Starting phenix.real_space_refine on Tue Dec 31 04:56:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y92_10732/12_2024/6y92_10732.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y92_10732/12_2024/6y92_10732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6y92_10732/12_2024/6y92_10732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y92_10732/12_2024/6y92_10732.map" model { file = "/net/cci-nas-00/data/ceres_data/6y92_10732/12_2024/6y92_10732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y92_10732/12_2024/6y92_10732.cif" } resolution = 4.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6498 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 6105 2.51 5 N 1550 2.21 5 O 1792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9497 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain: "D" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1632 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 198} Chain: "C" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1629 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain breaks: 1 Chain: "B" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 121 Unusual residues: {'Y01': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Restraints were copied for chains: H, L Time building chain proxies: 6.75, per 1000 atoms: 0.71 Number of scatterers: 9497 At special positions: 0 Unit cell: (91, 130, 147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1792 8.00 N 1550 7.00 C 6105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 205 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.1 seconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 20 sheets defined 22.5% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 49 through 70 removed outlier: 3.924A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N MET A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 85 removed outlier: 4.138A pdb=" N THR A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP A 85 " --> pdb=" O CYS A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 85' Processing helix chain 'A' and resid 85 through 101 removed outlier: 3.559A pdb=" N TRP A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 140 removed outlier: 3.596A pdb=" N ASN A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 183 through 216 Processing helix chain 'D' and resid 121 through 128 removed outlier: 3.741A pdb=" N GLY D 128 " --> pdb=" O GLN D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 188 removed outlier: 3.566A pdb=" N LYS D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.741A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 188 removed outlier: 3.566A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 70 removed outlier: 3.617A pdb=" N GLY B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N MET B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 removed outlier: 4.174A pdb=" N THR B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 84' Processing helix chain 'B' and resid 85 through 101 removed outlier: 3.893A pdb=" N TRP B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 140 removed outlier: 4.254A pdb=" N ILE B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 177 through 216 removed outlier: 3.794A pdb=" N GLU B 215 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP B 216 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'D' and resid 20 through 21 removed outlier: 4.045A pdb=" N LEU D 21 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU D 73 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 45 through 49 removed outlier: 7.008A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA D 34 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN D 89 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR D 36 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR D 87 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN D 38 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 130 through 139 removed outlier: 3.966A pdb=" N VAL D 132 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU D 179 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 153 through 154 removed outlier: 4.161A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS D 194 " --> pdb=" O LYS D 207 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS D 207 " --> pdb=" O CYS D 194 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL D 196 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.708A pdb=" N VAL C 5 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR C 80 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.850A pdb=" N GLY C 59 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR C 50 " --> pdb=" O GLY C 59 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N THR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N MET C 34 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 111 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AA9, first strand: chain 'C' and resid 129 through 133 removed outlier: 3.529A pdb=" N LEU C 150 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 133 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY C 148 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 147 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 189 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL C 151 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU C 187 " --> pdb=" O VAL C 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 160 through 163 removed outlier: 3.728A pdb=" N THR C 160 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N CYS C 205 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS C 218 " --> pdb=" O CYS C 205 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 207 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL C 216 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.709A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TYR H 80 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 59 through 60 removed outlier: 3.851A pdb=" N GLY H 59 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR H 50 " --> pdb=" O GLY H 59 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL H 111 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 93 through 94 Processing sheet with id=AB5, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.529A pdb=" N LEU H 150 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU H 133 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU H 147 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER H 189 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL H 151 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU H 187 " --> pdb=" O VAL H 151 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 160 through 163 removed outlier: 3.729A pdb=" N THR H 160 " --> pdb=" O ASN H 208 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYS H 205 " --> pdb=" O LYS H 218 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS H 218 " --> pdb=" O CYS H 205 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL H 207 " --> pdb=" O VAL H 216 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL H 216 " --> pdb=" O VAL H 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'L' and resid 20 through 21 removed outlier: 4.044A pdb=" N LEU L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU L 73 " --> pdb=" O LEU L 21 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 45 through 49 removed outlier: 7.008A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN L 38 " --> pdb=" O VAL L 85 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 130 through 139 removed outlier: 3.966A pdb=" N VAL L 132 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU L 179 " --> pdb=" O VAL L 132 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 153 through 154 removed outlier: 4.161A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL L 196 " --> pdb=" O VAL L 205 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2960 1.35 - 1.46: 2342 1.46 - 1.58: 4353 1.58 - 1.70: 0 1.70 - 1.81: 76 Bond restraints: 9731 Sorted by residual: bond pdb=" CAZ Y01 B 304 " pdb=" CBH Y01 B 304 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" CAZ Y01 B 302 " pdb=" CBH Y01 B 302 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" CAZ Y01 A 301 " pdb=" CBH Y01 A 301 " ideal model delta sigma weight residual 1.519 1.406 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" CAZ Y01 B 303 " pdb=" CBH Y01 B 303 " ideal model delta sigma weight residual 1.519 1.406 0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" CAZ Y01 B 301 " pdb=" CBH Y01 B 301 " ideal model delta sigma weight residual 1.519 1.407 0.112 2.00e-02 2.50e+03 3.16e+01 ... (remaining 9726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 12955 2.45 - 4.89: 242 4.89 - 7.34: 44 7.34 - 9.79: 10 9.79 - 12.24: 2 Bond angle restraints: 13253 Sorted by residual: angle pdb=" CB LYS L 190 " pdb=" CG LYS L 190 " pdb=" CD LYS L 190 " ideal model delta sigma weight residual 111.30 123.54 -12.24 2.30e+00 1.89e-01 2.83e+01 angle pdb=" CB LYS D 190 " pdb=" CG LYS D 190 " pdb=" CD LYS D 190 " ideal model delta sigma weight residual 111.30 123.53 -12.23 2.30e+00 1.89e-01 2.83e+01 angle pdb=" CG LYS L 190 " pdb=" CD LYS L 190 " pdb=" CE LYS L 190 " ideal model delta sigma weight residual 111.30 120.21 -8.91 2.30e+00 1.89e-01 1.50e+01 angle pdb=" CG LYS D 190 " pdb=" CD LYS D 190 " pdb=" CE LYS D 190 " ideal model delta sigma weight residual 111.30 120.21 -8.91 2.30e+00 1.89e-01 1.50e+01 angle pdb=" N VAL B 113 " pdb=" CA VAL B 113 " pdb=" C VAL B 113 " ideal model delta sigma weight residual 113.53 109.75 3.78 9.80e-01 1.04e+00 1.49e+01 ... (remaining 13248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.18: 5543 19.18 - 38.36: 433 38.36 - 57.54: 76 57.54 - 76.72: 28 76.72 - 95.91: 5 Dihedral angle restraints: 6085 sinusoidal: 2587 harmonic: 3498 Sorted by residual: dihedral pdb=" CB CYS C 149 " pdb=" SG CYS C 149 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual 93.00 29.28 63.72 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CB CYS A 167 " pdb=" SG CYS A 167 " pdb=" SG CYS A 183 " pdb=" CB CYS A 183 " ideal model delta sinusoidal sigma weight residual 93.00 148.52 -55.52 1 1.00e+01 1.00e-02 4.16e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 148.27 -55.27 1 1.00e+01 1.00e-02 4.13e+01 ... (remaining 6082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1419 0.097 - 0.194: 63 0.194 - 0.292: 3 0.292 - 0.389: 12 0.389 - 0.486: 11 Chirality restraints: 1508 Sorted by residual: chirality pdb=" CBG Y01 A 302 " pdb=" CAQ Y01 A 302 " pdb=" CBD Y01 A 302 " pdb=" CBI Y01 A 302 " both_signs ideal model delta sigma weight residual False -2.33 -2.82 0.49 2.00e-01 2.50e+01 5.90e+00 chirality pdb=" CBH Y01 A 301 " pdb=" CAT Y01 A 301 " pdb=" CAZ Y01 A 301 " pdb=" CBF Y01 A 301 " both_signs ideal model delta sigma weight residual False -2.85 -2.40 -0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" CBH Y01 B 304 " pdb=" CAT Y01 B 304 " pdb=" CAZ Y01 B 304 " pdb=" CBF Y01 B 304 " both_signs ideal model delta sigma weight residual False -2.85 -2.40 -0.45 2.00e-01 2.50e+01 5.16e+00 ... (remaining 1505 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 182 " 0.022 2.00e-02 2.50e+03 2.05e-02 8.44e+00 pdb=" CG TYR A 182 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 182 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 182 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 182 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 182 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 182 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 182 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 159 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO A 160 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 160 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 160 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 157 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO C 158 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 158 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 158 " 0.017 5.00e-02 4.00e+02 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 86 2.60 - 3.18: 7775 3.18 - 3.75: 13438 3.75 - 4.33: 16677 4.33 - 4.90: 27016 Nonbonded interactions: 64992 Sorted by model distance: nonbonded pdb=" SG CYS B 167 " pdb=" SG CYS B 183 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS H 149 " pdb=" SG CYS H 205 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " model vdw 2.033 3.760 ... (remaining 64987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 218 or (resid 301 and (name CAA or name CAB or \ name CAC or name CAD or name CAE or name CAI or name CAJ or name CAK or name CAN \ or name CAO or name CAP or name CAQ or name CAR or name CAS or name CAT or name \ CAU or name CAV or name CAZ or name CBA or name CBB or name CBC or name CBD or \ name CBE or name CBF or name CBG or name CBH or name CBI or name OAW)) or (resid \ 302 and (name CAC or name CAD or name CAE or name CAI or name CAK or name CAL o \ r name CAM or name CAO or name CAP or name CAQ or name CAR or name CAS or name C \ AT or name CAU or name CAV or name CAX or name CAY or name CAZ or name CBB or na \ me CBC or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI o \ r name OAF or name OAG or name OAH or name OAW)))) selection = (chain 'B' and (resid 41 through 218 or resid 301 through 302)) } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.000 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 9731 Z= 0.374 Angle : 0.774 12.237 13253 Z= 0.355 Chirality : 0.064 0.486 1508 Planarity : 0.003 0.038 1646 Dihedral : 14.344 95.906 3830 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.77 % Allowed : 0.19 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1194 helix: 0.94 (0.33), residues: 232 sheet: 1.24 (0.36), residues: 224 loop : -1.57 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 216 HIS 0.001 0.000 HIS A 145 PHE 0.021 0.001 PHE C 29 TYR 0.049 0.001 TYR A 182 ARG 0.002 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 243 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8849 (mmm) cc_final: 0.8534 (mmm) REVERT: H 16 ARG cc_start: 0.8117 (mmt-90) cc_final: 0.7858 (mmp80) REVERT: H 74 ASN cc_start: 0.8062 (t0) cc_final: 0.7812 (t0) REVERT: H 111 VAL cc_start: 0.8925 (t) cc_final: 0.8713 (m) REVERT: L 194 CYS cc_start: 0.4813 (p) cc_final: 0.4412 (p) REVERT: B 148 LYS cc_start: 0.9159 (tmmt) cc_final: 0.8582 (ttpt) outliers start: 8 outliers final: 1 residues processed: 245 average time/residue: 0.2080 time to fit residues: 72.8080 Evaluate side-chains 175 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 0.2980 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 214 ASN D 100 GLN L 100 GLN B 63 HIS B 171 ASN B 181 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9731 Z= 0.265 Angle : 0.629 6.123 13253 Z= 0.324 Chirality : 0.042 0.148 1508 Planarity : 0.005 0.046 1646 Dihedral : 7.541 57.808 1708 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.24), residues: 1194 helix: 0.82 (0.33), residues: 234 sheet: 0.78 (0.35), residues: 234 loop : -1.54 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 36 HIS 0.005 0.002 HIS A 63 PHE 0.019 0.002 PHE L 71 TYR 0.048 0.002 TYR A 182 ARG 0.007 0.001 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8337 (ppp) cc_final: 0.8117 (ppp) REVERT: D 47 LEU cc_start: 0.8561 (tp) cc_final: 0.8346 (tp) REVERT: D 181 LEU cc_start: 0.8434 (mm) cc_final: 0.7966 (pp) REVERT: D 192 TYR cc_start: 0.5806 (m-10) cc_final: 0.5402 (m-80) REVERT: H 16 ARG cc_start: 0.8228 (mmt-90) cc_final: 0.7929 (mmp80) REVERT: H 74 ASN cc_start: 0.8516 (t0) cc_final: 0.8191 (t0) REVERT: L 181 LEU cc_start: 0.8432 (mm) cc_final: 0.8043 (pp) REVERT: B 159 THR cc_start: 0.8251 (m) cc_final: 0.7980 (p) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1816 time to fit residues: 55.9084 Evaluate side-chains 167 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.2980 chunk 33 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN B 63 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9731 Z= 0.165 Angle : 0.574 6.640 13253 Z= 0.286 Chirality : 0.041 0.149 1508 Planarity : 0.004 0.044 1646 Dihedral : 7.172 59.051 1708 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.24), residues: 1194 helix: 1.05 (0.34), residues: 232 sheet: 0.45 (0.33), residues: 252 loop : -1.50 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 36 HIS 0.004 0.001 HIS B 63 PHE 0.014 0.002 PHE B 62 TYR 0.042 0.001 TYR A 182 ARG 0.003 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8266 (ppp) cc_final: 0.7990 (ppp) REVERT: A 71 MET cc_start: 0.8271 (mmm) cc_final: 0.7995 (tpp) REVERT: A 95 ILE cc_start: 0.8700 (pt) cc_final: 0.8500 (pt) REVERT: D 175 LEU cc_start: 0.7753 (mt) cc_final: 0.7152 (mp) REVERT: D 181 LEU cc_start: 0.8488 (mm) cc_final: 0.7997 (pp) REVERT: D 192 TYR cc_start: 0.5253 (m-10) cc_final: 0.4897 (m-80) REVERT: H 16 ARG cc_start: 0.8181 (mmt-90) cc_final: 0.7909 (mmp80) REVERT: H 74 ASN cc_start: 0.8599 (t0) cc_final: 0.8129 (t0) REVERT: H 188 SER cc_start: 0.8668 (m) cc_final: 0.8294 (t) REVERT: L 88 CYS cc_start: 0.6870 (p) cc_final: 0.6443 (t) REVERT: L 181 LEU cc_start: 0.8565 (mm) cc_final: 0.8117 (pp) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1875 time to fit residues: 61.0320 Evaluate side-chains 175 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN D 93 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9731 Z= 0.342 Angle : 0.711 8.399 13253 Z= 0.369 Chirality : 0.045 0.168 1508 Planarity : 0.005 0.081 1646 Dihedral : 7.413 59.321 1708 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.24), residues: 1194 helix: 0.78 (0.33), residues: 230 sheet: 0.01 (0.33), residues: 234 loop : -1.70 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 36 HIS 0.007 0.002 HIS A 63 PHE 0.033 0.003 PHE A 62 TYR 0.048 0.002 TYR A 182 ARG 0.004 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8354 (ppp) cc_final: 0.8137 (ppp) REVERT: A 95 ILE cc_start: 0.8849 (pt) cc_final: 0.8634 (pt) REVERT: A 159 THR cc_start: 0.9435 (m) cc_final: 0.9141 (p) REVERT: D 47 LEU cc_start: 0.8997 (tp) cc_final: 0.8794 (tp) REVERT: D 181 LEU cc_start: 0.8473 (mm) cc_final: 0.7948 (pp) REVERT: H 16 ARG cc_start: 0.8176 (mmt-90) cc_final: 0.7835 (mmp80) REVERT: H 84 ASN cc_start: 0.8717 (p0) cc_final: 0.8483 (p0) REVERT: H 203 TYR cc_start: 0.6415 (m-10) cc_final: 0.6076 (m-10) REVERT: H 213 ASN cc_start: 0.8775 (t0) cc_final: 0.8425 (t0) REVERT: L 47 LEU cc_start: 0.8865 (tp) cc_final: 0.8633 (tp) REVERT: L 118 PHE cc_start: 0.6544 (t80) cc_final: 0.6131 (t80) REVERT: L 175 LEU cc_start: 0.8079 (mt) cc_final: 0.7348 (mp) REVERT: B 181 GLN cc_start: 0.8892 (tt0) cc_final: 0.8623 (tt0) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2113 time to fit residues: 60.0002 Evaluate side-chains 161 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN C 30 ASN L 89 GLN B 63 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9731 Z= 0.192 Angle : 0.629 10.457 13253 Z= 0.314 Chirality : 0.042 0.147 1508 Planarity : 0.005 0.068 1646 Dihedral : 7.004 59.483 1708 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.10 % Allowed : 2.42 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.24), residues: 1194 helix: 1.06 (0.33), residues: 230 sheet: 0.04 (0.32), residues: 262 loop : -1.80 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 89 HIS 0.005 0.001 HIS B 63 PHE 0.024 0.002 PHE A 62 TYR 0.042 0.002 TYR A 182 ARG 0.003 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8331 (mmm) cc_final: 0.8090 (tpp) REVERT: A 95 ILE cc_start: 0.8824 (pt) cc_final: 0.8614 (pt) REVERT: A 194 LEU cc_start: 0.9061 (mm) cc_final: 0.8781 (mp) REVERT: D 181 LEU cc_start: 0.8639 (mm) cc_final: 0.8148 (pp) REVERT: C 16 ARG cc_start: 0.8074 (mmt-90) cc_final: 0.7751 (mmp80) REVERT: C 107 TYR cc_start: 0.8526 (m-80) cc_final: 0.8269 (m-80) REVERT: H 84 ASN cc_start: 0.8749 (p0) cc_final: 0.8534 (p0) REVERT: L 175 LEU cc_start: 0.7822 (mt) cc_final: 0.7166 (mp) REVERT: L 181 LEU cc_start: 0.8565 (mm) cc_final: 0.8143 (pp) REVERT: B 148 LYS cc_start: 0.9441 (tmmt) cc_final: 0.8706 (ttpt) REVERT: B 150 GLU cc_start: 0.7595 (tt0) cc_final: 0.6922 (tt0) REVERT: B 181 GLN cc_start: 0.8916 (mt0) cc_final: 0.8636 (tt0) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.2035 time to fit residues: 63.1570 Evaluate side-chains 163 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 28 optimal weight: 20.0000 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN C 30 ASN L 93 ASN B 63 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9731 Z= 0.170 Angle : 0.616 8.939 13253 Z= 0.305 Chirality : 0.042 0.144 1508 Planarity : 0.004 0.063 1646 Dihedral : 6.674 58.957 1708 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.10 % Allowed : 1.74 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.24), residues: 1194 helix: 1.13 (0.34), residues: 230 sheet: -0.03 (0.33), residues: 252 loop : -1.76 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 94 HIS 0.005 0.001 HIS B 63 PHE 0.009 0.001 PHE D 71 TYR 0.040 0.001 TYR A 182 ARG 0.003 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: A 95 ILE cc_start: 0.8841 (pt) cc_final: 0.8638 (pt) REVERT: A 138 ILE cc_start: 0.9289 (tp) cc_final: 0.9019 (tp) REVERT: D 181 LEU cc_start: 0.8503 (mm) cc_final: 0.8077 (pp) REVERT: H 16 ARG cc_start: 0.8025 (mmt-90) cc_final: 0.7754 (mmp80) REVERT: H 83 MET cc_start: 0.8213 (ptt) cc_final: 0.7952 (ptt) REVERT: H 213 ASN cc_start: 0.8637 (t0) cc_final: 0.8252 (t0) REVERT: L 175 LEU cc_start: 0.7755 (mt) cc_final: 0.7097 (mp) REVERT: L 181 LEU cc_start: 0.8572 (mm) cc_final: 0.8192 (pp) REVERT: B 181 GLN cc_start: 0.8863 (mt0) cc_final: 0.8442 (tt0) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.1982 time to fit residues: 61.0728 Evaluate side-chains 165 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 113 optimal weight: 0.0670 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN D 93 ASN C 30 ASN L 93 ASN B 63 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9731 Z= 0.155 Angle : 0.604 7.176 13253 Z= 0.297 Chirality : 0.041 0.178 1508 Planarity : 0.004 0.067 1646 Dihedral : 6.404 59.771 1708 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.10 % Allowed : 1.45 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.24), residues: 1194 helix: 1.25 (0.34), residues: 230 sheet: 0.03 (0.34), residues: 252 loop : -1.74 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 89 HIS 0.007 0.001 HIS B 63 PHE 0.021 0.001 PHE B 200 TYR 0.037 0.001 TYR A 182 ARG 0.003 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8141 (tpp) cc_final: 0.7669 (tpp) REVERT: A 119 MET cc_start: 0.8953 (mmm) cc_final: 0.8722 (mmm) REVERT: A 194 LEU cc_start: 0.9085 (mm) cc_final: 0.8837 (mt) REVERT: D 93 ASN cc_start: 0.8421 (m-40) cc_final: 0.7947 (m-40) REVERT: D 181 LEU cc_start: 0.8555 (mm) cc_final: 0.8125 (pp) REVERT: C 16 ARG cc_start: 0.7919 (mmt-90) cc_final: 0.7596 (mmp80) REVERT: H 213 ASN cc_start: 0.8595 (t0) cc_final: 0.8196 (t0) REVERT: L 93 ASN cc_start: 0.8552 (m-40) cc_final: 0.8041 (m-40) REVERT: L 175 LEU cc_start: 0.7761 (mt) cc_final: 0.7129 (mp) REVERT: L 181 LEU cc_start: 0.8564 (mm) cc_final: 0.8017 (tp) REVERT: B 181 GLN cc_start: 0.8780 (mt0) cc_final: 0.8423 (tt0) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.1947 time to fit residues: 60.2826 Evaluate side-chains 169 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 77 optimal weight: 0.3980 chunk 56 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN C 30 ASN B 181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9731 Z= 0.253 Angle : 0.668 7.207 13253 Z= 0.339 Chirality : 0.044 0.192 1508 Planarity : 0.005 0.062 1646 Dihedral : 6.537 57.527 1708 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.10 % Allowed : 1.74 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.24), residues: 1194 helix: 1.14 (0.34), residues: 230 sheet: -0.33 (0.33), residues: 252 loop : -1.87 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 36 HIS 0.003 0.001 HIS C 35 PHE 0.023 0.002 PHE B 62 TYR 0.043 0.002 TYR A 182 ARG 0.003 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8959 (mmm) cc_final: 0.8698 (mmm) REVERT: D 181 LEU cc_start: 0.8626 (mm) cc_final: 0.8186 (pp) REVERT: C 16 ARG cc_start: 0.7901 (mmt-90) cc_final: 0.7597 (mmp80) REVERT: C 107 TYR cc_start: 0.8593 (m-80) cc_final: 0.8315 (m-80) REVERT: H 16 ARG cc_start: 0.7992 (mmt-90) cc_final: 0.7702 (mmp80) REVERT: H 107 TYR cc_start: 0.8665 (m-80) cc_final: 0.8355 (m-80) REVERT: H 213 ASN cc_start: 0.8741 (t0) cc_final: 0.8407 (t0) REVERT: B 71 MET cc_start: 0.7964 (tpp) cc_final: 0.7514 (tpp) REVERT: B 181 GLN cc_start: 0.8993 (mt0) cc_final: 0.8638 (tt0) outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.2252 time to fit residues: 65.2571 Evaluate side-chains 157 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.0570 chunk 95 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 overall best weight: 1.0900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN B 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9731 Z= 0.171 Angle : 0.642 7.585 13253 Z= 0.316 Chirality : 0.042 0.183 1508 Planarity : 0.004 0.062 1646 Dihedral : 6.277 58.740 1708 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.24), residues: 1194 helix: 1.25 (0.34), residues: 230 sheet: -0.29 (0.33), residues: 252 loop : -1.85 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 89 HIS 0.006 0.001 HIS B 63 PHE 0.013 0.001 PHE A 62 TYR 0.031 0.001 TYR A 182 ARG 0.002 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7857 (tpp) cc_final: 0.7427 (tpp) REVERT: A 119 MET cc_start: 0.8933 (mmm) cc_final: 0.8719 (mmm) REVERT: D 93 ASN cc_start: 0.8501 (m-40) cc_final: 0.8160 (m-40) REVERT: C 107 TYR cc_start: 0.8510 (m-80) cc_final: 0.8271 (m-80) REVERT: H 13 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8191 (tm-30) REVERT: H 16 ARG cc_start: 0.7941 (mmt-90) cc_final: 0.7554 (mmt-90) REVERT: H 107 TYR cc_start: 0.8542 (m-80) cc_final: 0.8306 (m-80) REVERT: H 213 ASN cc_start: 0.8621 (t0) cc_final: 0.8279 (t0) REVERT: L 93 ASN cc_start: 0.8568 (m-40) cc_final: 0.8240 (m-40) REVERT: L 181 LEU cc_start: 0.8548 (mm) cc_final: 0.7986 (tp) REVERT: B 71 MET cc_start: 0.7927 (tpp) cc_final: 0.7629 (tpp) REVERT: B 148 LYS cc_start: 0.9427 (tmmt) cc_final: 0.8768 (pttt) REVERT: B 181 GLN cc_start: 0.8872 (mt0) cc_final: 0.8528 (tt0) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2182 time to fit residues: 67.6162 Evaluate side-chains 171 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 117 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS A 171 ASN ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN C 30 ASN B 63 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9731 Z= 0.195 Angle : 0.653 7.668 13253 Z= 0.325 Chirality : 0.043 0.192 1508 Planarity : 0.004 0.060 1646 Dihedral : 6.196 58.704 1708 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.10 % Allowed : 0.19 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.24), residues: 1194 helix: 1.25 (0.34), residues: 230 sheet: -0.35 (0.34), residues: 252 loop : -1.87 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 36 HIS 0.005 0.001 HIS B 63 PHE 0.014 0.001 PHE A 62 TYR 0.038 0.002 TYR A 182 ARG 0.002 0.000 ARG H 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8010 (tpp) cc_final: 0.7609 (tpp) REVERT: A 119 MET cc_start: 0.8924 (mmm) cc_final: 0.8686 (mmm) REVERT: A 138 ILE cc_start: 0.9169 (tp) cc_final: 0.8937 (tp) REVERT: C 13 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8322 (tm-30) REVERT: C 107 TYR cc_start: 0.8534 (m-80) cc_final: 0.8322 (m-80) REVERT: H 13 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8199 (tm-30) REVERT: H 16 ARG cc_start: 0.7944 (mmt-90) cc_final: 0.7549 (mmt-90) REVERT: H 91 THR cc_start: 0.7542 (p) cc_final: 0.7288 (t) REVERT: H 107 TYR cc_start: 0.8594 (m-80) cc_final: 0.8304 (m-80) REVERT: H 213 ASN cc_start: 0.8646 (t0) cc_final: 0.8324 (t0) REVERT: L 181 LEU cc_start: 0.8586 (mm) cc_final: 0.8119 (tp) REVERT: B 71 MET cc_start: 0.8159 (tpp) cc_final: 0.7769 (tpp) REVERT: B 148 LYS cc_start: 0.9462 (tmmt) cc_final: 0.8779 (pttt) REVERT: B 181 GLN cc_start: 0.8928 (mt0) cc_final: 0.8593 (tt0) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.2061 time to fit residues: 60.6075 Evaluate side-chains 165 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN C 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.137931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110307 restraints weight = 28398.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.110162 restraints weight = 19947.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110639 restraints weight = 20201.070| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9731 Z= 0.267 Angle : 0.707 8.888 13253 Z= 0.360 Chirality : 0.044 0.200 1508 Planarity : 0.005 0.060 1646 Dihedral : 6.417 57.363 1708 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.10 % Allowed : 0.48 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.24), residues: 1194 helix: 1.08 (0.34), residues: 230 sheet: -0.59 (0.32), residues: 262 loop : -1.98 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 36 HIS 0.004 0.001 HIS H 35 PHE 0.017 0.002 PHE B 200 TYR 0.056 0.002 TYR A 182 ARG 0.003 0.000 ARG D 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2036.60 seconds wall clock time: 39 minutes 43.29 seconds (2383.29 seconds total)