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.41 % Allowed : 22.54 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.41 (0.25), residues: 1206 helix: 0.87 (0.32), residues: 254 sheet: -0.01 (0.27), residues: 406 loop : -0.97 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 147 HIS 0.003 0.001 HIS H 208 PHE 0.011 0.002 PHE C 154 TYR 0.023 0.002 TYR A 94 ARG 0.002 0.000 ARG A 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.106 Fit side-chains REVERT: A 50 LYS cc_start: 0.8474 (ttmt) cc_final: 0.7059 (pttp) REVERT: D 32 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8074 (tp) outliers start: 25 outliers final: 21 residues processed: 165 average time/residue: 0.1857 time to fit residues: 44.6878 Evaluate side-chains 166 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 0.0470 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 166 ASN A 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.184546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.139297 restraints weight = 16694.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.139895 restraints weight = 8787.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.140495 restraints weight = 6503.750| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10018 Z= 0.179 Angle : 0.624 12.163 13590 Z= 0.300 Chirality : 0.044 0.210 1524 Planarity : 0.003 0.029 1642 Dihedral : 9.448 59.739 2050 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.02 % Allowed : 23.41 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.29 (0.25), residues: 1206 helix: 1.05 (0.33), residues: 248 sheet: 0.08 (0.26), residues: 418 loop : -0.95 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 147 HIS 0.003 0.001 HIS H 35 PHE 0.030 0.001 PHE H 64 TYR 0.035 0.001 TYR A 94 ARG 0.003 0.000 ARG B 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2029.30 seconds wall clock time: 37 minutes 36.24 seconds (2256.24 seconds total)