Starting phenix.real_space_refine on Thu Mar 14 17:41:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vja_21212/03_2024/6vja_21212.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vja_21212/03_2024/6vja_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_21212/03_2024/6vja_21212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vja_21212/03_2024/6vja_21212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vja_21212/03_2024/6vja_21212.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vja_21212/03_2024/6vja_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-dev-5265/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: 5.47, per 1000 atoms: 0.59 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: 3.39 Conformation dependent library (CDL) restraints added in 2.0 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: 1.42 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: 2.77 Time building geometry restraints manager: 3.72 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: 1.220 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: 6.910 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.460 Find NCS groups from input model: 0.490 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.010 ------------------------------------------------------------------------------- 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 : 1.061 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 REVERT: C 56 GLN cc_start: 0.8829 (mt0) cc_final: 0.8580 (mt0) REVERT: C 113 VAL cc_start: 0.5993 (m) cc_final: 0.5431 (t) REVERT: C 116 LYS cc_start: 0.8669 (mttt) cc_final: 0.8354 (mttt) REVERT: C 147 LEU cc_start: 0.7698 (mt) cc_final: 0.7359 (mp) REVERT: D 58 MET cc_start: 0.9273 (mmp) cc_final: 0.9008 (mmm) REVERT: D 89 TRP cc_start: 0.8880 (OUTLIER) cc_final: 0.8337 (p90) REVERT: H 5 GLN cc_start: 0.8690 (tt0) cc_final: 0.8434 (tp40) REVERT: H 64 LYS cc_start: 0.8666 (tttt) cc_final: 0.8323 (ttpp) REVERT: H 72 ASP cc_start: 0.8158 (t0) cc_final: 0.7737 (t0) REVERT: H 77 THR cc_start: 0.9088 (m) cc_final: 0.8497 (p) REVERT: H 86 ASP cc_start: 0.8579 (m-30) cc_final: 0.8012 (m-30) REVERT: H 154 TRP cc_start: 0.8131 (m100) cc_final: 0.7790 (m100) REVERT: I 64 LYS cc_start: 0.8730 (tttt) cc_final: 0.8386 (ttpp) REVERT: I 72 ASP cc_start: 0.8162 (t0) cc_final: 0.7791 (t0) REVERT: I 77 THR cc_start: 0.8981 (m) cc_final: 0.8433 (p) REVERT: I 86 ASP cc_start: 0.8475 (m-30) cc_final: 0.7910 (m-30) REVERT: I 154 TRP cc_start: 0.8036 (m100) cc_final: 0.7734 (m100) REVERT: I 161 SER cc_start: 0.8296 (m) cc_final: 0.7886 (p) REVERT: I 214 LYS cc_start: 0.8374 (mttt) cc_final: 0.7822 (tptt) REVERT: L 82 ASP cc_start: 0.8242 (m-30) cc_final: 0.7847 (m-30) REVERT: L 117 ILE cc_start: 0.8791 (tt) cc_final: 0.8457 (tt) REVERT: L 118 PHE cc_start: 0.8244 (m-80) cc_final: 0.7475 (m-80) REVERT: L 124 GLN cc_start: 0.8046 (tt0) cc_final: 0.7758 (tt0) REVERT: L 126 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7628 (tppt) REVERT: M 24 ARG cc_start: 0.8363 (ttm110) cc_final: 0.7959 (ttp80) REVERT: M 82 ASP cc_start: 0.8188 (m-30) cc_final: 0.7828 (m-30) REVERT: M 118 PHE cc_start: 0.8278 (m-80) cc_final: 0.7451 (m-80) REVERT: M 124 GLN cc_start: 0.7880 (tt0) cc_final: 0.7628 (tt0) REVERT: M 126 LYS cc_start: 0.8047 (mtmt) cc_final: 0.7822 (tppt) REVERT: M 214 CYS cc_start: 0.3960 (t) cc_final: 0.3738 (t) outliers start: 5 outliers final: 1 residues processed: 306 average time/residue: 0.2006 time to fit residues: 85.0150 Evaluate side-chains 226 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain D residue 89 TRP 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: 2.9990 chunk 49 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN D 56 GLN D 63 HIS D 181 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN L 124 GLN M 53 ASN M 124 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9582 Z= 0.188 Angle : 0.648 8.282 13058 Z= 0.329 Chirality : 0.043 0.215 1490 Planarity : 0.004 0.043 1608 Dihedral : 7.665 59.810 1710 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.25 % Allowed : 10.55 % Favored : 87.21 % 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: 1.65 (0.24), residues: 1192 helix: 1.05 (0.33), residues: 248 sheet: 2.15 (0.25), residues: 404 loop : 0.35 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 89 HIS 0.003 0.001 HIS D 145 PHE 0.015 0.001 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 283 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 260 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 85 TRP cc_start: 0.8401 (m100) cc_final: 0.8168 (m100) REVERT: C 89 TRP cc_start: 0.8892 (OUTLIER) cc_final: 0.7874 (p90) REVERT: C 99 SER cc_start: 0.8655 (t) cc_final: 0.8440 (p) REVERT: C 116 LYS cc_start: 0.8388 (mttt) cc_final: 0.8063 (mmmt) REVERT: C 137 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8393 (m-30) REVERT: C 139 LEU cc_start: 0.9024 (mm) cc_final: 0.8719 (mm) REVERT: C 175 LYS cc_start: 0.8586 (mmtp) cc_final: 0.8359 (mmtp) REVERT: D 62 PHE cc_start: 0.8734 (t80) cc_final: 0.8383 (t80) REVERT: D 89 TRP cc_start: 0.8862 (OUTLIER) cc_final: 0.7784 (p90) REVERT: D 116 LYS cc_start: 0.8261 (mttt) cc_final: 0.7637 (mttt) REVERT: D 175 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8380 (mmtp) REVERT: H 64 LYS cc_start: 0.8559 (tttt) cc_final: 0.8239 (ttpp) REVERT: H 72 ASP cc_start: 0.8236 (t0) cc_final: 0.7910 (t0) REVERT: H 77 THR cc_start: 0.9018 (m) cc_final: 0.8476 (p) REVERT: H 86 ASP cc_start: 0.8243 (m-30) cc_final: 0.8040 (m-30) REVERT: H 154 TRP cc_start: 0.8241 (m100) cc_final: 0.7835 (m100) REVERT: I 5 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7454 (mp10) REVERT: I 64 LYS cc_start: 0.8611 (tttt) cc_final: 0.8305 (ttpp) REVERT: I 72 ASP cc_start: 0.8166 (t0) cc_final: 0.7922 (t0) REVERT: I 77 THR cc_start: 0.8993 (m) cc_final: 0.8445 (p) REVERT: I 86 ASP cc_start: 0.8146 (m-30) cc_final: 0.7799 (m-30) REVERT: I 122 PHE cc_start: 0.7352 (m-10) cc_final: 0.7093 (m-10) REVERT: I 154 TRP cc_start: 0.8160 (m100) cc_final: 0.7805 (m100) REVERT: I 161 SER cc_start: 0.8321 (m) cc_final: 0.7936 (p) REVERT: I 214 LYS cc_start: 0.8526 (mttt) cc_final: 0.8032 (tptt) REVERT: L 24 ARG cc_start: 0.8046 (ttp-110) cc_final: 0.7828 (ttp80) REVERT: L 79 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6778 (mt-10) REVERT: L 82 ASP cc_start: 0.8126 (m-30) cc_final: 0.7822 (m-30) REVERT: L 118 PHE cc_start: 0.8643 (m-80) cc_final: 0.7885 (m-80) REVERT: L 124 GLN cc_start: 0.7960 (tt0) cc_final: 0.7430 (tt0) REVERT: M 24 ARG cc_start: 0.8249 (ttm110) cc_final: 0.8013 (ttp80) REVERT: M 79 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6588 (mt-10) REVERT: M 82 ASP cc_start: 0.8056 (m-30) cc_final: 0.7731 (m-30) REVERT: M 118 PHE cc_start: 0.8554 (m-80) cc_final: 0.7876 (m-80) REVERT: M 124 GLN cc_start: 0.7941 (tt0) cc_final: 0.7409 (tt0) REVERT: M 214 CYS cc_start: 0.4367 (t) cc_final: 0.4129 (t) outliers start: 23 outliers final: 15 residues processed: 275 average time/residue: 0.1896 time to fit residues: 73.4581 Evaluate side-chains 236 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 217 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain L residue 158 ASN Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.0000 chunk 89 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN D 181 GLN L 160 GLN M 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9582 Z= 0.226 Angle : 0.618 7.371 13058 Z= 0.311 Chirality : 0.043 0.178 1490 Planarity : 0.005 0.048 1608 Dihedral : 7.369 54.972 1710 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.30 % Allowed : 12.11 % Favored : 83.59 % 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: 1.70 (0.24), residues: 1192 helix: 1.39 (0.34), residues: 246 sheet: 2.07 (0.25), residues: 384 loop : 0.40 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 89 HIS 0.004 0.001 HIS C 145 PHE 0.013 0.001 PHE H 100D TYR 0.039 0.002 TYR C 94 ARG 0.002 0.000 ARG D 109 *********************** 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 276 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 232 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 SER cc_start: 0.8706 (t) cc_final: 0.8504 (p) REVERT: C 116 LYS cc_start: 0.8319 (mttt) cc_final: 0.8043 (mmmt) REVERT: C 137 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8071 (m-30) REVERT: D 62 PHE cc_start: 0.8631 (t80) cc_final: 0.8138 (t80) REVERT: D 116 LYS cc_start: 0.8349 (mttt) cc_final: 0.7692 (mttt) REVERT: D 137 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8455 (m-30) REVERT: H 64 LYS cc_start: 0.8743 (tttt) cc_final: 0.8393 (ttpp) REVERT: H 72 ASP cc_start: 0.8253 (t0) cc_final: 0.7881 (t0) REVERT: H 77 THR cc_start: 0.8999 (m) cc_final: 0.8479 (p) REVERT: H 86 ASP cc_start: 0.8273 (m-30) cc_final: 0.7945 (m-30) REVERT: H 154 TRP cc_start: 0.8336 (m100) cc_final: 0.7944 (m100) REVERT: H 161 SER cc_start: 0.8278 (m) cc_final: 0.7902 (p) REVERT: I 64 LYS cc_start: 0.8700 (tttt) cc_final: 0.8366 (ttpp) REVERT: I 72 ASP cc_start: 0.8234 (t0) cc_final: 0.7888 (t0) REVERT: I 77 THR cc_start: 0.8995 (m) cc_final: 0.8465 (p) REVERT: I 86 ASP cc_start: 0.8235 (m-30) cc_final: 0.7867 (m-30) REVERT: I 154 TRP cc_start: 0.8286 (m100) cc_final: 0.7927 (m100) REVERT: I 161 SER cc_start: 0.8347 (m) cc_final: 0.8032 (p) REVERT: I 214 LYS cc_start: 0.8554 (mttt) cc_final: 0.8033 (tptt) REVERT: L 79 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6807 (mt-10) REVERT: L 82 ASP cc_start: 0.8038 (m-30) cc_final: 0.7626 (m-30) REVERT: L 118 PHE cc_start: 0.8585 (m-80) cc_final: 0.7929 (m-80) REVERT: L 124 GLN cc_start: 0.7897 (tt0) cc_final: 0.7267 (tt0) REVERT: M 24 ARG cc_start: 0.8251 (ttm110) cc_final: 0.8001 (ttp80) REVERT: M 79 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6790 (mt-10) REVERT: M 82 ASP cc_start: 0.8023 (m-30) cc_final: 0.7665 (m-30) REVERT: M 118 PHE cc_start: 0.8557 (m-80) cc_final: 0.7940 (m-80) REVERT: M 124 GLN cc_start: 0.7771 (tt0) cc_final: 0.7412 (tt0) REVERT: M 211 ARG cc_start: 0.6490 (ttp80) cc_final: 0.6033 (ptt180) REVERT: M 213 GLU cc_start: 0.6575 (pt0) cc_final: 0.6173 (pt0) outliers start: 44 outliers final: 32 residues processed: 257 average time/residue: 0.1905 time to fit residues: 69.0452 Evaluate side-chains 246 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 212 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain D residue 63 HIS Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 158 ASN Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 170 ASP Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL 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: 0.0870 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 0.0040 chunk 72 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 56 optimal weight: 0.0970 chunk 102 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9582 Z= 0.187 Angle : 0.579 7.333 13058 Z= 0.287 Chirality : 0.042 0.155 1490 Planarity : 0.004 0.046 1608 Dihedral : 7.169 55.033 1710 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.30 % Allowed : 13.38 % Favored : 82.32 % 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: 1.71 (0.25), residues: 1192 helix: 1.61 (0.34), residues: 246 sheet: 1.96 (0.25), residues: 392 loop : 0.37 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 89 HIS 0.003 0.001 HIS C 145 PHE 0.013 0.001 PHE C 62 TYR 0.041 0.002 TYR C 94 ARG 0.001 0.000 ARG D 109 *********************** 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 255 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 211 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8738 (OUTLIER) cc_final: 0.7646 (p90) REVERT: C 116 LYS cc_start: 0.8335 (mttt) cc_final: 0.8046 (mmmt) REVERT: C 175 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8372 (mmtp) REVERT: D 116 LYS cc_start: 0.8391 (mttt) cc_final: 0.7726 (mttt) REVERT: D 137 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8264 (m-30) REVERT: H 64 LYS cc_start: 0.8683 (tttt) cc_final: 0.8352 (ttpp) REVERT: H 72 ASP cc_start: 0.8170 (t0) cc_final: 0.7762 (t0) REVERT: H 77 THR cc_start: 0.8996 (m) cc_final: 0.8536 (p) REVERT: H 86 ASP cc_start: 0.8145 (m-30) cc_final: 0.7834 (m-30) REVERT: H 161 SER cc_start: 0.8310 (m) cc_final: 0.7958 (p) REVERT: H 195 ILE cc_start: 0.7027 (mm) cc_final: 0.6733 (tp) REVERT: I 64 LYS cc_start: 0.8726 (tttt) cc_final: 0.8368 (ttpp) REVERT: I 72 ASP cc_start: 0.8205 (t0) cc_final: 0.7823 (t0) REVERT: I 77 THR cc_start: 0.8992 (m) cc_final: 0.8465 (p) REVERT: I 86 ASP cc_start: 0.8127 (m-30) cc_final: 0.7772 (m-30) REVERT: I 154 TRP cc_start: 0.8291 (m100) cc_final: 0.7910 (m100) REVERT: I 161 SER cc_start: 0.8232 (m) cc_final: 0.7928 (p) REVERT: I 195 ILE cc_start: 0.6648 (OUTLIER) cc_final: 0.6211 (mm) REVERT: I 214 LYS cc_start: 0.8524 (mttt) cc_final: 0.8018 (tptt) REVERT: L 82 ASP cc_start: 0.8102 (m-30) cc_final: 0.7786 (m-30) REVERT: L 118 PHE cc_start: 0.8548 (m-80) cc_final: 0.7945 (m-80) REVERT: L 124 GLN cc_start: 0.7844 (tt0) cc_final: 0.7151 (tt0) REVERT: L 165 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8837 (tp30) REVERT: M 24 ARG cc_start: 0.8226 (ttm110) cc_final: 0.7983 (ttp80) REVERT: M 79 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6765 (mt-10) REVERT: M 82 ASP cc_start: 0.8031 (m-30) cc_final: 0.7685 (m-30) REVERT: M 118 PHE cc_start: 0.8541 (m-80) cc_final: 0.7964 (m-80) REVERT: M 124 GLN cc_start: 0.7644 (tt0) cc_final: 0.7215 (tt0) outliers start: 44 outliers final: 29 residues processed: 237 average time/residue: 0.1884 time to fit residues: 63.4145 Evaluate side-chains 233 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain L residue 158 ASN Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 170 ASP Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 97 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9582 Z= 0.143 Angle : 0.552 6.849 13058 Z= 0.271 Chirality : 0.041 0.148 1490 Planarity : 0.004 0.046 1608 Dihedral : 7.000 56.723 1710 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.52 % Allowed : 14.26 % 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: 1.79 (0.25), residues: 1192 helix: 1.76 (0.35), residues: 246 sheet: 1.96 (0.25), residues: 394 loop : 0.40 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 89 HIS 0.002 0.000 HIS M 189 PHE 0.013 0.001 PHE C 62 TYR 0.040 0.001 TYR C 94 ARG 0.002 0.000 ARG L 211 *********************** 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 246 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8543 (OUTLIER) cc_final: 0.7527 (p90) REVERT: C 116 LYS cc_start: 0.8372 (mttt) cc_final: 0.8080 (mmmt) REVERT: C 175 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8361 (mmtp) REVERT: D 89 TRP cc_start: 0.8654 (OUTLIER) cc_final: 0.7406 (p90) REVERT: D 116 LYS cc_start: 0.8373 (mttt) cc_final: 0.7720 (mttt) REVERT: D 137 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: D 175 LYS cc_start: 0.8688 (mmtp) cc_final: 0.8388 (mmtp) REVERT: H 64 LYS cc_start: 0.8550 (tttt) cc_final: 0.8236 (ttpp) REVERT: H 72 ASP cc_start: 0.8155 (t0) cc_final: 0.7707 (t0) REVERT: H 77 THR cc_start: 0.8986 (m) cc_final: 0.8552 (p) REVERT: H 86 ASP cc_start: 0.8043 (m-30) cc_final: 0.7764 (m-30) REVERT: H 161 SER cc_start: 0.8212 (m) cc_final: 0.7883 (p) REVERT: H 195 ILE cc_start: 0.7115 (mm) cc_final: 0.6844 (tp) REVERT: I 64 LYS cc_start: 0.8546 (tttt) cc_final: 0.8194 (ttpp) REVERT: I 72 ASP cc_start: 0.8159 (t0) cc_final: 0.7725 (t0) REVERT: I 77 THR cc_start: 0.8984 (m) cc_final: 0.8543 (p) REVERT: I 161 SER cc_start: 0.8279 (m) cc_final: 0.7942 (p) REVERT: I 195 ILE cc_start: 0.6563 (OUTLIER) cc_final: 0.6324 (mm) REVERT: I 214 LYS cc_start: 0.8465 (mttt) cc_final: 0.7963 (tptt) REVERT: L 79 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6826 (mt-10) REVERT: L 82 ASP cc_start: 0.8095 (m-30) cc_final: 0.7697 (m-30) REVERT: L 118 PHE cc_start: 0.8556 (m-80) cc_final: 0.8031 (m-80) REVERT: L 124 GLN cc_start: 0.7822 (tt0) cc_final: 0.7123 (tt0) REVERT: L 165 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8837 (tp30) REVERT: M 24 ARG cc_start: 0.8213 (ttm110) cc_final: 0.7985 (ttp80) REVERT: M 82 ASP cc_start: 0.8001 (m-30) cc_final: 0.7735 (m-30) REVERT: M 118 PHE cc_start: 0.8532 (m-80) cc_final: 0.8048 (m-80) REVERT: M 124 GLN cc_start: 0.7658 (tt0) cc_final: 0.7010 (tt0) REVERT: M 126 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7638 (tppt) outliers start: 36 outliers final: 27 residues processed: 227 average time/residue: 0.1859 time to fit residues: 60.1202 Evaluate side-chains 231 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 200 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 63 HIS Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain L residue 158 ASN Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 170 ASP Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN 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: 0.7892 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9582 Z= 0.357 Angle : 0.661 9.835 13058 Z= 0.331 Chirality : 0.044 0.173 1490 Planarity : 0.005 0.048 1608 Dihedral : 7.300 58.606 1710 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.30 % Allowed : 15.43 % Favored : 80.27 % 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: 1.46 (0.24), residues: 1192 helix: 1.44 (0.34), residues: 246 sheet: 1.86 (0.25), residues: 378 loop : 0.19 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I 154 HIS 0.004 0.001 HIS L 34 PHE 0.016 0.002 PHE I 122 TYR 0.043 0.002 TYR C 94 ARG 0.004 0.001 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 241 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 197 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8753 (OUTLIER) cc_final: 0.7685 (p90) REVERT: C 197 MET cc_start: 0.9544 (ttm) cc_final: 0.9231 (ttp) REVERT: D 116 LYS cc_start: 0.8507 (mttt) cc_final: 0.7941 (mttt) REVERT: D 197 MET cc_start: 0.9487 (ttm) cc_final: 0.9181 (ttp) REVERT: H 64 LYS cc_start: 0.8852 (tttt) cc_final: 0.8471 (ttpp) REVERT: H 72 ASP cc_start: 0.8196 (t0) cc_final: 0.7766 (t0) REVERT: H 77 THR cc_start: 0.8976 (m) cc_final: 0.8352 (p) REVERT: H 86 ASP cc_start: 0.8219 (m-30) cc_final: 0.7913 (m-30) REVERT: H 154 TRP cc_start: 0.8378 (m100) cc_final: 0.8006 (m100) REVERT: H 161 SER cc_start: 0.8279 (m) cc_final: 0.7980 (p) REVERT: I 64 LYS cc_start: 0.8864 (tttt) cc_final: 0.8481 (ttpp) REVERT: I 72 ASP cc_start: 0.8231 (t0) cc_final: 0.7802 (t0) REVERT: I 77 THR cc_start: 0.8970 (m) cc_final: 0.8334 (p) REVERT: I 86 ASP cc_start: 0.8385 (m-30) cc_final: 0.8174 (m-30) REVERT: I 161 SER cc_start: 0.8307 (m) cc_final: 0.7993 (p) REVERT: I 195 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6344 (mm) REVERT: I 214 LYS cc_start: 0.8447 (mttt) cc_final: 0.7892 (tptt) REVERT: L 82 ASP cc_start: 0.8109 (m-30) cc_final: 0.7822 (m-30) REVERT: L 118 PHE cc_start: 0.8607 (m-80) cc_final: 0.7977 (m-80) REVERT: L 124 GLN cc_start: 0.7785 (tt0) cc_final: 0.7080 (tt0) REVERT: L 165 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8808 (tp30) REVERT: M 24 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7966 (ttp80) REVERT: M 79 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6647 (mt-10) REVERT: M 82 ASP cc_start: 0.8133 (m-30) cc_final: 0.7762 (m-30) REVERT: M 118 PHE cc_start: 0.8503 (m-80) cc_final: 0.7925 (m-80) REVERT: M 124 GLN cc_start: 0.7445 (tt0) cc_final: 0.6778 (tt0) REVERT: M 126 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7615 (tppt) outliers start: 44 outliers final: 33 residues processed: 223 average time/residue: 0.1901 time to fit residues: 59.8118 Evaluate side-chains 229 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 193 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain L residue 158 ASN Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 170 ASP Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN 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: 0.7870 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9582 Z= 0.268 Angle : 0.615 8.551 13058 Z= 0.305 Chirality : 0.043 0.151 1490 Planarity : 0.005 0.056 1608 Dihedral : 7.161 55.065 1710 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.20 % Allowed : 16.70 % Favored : 79.10 % 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: 1.41 (0.24), residues: 1192 helix: 1.49 (0.34), residues: 246 sheet: 1.83 (0.25), residues: 380 loop : 0.11 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 89 HIS 0.003 0.001 HIS M 34 PHE 0.020 0.001 PHE D 62 TYR 0.042 0.002 TYR C 94 ARG 0.002 0.000 ARG I 94 *********************** 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 238 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 195 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8710 (OUTLIER) cc_final: 0.7591 (p90) REVERT: C 116 LYS cc_start: 0.8462 (mttt) cc_final: 0.8189 (mmmt) REVERT: C 175 LYS cc_start: 0.8777 (mmtp) cc_final: 0.8576 (mmtm) REVERT: C 197 MET cc_start: 0.9536 (ttm) cc_final: 0.9206 (ttp) REVERT: D 116 LYS cc_start: 0.8481 (mttt) cc_final: 0.7893 (mttt) REVERT: D 137 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.7748 (m-30) REVERT: D 197 MET cc_start: 0.9473 (ttm) cc_final: 0.9181 (ttp) REVERT: H 64 LYS cc_start: 0.8819 (tttt) cc_final: 0.8443 (ttpp) REVERT: H 72 ASP cc_start: 0.8170 (t0) cc_final: 0.7743 (t0) REVERT: H 77 THR cc_start: 0.8993 (m) cc_final: 0.8403 (p) REVERT: H 86 ASP cc_start: 0.8115 (m-30) cc_final: 0.7836 (m-30) REVERT: H 161 SER cc_start: 0.8256 (m) cc_final: 0.7935 (p) REVERT: I 64 LYS cc_start: 0.8787 (tttt) cc_final: 0.8418 (ttpp) REVERT: I 72 ASP cc_start: 0.8196 (t0) cc_final: 0.7767 (t0) REVERT: I 77 THR cc_start: 0.8989 (m) cc_final: 0.8383 (p) REVERT: I 86 ASP cc_start: 0.8350 (m-30) cc_final: 0.8140 (m-30) REVERT: I 161 SER cc_start: 0.8372 (m) cc_final: 0.8073 (p) REVERT: I 195 ILE cc_start: 0.6732 (OUTLIER) cc_final: 0.6429 (mm) REVERT: I 214 LYS cc_start: 0.8441 (mttt) cc_final: 0.7921 (tptt) REVERT: L 79 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6893 (mt-10) REVERT: L 82 ASP cc_start: 0.8091 (m-30) cc_final: 0.7706 (m-30) REVERT: L 118 PHE cc_start: 0.8607 (m-80) cc_final: 0.7924 (m-80) REVERT: L 124 GLN cc_start: 0.7808 (tt0) cc_final: 0.7118 (tt0) REVERT: L 165 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8833 (tp30) REVERT: L 211 ARG cc_start: 0.7325 (ptm-80) cc_final: 0.6994 (ptm-80) REVERT: M 24 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7935 (ttp80) REVERT: M 79 GLU cc_start: 0.7476 (mt-10) cc_final: 0.6824 (mt-10) REVERT: M 82 ASP cc_start: 0.8112 (m-30) cc_final: 0.7742 (m-30) REVERT: M 118 PHE cc_start: 0.8534 (m-80) cc_final: 0.7931 (m-80) REVERT: M 124 GLN cc_start: 0.7461 (tt0) cc_final: 0.6891 (tt0) REVERT: M 126 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7596 (tppt) outliers start: 43 outliers final: 32 residues processed: 223 average time/residue: 0.1854 time to fit residues: 59.0714 Evaluate side-chains 229 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 193 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain L residue 158 ASN Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 170 ASP Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN H 6 GLN I 6 GLN M 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9582 Z= 0.308 Angle : 0.637 8.550 13058 Z= 0.318 Chirality : 0.043 0.148 1490 Planarity : 0.005 0.053 1608 Dihedral : 7.222 54.258 1710 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.10 % Allowed : 16.60 % 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: 1.21 (0.24), residues: 1192 helix: 1.30 (0.34), residues: 246 sheet: 1.72 (0.25), residues: 380 loop : -0.02 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 89 HIS 0.003 0.001 HIS M 189 PHE 0.021 0.002 PHE D 62 TYR 0.042 0.002 TYR C 94 ARG 0.002 0.000 ARG I 94 *********************** 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 239 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 197 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8733 (OUTLIER) cc_final: 0.7597 (p90) REVERT: C 197 MET cc_start: 0.9538 (ttm) cc_final: 0.9203 (ttp) REVERT: D 116 LYS cc_start: 0.8483 (mttt) cc_final: 0.7900 (mttt) REVERT: D 133 LEU cc_start: 0.8727 (mt) cc_final: 0.8255 (mp) REVERT: D 137 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: D 197 MET cc_start: 0.9480 (ttm) cc_final: 0.9174 (ttp) REVERT: H 64 LYS cc_start: 0.8839 (tttt) cc_final: 0.8477 (ttpp) REVERT: H 72 ASP cc_start: 0.8167 (t0) cc_final: 0.7679 (t0) REVERT: H 77 THR cc_start: 0.8986 (m) cc_final: 0.8353 (p) REVERT: H 86 ASP cc_start: 0.8069 (m-30) cc_final: 0.7793 (m-30) REVERT: H 154 TRP cc_start: 0.8357 (m100) cc_final: 0.7992 (m100) REVERT: H 161 SER cc_start: 0.8278 (m) cc_final: 0.8055 (p) REVERT: I 64 LYS cc_start: 0.8806 (tttt) cc_final: 0.8452 (ttpp) REVERT: I 72 ASP cc_start: 0.8188 (t0) cc_final: 0.7763 (t0) REVERT: I 77 THR cc_start: 0.8970 (m) cc_final: 0.8311 (p) REVERT: I 86 ASP cc_start: 0.8338 (m-30) cc_final: 0.8121 (m-30) REVERT: I 161 SER cc_start: 0.8459 (m) cc_final: 0.8185 (p) REVERT: I 195 ILE cc_start: 0.6668 (OUTLIER) cc_final: 0.6367 (mm) REVERT: I 214 LYS cc_start: 0.8467 (mttt) cc_final: 0.7894 (tptt) REVERT: L 24 ARG cc_start: 0.8123 (ttp-110) cc_final: 0.7780 (ttp80) REVERT: L 79 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6912 (mt-10) REVERT: L 82 ASP cc_start: 0.8121 (m-30) cc_final: 0.7717 (m-30) REVERT: L 118 PHE cc_start: 0.8589 (m-80) cc_final: 0.7916 (m-80) REVERT: L 124 GLN cc_start: 0.7631 (tt0) cc_final: 0.6910 (tt0) REVERT: L 211 ARG cc_start: 0.7279 (ptm-80) cc_final: 0.6863 (ptm-80) REVERT: M 24 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7923 (ttp80) REVERT: M 79 GLU cc_start: 0.7607 (mt-10) cc_final: 0.6895 (mt-10) REVERT: M 82 ASP cc_start: 0.8120 (m-30) cc_final: 0.7741 (m-30) REVERT: M 102 THR cc_start: 0.8837 (m) cc_final: 0.8630 (m) REVERT: M 118 PHE cc_start: 0.8513 (m-80) cc_final: 0.7957 (m-80) REVERT: M 126 LYS cc_start: 0.7991 (mtmt) cc_final: 0.7595 (tppt) outliers start: 42 outliers final: 33 residues processed: 224 average time/residue: 0.1885 time to fit residues: 60.2007 Evaluate side-chains 229 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 193 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain L residue 158 ASN Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 170 ASP Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 0.0970 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 112 optimal weight: 30.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9582 Z= 0.183 Angle : 0.584 8.589 13058 Z= 0.285 Chirality : 0.042 0.147 1490 Planarity : 0.005 0.042 1608 Dihedral : 7.035 55.975 1710 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.52 % Allowed : 17.38 % Favored : 79.10 % 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: 1.49 (0.25), residues: 1192 helix: 1.88 (0.35), residues: 238 sheet: 1.78 (0.25), residues: 378 loop : 0.09 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP I 154 HIS 0.002 0.000 HIS M 189 PHE 0.014 0.001 PHE I 122 TYR 0.040 0.001 TYR C 94 ARG 0.002 0.000 ARG L 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 241 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 205 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8566 (OUTLIER) cc_final: 0.7533 (p90) REVERT: C 116 LYS cc_start: 0.8455 (mttt) cc_final: 0.8179 (mmmt) REVERT: C 204 GLN cc_start: 0.8935 (tp40) cc_final: 0.8533 (tp-100) REVERT: D 116 LYS cc_start: 0.8355 (mttt) cc_final: 0.7738 (mttt) REVERT: D 133 LEU cc_start: 0.8630 (mt) cc_final: 0.8324 (mp) REVERT: D 137 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.7677 (m-30) REVERT: H 64 LYS cc_start: 0.8674 (tttt) cc_final: 0.8321 (ttpp) REVERT: H 72 ASP cc_start: 0.8112 (t0) cc_final: 0.7627 (t0) REVERT: H 77 THR cc_start: 0.9000 (m) cc_final: 0.8489 (p) REVERT: H 86 ASP cc_start: 0.7881 (m-30) cc_final: 0.7648 (m-30) REVERT: I 64 LYS cc_start: 0.8635 (tttt) cc_final: 0.8267 (ttpp) REVERT: I 72 ASP cc_start: 0.8141 (t0) cc_final: 0.7719 (t0) REVERT: I 77 THR cc_start: 0.8991 (m) cc_final: 0.8458 (p) REVERT: I 97 TYR cc_start: 0.8843 (t80) cc_final: 0.8358 (t80) REVERT: I 161 SER cc_start: 0.8479 (m) cc_final: 0.8266 (p) REVERT: I 195 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6484 (mm) REVERT: I 214 LYS cc_start: 0.8521 (mttt) cc_final: 0.7944 (tptt) REVERT: L 24 ARG cc_start: 0.7998 (ttp-110) cc_final: 0.7702 (ttp80) REVERT: L 82 ASP cc_start: 0.8169 (m-30) cc_final: 0.7861 (m-30) REVERT: L 118 PHE cc_start: 0.8599 (m-80) cc_final: 0.7959 (m-80) REVERT: L 124 GLN cc_start: 0.7777 (tt0) cc_final: 0.7113 (tt0) REVERT: M 24 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7935 (ttp80) REVERT: M 82 ASP cc_start: 0.8136 (m-30) cc_final: 0.7848 (m-30) REVERT: M 118 PHE cc_start: 0.8537 (m-80) cc_final: 0.8076 (m-80) REVERT: M 124 GLN cc_start: 0.6911 (tt0) cc_final: 0.6550 (tt0) REVERT: M 126 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7637 (tppt) outliers start: 36 outliers final: 31 residues processed: 226 average time/residue: 0.1859 time to fit residues: 60.0782 Evaluate side-chains 237 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 203 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 158 ASN Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 170 ASP Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 9 optimal weight: 0.0870 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.6962 ------------------------------------------------------------------------------- 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 L 6 GLN M 6 GLN M 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9582 Z= 0.206 Angle : 0.591 8.654 13058 Z= 0.289 Chirality : 0.041 0.142 1490 Planarity : 0.005 0.046 1608 Dihedral : 6.994 55.711 1710 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.52 % Allowed : 17.48 % Favored : 79.00 % 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: 1.50 (0.25), residues: 1192 helix: 1.95 (0.35), residues: 238 sheet: 1.79 (0.25), residues: 392 loop : 0.02 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP I 154 HIS 0.002 0.000 HIS M 34 PHE 0.015 0.001 PHE D 62 TYR 0.041 0.002 TYR C 94 ARG 0.002 0.000 ARG H 94 ********************** 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 240 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 204 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 TRP cc_start: 0.8532 (OUTLIER) cc_final: 0.7531 (p90) REVERT: C 116 LYS cc_start: 0.8470 (mttt) cc_final: 0.8215 (mmmt) REVERT: C 204 GLN cc_start: 0.8908 (tp40) cc_final: 0.8529 (tp-100) REVERT: D 116 LYS cc_start: 0.8379 (mttt) cc_final: 0.7775 (mttt) REVERT: D 133 LEU cc_start: 0.8676 (mt) cc_final: 0.8172 (mp) REVERT: D 137 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.7718 (m-30) REVERT: D 197 MET cc_start: 0.9486 (ttm) cc_final: 0.9174 (ttp) REVERT: H 64 LYS cc_start: 0.8694 (tttt) cc_final: 0.8335 (ttpp) REVERT: H 72 ASP cc_start: 0.8186 (t0) cc_final: 0.7665 (t0) REVERT: H 77 THR cc_start: 0.9011 (m) cc_final: 0.8493 (p) REVERT: H 86 ASP cc_start: 0.7902 (m-30) cc_final: 0.7635 (m-30) REVERT: I 64 LYS cc_start: 0.8705 (tttt) cc_final: 0.8339 (ttpp) REVERT: I 72 ASP cc_start: 0.8123 (t0) cc_final: 0.7654 (t0) REVERT: I 77 THR cc_start: 0.8996 (m) cc_final: 0.8460 (p) REVERT: I 97 TYR cc_start: 0.8872 (t80) cc_final: 0.8402 (t80) REVERT: I 161 SER cc_start: 0.8681 (m) cc_final: 0.8434 (p) REVERT: I 214 LYS cc_start: 0.8516 (mttt) cc_final: 0.7933 (tptt) REVERT: L 24 ARG cc_start: 0.8013 (ttp-110) cc_final: 0.7689 (ttp80) REVERT: L 82 ASP cc_start: 0.8153 (m-30) cc_final: 0.7853 (m-30) REVERT: L 118 PHE cc_start: 0.8577 (m-80) cc_final: 0.7976 (m-80) REVERT: L 124 GLN cc_start: 0.7798 (tt0) cc_final: 0.7123 (tt0) REVERT: M 24 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7931 (ttp80) REVERT: M 82 ASP cc_start: 0.8156 (m-30) cc_final: 0.7862 (m-30) REVERT: M 118 PHE cc_start: 0.8522 (m-80) cc_final: 0.8080 (m-80) REVERT: M 124 GLN cc_start: 0.6740 (tt0) cc_final: 0.6193 (tt0) REVERT: M 211 ARG cc_start: 0.7704 (ptm-80) cc_final: 0.7358 (ptm-80) outliers start: 36 outliers final: 30 residues processed: 226 average time/residue: 0.1720 time to fit residues: 56.0021 Evaluate side-chains 233 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 TRP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 89 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 158 ASN Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 170 ASP Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.0770 chunk 86 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 39 optimal weight: 0.0050 chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.4552 ------------------------------------------------------------------------------- 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 6 GLN M 6 GLN M 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.162799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.113530 restraints weight = 15913.608| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.53 r_work: 0.3287 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9582 Z= 0.118 Angle : 0.549 8.285 13058 Z= 0.265 Chirality : 0.041 0.159 1490 Planarity : 0.004 0.042 1608 Dihedral : 6.718 57.295 1710 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.44 % Allowed : 18.65 % Favored : 78.91 % 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: 1.59 (0.25), residues: 1192 helix: 1.82 (0.35), residues: 250 sheet: 1.90 (0.25), residues: 388 loop : 0.12 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP I 154 HIS 0.004 0.001 HIS C 63 PHE 0.019 0.001 PHE D 62 TYR 0.038 0.001 TYR C 94 ARG 0.001 0.000 ARG L 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2300.28 seconds wall clock time: 41 minutes 59.93 seconds (2519.93 seconds total)