Starting phenix.real_space_refine on Fri Dec 8 23:06:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vja_21212/12_2023/6vja_21212.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vja_21212/12_2023/6vja_21212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vja_21212/12_2023/6vja_21212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vja_21212/12_2023/6vja_21212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vja_21212/12_2023/6vja_21212.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vja_21212/12_2023/6vja_21212.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6004 2.51 5 N 1500 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 48": "OE1" <-> "OE2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H GLU 212": "OE1" <-> "OE2" Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "I GLU 212": "OE1" <-> "OE2" Residue "L TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 142": "NH1" <-> "NH2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 195": "OE1" <-> "OE2" Residue "L PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 213": "OE1" <-> "OE2" Residue "M TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 77": "NH1" <-> "NH2" Residue "M PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M GLU 161": "OE1" <-> "OE2" Residue "M TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 195": "OE1" <-> "OE2" Residue "M PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 213": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9342 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1275 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain: "D" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1275 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1668 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "I" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1668 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, '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: "M" 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: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.96, per 1000 atoms: 0.64 Number of scatterers: 9342 At special positions: 0 Unit cell: (161, 70, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1782 8.00 N 1500 7.00 C 6004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS C 167 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS D 167 " - pdb=" SG CYS D 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.05 Simple disulfide: pdb=" SG CYS H 216 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 196 " distance=2.05 Simple disulfide: pdb=" SG CYS I 216 " - pdb=" SG CYS M 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.9 seconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 22 sheets defined 27.6% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'C' and resid 47 through 71 removed outlier: 4.541A pdb=" N THR C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS C 63 " --> pdb=" O ASN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'C' and resid 85 through 97 removed outlier: 3.867A pdb=" N TRP C 89 " --> pdb=" O TRP C 85 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 114 through 143 removed outlier: 3.759A pdb=" N ILE C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 177 through 206 removed outlier: 3.770A pdb=" N GLN C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN C 204 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 71 removed outlier: 4.406A pdb=" N THR D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS D 63 " --> pdb=" O ASN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.606A pdb=" N TRP D 89 " --> pdb=" O TRP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 114 through 141 removed outlier: 3.559A pdb=" N ILE D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 124 " --> pdb=" O ASN D 120 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 177 through 206 removed outlier: 3.591A pdb=" N GLN D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU D 205 " --> pdb=" O ALA D 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.838A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 65 removed outlier: 4.458A pdb=" N GLY H 65 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.707A pdb=" N SER H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 129 No H-bonds generated for 'chain 'H' and resid 127 through 129' Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.797A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 65 removed outlier: 4.410A pdb=" N GLY I 65 " --> pdb=" O GLN I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.706A pdb=" N SER I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 129 No H-bonds generated for 'chain 'I' and resid 127 through 129' Processing helix chain 'I' and resid 156 through 158 No H-bonds generated for 'chain 'I' and resid 156 through 158' Processing helix chain 'I' and resid 187 through 189 No H-bonds generated for 'chain 'I' and resid 187 through 189' Processing helix chain 'I' and resid 201 through 204 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.970A pdb=" N ALA L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.928A pdb=" N ALA M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.863A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.554A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN H 33 " --> pdb=" O SER H 95 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.554A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG H 94 " --> pdb=" O ASN H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.572A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 131 through 132 removed outlier: 6.011A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.020A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.882A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.552A pdb=" N VAL I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN I 33 " --> pdb=" O SER I 95 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.552A pdb=" N VAL I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG I 94 " --> pdb=" O ASN I 101 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP I 100A" --> pdb=" O TYR I 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 120 through 124 removed outlier: 5.978A pdb=" N TYR I 176 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 131 through 132 removed outlier: 5.978A pdb=" N TYR I 176 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 151 through 154 removed outlier: 4.019A pdb=" N TYR I 194 " --> pdb=" O VAL I 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.544A pdb=" N TRP L 35 " --> pdb=" O TRP L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.582A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.790A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA L 130 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.518A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'M' and resid 10 through 13 removed outlier: 4.158A pdb=" N ALA M 13 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP M 35 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 10 through 13 removed outlier: 4.158A pdb=" N ALA M 13 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 114 through 118 removed outlier: 3.781A pdb=" N VAL M 133 " --> pdb=" O PHE M 118 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA M 130 " --> pdb=" O LEU M 181 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR M 173 " --> pdb=" O ASN M 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 153 through 154 removed outlier: 3.507A pdb=" N CYS M 194 " --> pdb=" O LYS M 207 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS M 207 " --> pdb=" O CYS M 194 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.37 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2301 1.33 - 1.46: 2388 1.46 - 1.58: 4809 1.58 - 1.71: 0 1.71 - 1.84: 84 Bond restraints: 9582 Sorted by residual: bond pdb=" CAX Y01 D 402 " pdb=" OAH Y01 D 402 " ideal model delta sigma weight residual 1.248 1.343 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" CAX Y01 C1001 " pdb=" OAH Y01 C1001 " ideal model delta sigma weight residual 1.248 1.341 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" CAX Y01 D 403 " pdb=" OAH Y01 D 403 " ideal model delta sigma weight residual 1.248 1.340 -0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" CAX Y01 D 401 " pdb=" OAH Y01 D 401 " ideal model delta sigma weight residual 1.248 1.340 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" CAX Y01 C1003 " pdb=" OAH Y01 C1003 " ideal model delta sigma weight residual 1.248 1.338 -0.090 2.00e-02 2.50e+03 2.03e+01 ... (remaining 9577 not shown) Histogram of bond angle deviations from ideal: 96.87 - 104.33: 220 104.33 - 111.79: 4551 111.79 - 119.25: 3407 119.25 - 126.71: 4730 126.71 - 134.17: 150 Bond angle restraints: 13058 Sorted by residual: angle pdb=" CA TRP M 91 " pdb=" CB TRP M 91 " pdb=" CG TRP M 91 " ideal model delta sigma weight residual 113.60 122.09 -8.49 1.90e+00 2.77e-01 2.00e+01 angle pdb=" CA TYR H 100C" pdb=" CB TYR H 100C" pdb=" CG TYR H 100C" ideal model delta sigma weight residual 113.90 121.28 -7.38 1.80e+00 3.09e-01 1.68e+01 angle pdb=" CA TRP L 91 " pdb=" CB TRP L 91 " pdb=" CG TRP L 91 " ideal model delta sigma weight residual 113.60 121.04 -7.44 1.90e+00 2.77e-01 1.53e+01 angle pdb=" CA TYR I 100C" pdb=" CB TYR I 100C" pdb=" CG TYR I 100C" ideal model delta sigma weight residual 113.90 120.93 -7.03 1.80e+00 3.09e-01 1.53e+01 angle pdb=" N LEU D 112 " pdb=" CA LEU D 112 " pdb=" C LEU D 112 " ideal model delta sigma weight residual 110.80 102.49 8.31 2.13e+00 2.20e-01 1.52e+01 ... (remaining 13053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5658 17.90 - 35.80: 272 35.80 - 53.70: 51 53.70 - 71.60: 30 71.60 - 89.49: 12 Dihedral angle restraints: 6023 sinusoidal: 2543 harmonic: 3480 Sorted by residual: dihedral pdb=" CB CYS C 167 " pdb=" SG CYS C 167 " pdb=" SG CYS C 183 " pdb=" CB CYS C 183 " ideal model delta sinusoidal sigma weight residual -86.00 -149.42 63.42 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" CB CYS D 167 " pdb=" SG CYS D 167 " pdb=" SG CYS D 183 " pdb=" CB CYS D 183 " ideal model delta sinusoidal sigma weight residual -86.00 -148.59 62.59 1 1.00e+01 1.00e-02 5.18e+01 dihedral pdb=" CA ASN D 166 " pdb=" C ASN D 166 " pdb=" N CYS D 167 " pdb=" CA CYS D 167 " ideal model delta harmonic sigma weight residual -180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 6020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1277 0.100 - 0.199: 187 0.199 - 0.299: 10 0.299 - 0.398: 10 0.398 - 0.498: 6 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CBG Y01 D 403 " pdb=" CAQ Y01 D 403 " pdb=" CBD Y01 D 403 " pdb=" CBI Y01 D 403 " both_signs ideal model delta sigma weight residual False -2.33 -2.83 0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CBG Y01 C1003 " pdb=" CAQ Y01 C1003 " pdb=" CBD Y01 C1003 " pdb=" CBI Y01 C1003 " both_signs ideal model delta sigma weight residual False -2.33 -2.82 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" CBG Y01 D 401 " pdb=" CAQ Y01 D 401 " pdb=" CBD Y01 D 401 " pdb=" CBI Y01 D 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.81 0.48 2.00e-01 2.50e+01 5.74e+00 ... (remaining 1487 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 94 " 0.099 9.50e-02 1.11e+02 5.41e-02 1.32e+01 pdb=" NE ARG H 94 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG H 94 " 0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG H 94 " -0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG H 94 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 120 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.53e+00 pdb=" C ASN D 120 " 0.053 2.00e-02 2.50e+03 pdb=" O ASN D 120 " -0.020 2.00e-02 2.50e+03 pdb=" N SER D 121 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 91 " -0.027 2.00e-02 2.50e+03 1.94e-02 9.44e+00 pdb=" CG TRP M 91 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP M 91 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP M 91 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP M 91 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP M 91 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP M 91 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 91 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 91 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP M 91 " -0.004 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1000 2.73 - 3.28: 8990 3.28 - 3.82: 14171 3.82 - 4.36: 17033 4.36 - 4.90: 29761 Nonbonded interactions: 70955 Sorted by model distance: nonbonded pdb=" OE2 GLU M 105 " pdb=" OH TYR M 173 " model vdw 2.193 2.440 nonbonded pdb=" OE1 GLU D 168 " pdb=" OH TYR D 184 " model vdw 2.271 2.440 nonbonded pdb=" OE2 GLU L 105 " pdb=" OH TYR L 173 " model vdw 2.296 2.440 nonbonded pdb=" ND2 ASN M 210 " pdb=" OE1 GLU M 213 " model vdw 2.299 2.520 nonbonded pdb=" N GLU L 79 " pdb=" OD2 ASP L 82 " model vdw 2.328 2.520 ... (remaining 70950 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 'C' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 6.920 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.050 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.014 0.117 9582 Z= 0.883 Angle : 1.270 10.980 13058 Z= 0.673 Chirality : 0.078 0.498 1490 Planarity : 0.007 0.060 1608 Dihedral : 12.613 89.494 3766 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 0.49 % Allowed : 1.46 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % 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: 0.64 (0.23), residues: 1192 helix: -0.71 (0.29), residues: 234 sheet: 1.98 (0.26), residues: 372 loop : -0.07 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.005 TRP M 91 HIS 0.011 0.003 HIS D 145 PHE 0.040 0.004 PHE H 100D TYR 0.038 0.007 TYR I 100C ARG 0.060 0.007 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 301 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 306 average time/residue: 0.2028 time to fit residues: 85.9479 Evaluate side-chains 210 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1266 time to fit residues: 1.6496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN C 181 GLN D 56 GLN D 63 HIS D 181 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN M 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9582 Z= 0.205 Angle : 0.655 8.094 13058 Z= 0.333 Chirality : 0.044 0.213 1490 Planarity : 0.005 0.043 1608 Dihedral : 7.439 59.020 1706 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.22 % Allowed : 10.35 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.24), residues: 1192 helix: 0.98 (0.33), residues: 248 sheet: 2.24 (0.25), residues: 402 loop : 0.29 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 89 HIS 0.004 0.001 HIS D 145 PHE 0.017 0.002 PHE I 122 TYR 0.027 0.002 TYR D 94 ARG 0.003 0.000 ARG D 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 247 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 22 residues processed: 269 average time/residue: 0.1897 time to fit residues: 72.4777 Evaluate side-chains 233 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 211 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.0881 time to fit residues: 5.0427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.0060 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 181 GLN L 160 GLN M 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9582 Z= 0.267 Angle : 0.639 7.483 13058 Z= 0.324 Chirality : 0.043 0.180 1490 Planarity : 0.005 0.048 1608 Dihedral : 7.223 53.571 1706 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.54 % Allowed : 13.28 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1192 helix: 1.24 (0.34), residues: 246 sheet: 1.98 (0.25), residues: 394 loop : 0.21 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 89 HIS 0.004 0.001 HIS C 145 PHE 0.016 0.002 PHE D 62 TYR 0.045 0.002 TYR D 94 ARG 0.006 0.000 ARG L 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 225 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 238 average time/residue: 0.1930 time to fit residues: 65.2304 Evaluate side-chains 206 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 192 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1001 time to fit residues: 4.0728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 102 optimal weight: 0.0070 chunk 30 optimal weight: 3.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN L 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9582 Z= 0.257 Angle : 0.615 7.123 13058 Z= 0.311 Chirality : 0.043 0.170 1490 Planarity : 0.005 0.046 1608 Dihedral : 7.142 55.668 1706 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.54 % Allowed : 14.55 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.24), residues: 1192 helix: 1.42 (0.34), residues: 246 sheet: 1.91 (0.25), residues: 394 loop : 0.07 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 89 HIS 0.003 0.001 HIS C 145 PHE 0.016 0.002 PHE D 62 TYR 0.017 0.002 TYR I 100C ARG 0.002 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 199 time to evaluate : 0.998 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 213 average time/residue: 0.1925 time to fit residues: 58.0388 Evaluate side-chains 194 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0907 time to fit residues: 4.1233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 HIS H 1 GLN H 6 GLN I 1 GLN L 89 GLN M 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9582 Z= 0.324 Angle : 0.646 7.294 13058 Z= 0.329 Chirality : 0.044 0.195 1490 Planarity : 0.005 0.046 1608 Dihedral : 7.217 59.164 1706 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.95 % Allowed : 15.82 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.24), residues: 1192 helix: 1.27 (0.33), residues: 246 sheet: 1.78 (0.25), residues: 382 loop : -0.07 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP H 154 HIS 0.003 0.001 HIS L 34 PHE 0.025 0.002 PHE C 62 TYR 0.020 0.002 TYR H 100C ARG 0.003 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 1.182 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 202 average time/residue: 0.1991 time to fit residues: 57.1966 Evaluate side-chains 192 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 183 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1268 time to fit residues: 3.2754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN M 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9582 Z= 0.147 Angle : 0.558 7.212 13058 Z= 0.279 Chirality : 0.042 0.152 1490 Planarity : 0.004 0.043 1608 Dihedral : 6.843 57.958 1706 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.37 % Allowed : 16.99 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1192 helix: 1.69 (0.34), residues: 250 sheet: 1.87 (0.25), residues: 384 loop : 0.10 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 89 HIS 0.001 0.000 HIS D 63 PHE 0.038 0.001 PHE C 62 TYR 0.015 0.001 TYR D 94 ARG 0.002 0.000 ARG L 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 211 time to evaluate : 1.121 Fit side-chains outliers start: 14 outliers final: 3 residues processed: 218 average time/residue: 0.1925 time to fit residues: 60.4395 Evaluate side-chains 200 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 197 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0994 time to fit residues: 2.2112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 6.9990 chunk 12 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 HIS H 6 GLN I 6 GLN L 89 GLN M 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9582 Z= 0.323 Angle : 0.653 9.027 13058 Z= 0.329 Chirality : 0.044 0.159 1490 Planarity : 0.005 0.049 1608 Dihedral : 7.070 54.831 1706 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.46 % Allowed : 18.95 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.24), residues: 1192 helix: 1.73 (0.33), residues: 238 sheet: 1.72 (0.25), residues: 382 loop : -0.01 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP I 154 HIS 0.003 0.001 HIS M 34 PHE 0.023 0.002 PHE I 122 TYR 0.027 0.002 TYR I 100C ARG 0.004 0.001 ARG M 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 1.141 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 202 average time/residue: 0.1951 time to fit residues: 56.0696 Evaluate side-chains 194 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0850 time to fit residues: 2.3980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.0050 chunk 45 optimal weight: 0.0670 chunk 67 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.0030 chunk 89 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 HIS H 6 GLN I 6 GLN L 89 GLN M 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9582 Z= 0.130 Angle : 0.572 8.740 13058 Z= 0.279 Chirality : 0.041 0.152 1490 Planarity : 0.004 0.043 1608 Dihedral : 6.692 57.404 1706 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.78 % Allowed : 18.75 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1192 helix: 1.76 (0.34), residues: 248 sheet: 1.92 (0.25), residues: 382 loop : 0.18 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP I 154 HIS 0.002 0.001 HIS H 35 PHE 0.016 0.001 PHE I 122 TYR 0.012 0.001 TYR C 182 ARG 0.002 0.000 ARG M 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 216 time to evaluate : 1.302 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 220 average time/residue: 0.2103 time to fit residues: 67.0063 Evaluate side-chains 190 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1012 time to fit residues: 1.8542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 HIS H 6 GLN I 6 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 9582 Z= 0.357 Angle : 0.676 8.971 13058 Z= 0.340 Chirality : 0.044 0.176 1490 Planarity : 0.005 0.050 1608 Dihedral : 7.015 53.908 1706 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.27 % Allowed : 19.04 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.24), residues: 1192 helix: 1.63 (0.33), residues: 242 sheet: 1.66 (0.25), residues: 382 loop : -0.15 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP I 154 HIS 0.003 0.001 HIS M 34 PHE 0.016 0.002 PHE I 122 TYR 0.027 0.002 TYR I 100C ARG 0.007 0.001 ARG M 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 1.018 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 195 average time/residue: 0.1970 time to fit residues: 55.0419 Evaluate side-chains 186 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 181 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0975 time to fit residues: 2.2987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 117 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN I 6 GLN M 6 GLN M 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9582 Z= 0.224 Angle : 0.626 9.367 13058 Z= 0.310 Chirality : 0.043 0.154 1490 Planarity : 0.005 0.043 1608 Dihedral : 6.952 59.140 1706 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.49 % Allowed : 19.63 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.24), residues: 1192 helix: 1.80 (0.34), residues: 242 sheet: 1.69 (0.25), residues: 382 loop : -0.12 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 89 HIS 0.002 0.001 HIS M 198 PHE 0.018 0.001 PHE I 122 TYR 0.034 0.002 TYR D 94 ARG 0.004 0.001 ARG M 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 1.191 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 190 average time/residue: 0.2054 time to fit residues: 56.4897 Evaluate side-chains 186 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 184 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0892 time to fit residues: 1.6899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.7980 chunk 86 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN M 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.160241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110394 restraints weight = 15772.759| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.53 r_work: 0.3241 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9582 Z= 0.174 Angle : 0.619 10.547 13058 Z= 0.302 Chirality : 0.042 0.158 1490 Planarity : 0.005 0.046 1608 Dihedral : 6.852 59.499 1706 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.29 % Allowed : 20.41 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1192 helix: 1.79 (0.34), residues: 242 sheet: 1.75 (0.25), residues: 378 loop : -0.05 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 89 HIS 0.003 0.001 HIS D 63 PHE 0.015 0.001 PHE I 122 TYR 0.034 0.002 TYR C 94 ARG 0.003 0.000 ARG M 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2289.81 seconds wall clock time: 42 minutes 28.62 seconds (2548.62 seconds total)