Starting phenix.real_space_refine (version: dev) on Mon Dec 12 09:17:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y90_10731/12_2022/6y90_10731_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y90_10731/12_2022/6y90_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_10731/12_2022/6y90_10731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y90_10731/12_2022/6y90_10731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y90_10731/12_2022/6y90_10731_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y90_10731/12_2022/6y90_10731_updated.pdb" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 12 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: 12 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.16, per 1000 atoms: 0.63 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: 4.09 Conformation dependent library (CDL) restraints added in 1.4 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... running ksdssp... Secondary structure from input PDB file: 20 helices and 22 sheets defined 21.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 49 through 71 Processing helix chain 'A' and resid 80 through 83 No H-bonds generated for 'chain 'A' and resid 80 through 83' Processing helix chain 'A' and resid 86 through 102 Processing helix chain 'A' and resid 113 through 142 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 153 through 156 No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 178 through 214 removed outlier: 3.859A pdb=" N CYS A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 70 Processing helix chain 'B' and resid 80 through 83 No H-bonds generated for 'chain 'B' and resid 80 through 83' Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 113 through 142 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 153 through 156 No H-bonds generated for 'chain 'B' and resid 153 through 156' Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 178 through 214 removed outlier: 3.729A pdb=" N CYS B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 81 No H-bonds generated for 'chain 'D' and resid 79 through 81' Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'L' and resid 79 through 81 No H-bonds generated for 'chain 'L' and resid 79 through 81' Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 182 through 187 Processing sheet with id= A, first strand: chain 'C' and resid 3 through 6 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= B, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.713A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LYS C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TRP C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 40 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU C 45 " --> pdb=" O THR C 40 " (cutoff:3.500A) Processing sheet with id= C, 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= D, 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: 3.828A pdb=" N SER C 187 " --> pdb=" O PHE C 174 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 203 through 208 Processing sheet with id= F, first strand: chain 'C' and resid 150 through 153 removed outlier: 6.856A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id= G, 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= H, first strand: chain 'D' and resid 10 through 13 removed outlier: 5.744A pdb=" N LYS D 102 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA D 13 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLU D 104 " --> pdb=" O ALA D 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'D' and resid 84 through 89 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) Processing sheet with id= J, 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= K, 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= L, first strand: chain 'H' and resid 3 through 6 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= M, first strand: chain 'H' and resid 93 through 96 removed outlier: 3.713A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id= N, 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= O, 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: 3.828A pdb=" N SER H 187 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 203 through 208 Processing sheet with id= Q, first strand: chain 'H' and resid 150 through 153 removed outlier: 6.855A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id= R, 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= S, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.744A pdb=" N LYS L 102 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA L 13 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLU L 104 " --> pdb=" O ALA L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'L' and resid 84 through 89 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) Processing sheet with id= U, 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= V, 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) 330 hydrogen bonds defined for protein. 948 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: 2.74 Time building geometry restraints manager: 4.40 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 - 17.33: 5311 17.33 - 34.66: 506 34.66 - 52.00: 109 52.00 - 69.33: 14 69.33 - 86.66: 12 Dihedral angle restraints: 5952 sinusoidal: 2430 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=" N MET H 34 " pdb=" CA MET H 34 " pdb=" CB MET H 34 " pdb=" CG MET H 34 " ideal model delta sinusoidal sigma weight residual -60.00 -119.83 59.83 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N MET C 34 " pdb=" CA MET C 34 " pdb=" CB MET C 34 " pdb=" CG MET C 34 " ideal model delta sinusoidal sigma weight residual -60.00 -119.81 59.81 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5949 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: 2188 2.79 - 3.32: 8719 3.32 - 3.85: 15267 3.85 - 4.37: 16879 4.37 - 4.90: 29896 Nonbonded interactions: 72949 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 72944 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 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. 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: 1.260 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: 6.260 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.090 Process input model: 29.600 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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= 0.414 Angle : 0.903 14.163 13590 Z= 0.356 Chirality : 0.068 0.480 1524 Planarity : 0.003 0.032 1642 Dihedral : 14.160 86.662 3664 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 % 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 *********************** 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 : 1.129 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 191 average time/residue: 0.2035 time to fit residues: 55.2186 Evaluate side-chains 153 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1114 time to fit residues: 1.9425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 4.9990 chunk 90 optimal weight: 30.0000 chunk 50 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 40.0000 chunk 94 optimal weight: 20.0000 chunk 36 optimal weight: 0.0470 chunk 57 optimal weight: 0.1980 chunk 70 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 B 158 HIS B 166 ASN B 181 GLN B 214 ASN C 207 ASN H 33 ASN H 39 GLN H 207 ASN L 1 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 10018 Z= 0.157 Angle : 0.571 9.120 13590 Z= 0.268 Chirality : 0.042 0.243 1524 Planarity : 0.003 0.035 1642 Dihedral : 9.121 70.289 1574 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.96 % 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: 0.27 (0.26), residues: 1206 helix: 1.98 (0.34), residues: 238 sheet: 0.20 (0.28), residues: 392 loop : -0.56 (0.27), residues: 576 *********************** 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 169 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 159 time to evaluate : 1.171 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 165 average time/residue: 0.1966 time to fit residues: 47.1951 Evaluate side-chains 151 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1060 time to fit residues: 2.3684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 74 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 C 33 ASN D 37 GLN H 39 GLN ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2437 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= 0.276 Angle : 0.616 8.529 13590 Z= 0.299 Chirality : 0.044 0.223 1524 Planarity : 0.004 0.036 1642 Dihedral : 9.030 73.196 1574 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 1.54 % 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: 0.21 (0.26), residues: 1206 helix: 1.86 (0.34), residues: 236 sheet: 0.15 (0.26), residues: 424 loop : -0.58 (0.28), residues: 546 *********************** 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 173 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 1.220 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 166 average time/residue: 0.1990 time to fit residues: 48.0694 Evaluate side-chains 152 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 1.155 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0859 time to fit residues: 2.4997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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 181 GLN A 214 ASN B 166 ASN B 181 GLN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 10018 Z= 0.267 Angle : 0.606 8.793 13590 Z= 0.289 Chirality : 0.043 0.253 1524 Planarity : 0.003 0.037 1642 Dihedral : 9.100 71.793 1574 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 1.35 % 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: 0.03 (0.25), residues: 1206 helix: 1.87 (0.34), residues: 232 sheet: 0.10 (0.27), residues: 410 loop : -0.79 (0.27), residues: 564 *********************** 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 172 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 1.118 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 169 average time/residue: 0.1994 time to fit residues: 49.4778 Evaluate side-chains 148 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 141 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0950 time to fit residues: 2.7920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 1 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 50.0000 chunk 98 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 63 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10018 Z= 0.171 Angle : 0.563 9.656 13590 Z= 0.265 Chirality : 0.042 0.234 1524 Planarity : 0.003 0.029 1642 Dihedral : 8.854 70.486 1574 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 1.45 % 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: 0.03 (0.25), residues: 1206 helix: 1.82 (0.33), residues: 234 sheet: 0.12 (0.26), residues: 410 loop : -0.79 (0.28), residues: 562 *********************** 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 169 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 1.193 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 163 average time/residue: 0.1949 time to fit residues: 46.2308 Evaluate side-chains 145 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0988 time to fit residues: 2.2636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 0.5980 chunk 116 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 63 HIS C 172 HIS D 37 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 10018 Z= 0.318 Angle : 0.651 10.012 13590 Z= 0.313 Chirality : 0.045 0.221 1524 Planarity : 0.004 0.029 1642 Dihedral : 9.222 73.432 1574 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 1.83 % 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: -0.11 (0.25), residues: 1206 helix: 1.61 (0.34), residues: 232 sheet: 0.08 (0.26), residues: 434 loop : -0.91 (0.28), residues: 540 *********************** 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 172 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 1.208 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 165 average time/residue: 0.1946 time to fit residues: 46.4475 Evaluate side-chains 152 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0865 time to fit residues: 3.0066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 181 GLN C 179 GLN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 10018 Z= 0.387 Angle : 0.715 12.103 13590 Z= 0.346 Chirality : 0.047 0.229 1524 Planarity : 0.004 0.032 1642 Dihedral : 9.800 73.293 1574 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 2.02 % 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: -0.37 (0.25), residues: 1206 helix: 1.28 (0.33), residues: 232 sheet: -0.07 (0.26), residues: 450 loop : -1.04 (0.29), residues: 524 *********************** 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 177 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 1.205 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 171 average time/residue: 0.2052 time to fit residues: 51.1105 Evaluate side-chains 161 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0896 time to fit residues: 3.5060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 40.0000 chunk 105 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** B 63 HIS B 214 ASN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 10018 Z= 0.336 Angle : 0.692 13.106 13590 Z= 0.332 Chirality : 0.046 0.216 1524 Planarity : 0.004 0.032 1642 Dihedral : 9.708 71.077 1574 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 1.06 % 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: -0.50 (0.25), residues: 1206 helix: 1.18 (0.33), residues: 232 sheet: -0.18 (0.26), residues: 404 loop : -1.04 (0.28), residues: 570 *********************** 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 169 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 1.146 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 165 average time/residue: 0.1989 time to fit residues: 47.6887 Evaluate side-chains 157 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1030 time to fit residues: 2.8626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 145 HIS A 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 1 GLN D 137 ASN ** H 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 10018 Z= 0.311 Angle : 0.689 13.502 13590 Z= 0.332 Chirality : 0.046 0.202 1524 Planarity : 0.004 0.032 1642 Dihedral : 9.735 71.979 1574 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 0.87 % 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: -0.55 (0.25), residues: 1206 helix: 1.05 (0.33), residues: 234 sheet: -0.25 (0.27), residues: 392 loop : -0.98 (0.27), residues: 580 *********************** 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 170 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 1.162 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 165 average time/residue: 0.2046 time to fit residues: 48.9415 Evaluate side-chains 157 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 1.164 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0902 time to fit residues: 2.2451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 29 optimal weight: 0.0770 overall best weight: 1.6144 ------------------------------------------------------------------------------- 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 145 HIS A 166 ASN A 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 10018 Z= 0.257 Angle : 0.671 10.753 13590 Z= 0.324 Chirality : 0.045 0.207 1524 Planarity : 0.004 0.031 1642 Dihedral : 9.534 71.605 1574 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 0.87 % 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: -0.50 (0.25), residues: 1206 helix: 1.07 (0.33), residues: 234 sheet: -0.22 (0.27), residues: 392 loop : -0.94 (0.28), residues: 580 ********************** 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 168 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 159 time to evaluate : 1.125 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 165 average time/residue: 0.2013 time to fit residues: 48.3176 Evaluate side-chains 159 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 153 time to evaluate : 1.102 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0917 time to fit residues: 2.4839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** B 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.182442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.138545 restraints weight = 17111.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.137382 restraints weight = 9680.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.138435 restraints weight = 7005.615| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 10018 Z= 0.250 Angle : 0.661 10.462 13590 Z= 0.319 Chirality : 0.044 0.196 1524 Planarity : 0.003 0.032 1642 Dihedral : 9.298 71.711 1574 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.29 % 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: -0.49 (0.25), residues: 1206 helix: 1.14 (0.33), residues: 234 sheet: -0.23 (0.27), residues: 388 loop : -0.95 (0.27), residues: 584 =============================================================================== Job complete usr+sys time: 1974.30 seconds wall clock time: 36 minutes 59.32 seconds (2219.32 seconds total)