Starting phenix.real_space_refine on Wed Mar 4 16:27:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y92_10732/03_2026/6y92_10732.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y92_10732/03_2026/6y92_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_10732/03_2026/6y92_10732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y92_10732/03_2026/6y92_10732.map" model { file = "/net/cci-nas-00/data/ceres_data/6y92_10732/03_2026/6y92_10732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y92_10732/03_2026/6y92_10732.cif" } resolution = 4.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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-1': 2, 'Y01:plan-2': 2} Unresolved non-hydrogen planarities: 14 Restraints were copied for chains: H, L Time building chain proxies: 2.81, per 1000 atoms: 0.30 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=9, 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 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 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: 0.83 Conformation dependent library (CDL) restraints added in 495.9 milliseconds 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: 0.33 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: 1.22 Time building geometry restraints manager: 1.12 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: 5544 19.18 - 38.36: 440 38.36 - 57.54: 79 57.54 - 76.72: 29 76.72 - 95.91: 5 Dihedral angle restraints: 6097 sinusoidal: 2599 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 H 149 " pdb=" SG CYS H 149 " pdb=" SG CYS H 205 " pdb=" CB CYS H 205 " ideal model delta sinusoidal sigma weight residual 93.00 29.29 63.71 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 ... (remaining 6094 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: 82 2.60 - 3.18: 7767 3.18 - 3.75: 13438 3.75 - 4.33: 16677 4.33 - 4.90: 27016 Nonbonded interactions: 64980 Sorted by model distance: nonbonded pdb=" SG CYS B 167 " pdb=" SG CYS B 183 " model vdw 2.028 3.760 nonbonded pdb=" O PHE A 45 " pdb=" OG SER A 49 " model vdw 2.265 3.040 nonbonded pdb=" OE1 GLN D 124 " pdb=" OG SER D 131 " model vdw 2.276 3.040 nonbonded pdb=" OE1 GLN L 124 " pdb=" OG SER L 131 " model vdw 2.277 3.040 nonbonded pdb=" OE2 GLU H 6 " pdb=" OG1 THR H 116 " model vdw 2.303 3.040 ... (remaining 64975 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 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.580 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 14.160 ------------------------------------------------------------------------------- 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 9743 Z= 0.287 Angle : 0.774 12.237 13271 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG C 87 TYR 0.049 0.001 TYR A 182 PHE 0.021 0.001 PHE C 29 TRP 0.012 0.001 TRP B 216 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 9731) covalent geometry : angle 0.77368 (13253) SS BOND : bond 0.00228 ( 9) SS BOND : angle 0.64407 ( 18) hydrogen bonds : bond 0.20760 ( 274) hydrogen bonds : angle 7.76820 ( 768) Misc. bond : bond 0.00058 ( 3) *********************** 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 : 0.353 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: 0.7859 (mmp80) REVERT: H 74 ASN cc_start: 0.8062 (t0) cc_final: 0.7812 (t0) REVERT: H 111 VAL cc_start: 0.8924 (t) cc_final: 0.8713 (m) REVERT: L 194 CYS cc_start: 0.4814 (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: 0.0827 time to fit residues: 29.7441 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 : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 0.1980 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 0.1980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN D 100 GLN L 100 GLN B 63 HIS B 171 ASN B 181 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.159536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.130123 restraints weight = 28551.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.133507 restraints weight = 18493.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.134828 restraints weight = 11269.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.136391 restraints weight = 10019.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.136349 restraints weight = 9433.394| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9743 Z= 0.111 Angle : 0.564 7.132 13271 Z= 0.284 Chirality : 0.040 0.139 1508 Planarity : 0.004 0.034 1646 Dihedral : 7.398 58.252 1708 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.25), residues: 1194 helix: 1.02 (0.33), residues: 234 sheet: 1.00 (0.36), residues: 234 loop : -1.45 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 87 TYR 0.044 0.001 TYR A 182 PHE 0.016 0.001 PHE A 202 TRP 0.012 0.001 TRP B 89 HIS 0.008 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9731) covalent geometry : angle 0.56367 (13253) SS BOND : bond 0.00421 ( 9) SS BOND : angle 0.79085 ( 18) hydrogen bonds : bond 0.03991 ( 274) hydrogen bonds : angle 5.65738 ( 768) Misc. bond : bond 0.00014 ( 3) *********************** 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 215 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8401 (ppp) cc_final: 0.8168 (ppp) REVERT: A 137 ASP cc_start: 0.8681 (t70) cc_final: 0.8390 (p0) REVERT: A 194 LEU cc_start: 0.9170 (mm) cc_final: 0.8511 (mm) REVERT: D 181 LEU cc_start: 0.8379 (mm) cc_final: 0.7950 (pp) REVERT: D 192 TYR cc_start: 0.4902 (m-10) cc_final: 0.4654 (m-80) REVERT: H 16 ARG cc_start: 0.8213 (mmt-90) cc_final: 0.7933 (mmp80) REVERT: H 74 ASN cc_start: 0.8192 (t0) cc_final: 0.7886 (t0) REVERT: L 181 LEU cc_start: 0.8501 (mm) cc_final: 0.8149 (pp) REVERT: L 194 CYS cc_start: 0.3917 (p) cc_final: 0.3514 (p) REVERT: B 137 ASP cc_start: 0.8401 (t0) cc_final: 0.8097 (p0) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.0758 time to fit residues: 24.7643 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 : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 102 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 41 optimal weight: 0.2980 chunk 82 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.156304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.128147 restraints weight = 29300.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.128107 restraints weight = 19753.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.129595 restraints weight = 15447.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.131279 restraints weight = 12144.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.130901 restraints weight = 10392.461| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9743 Z= 0.124 Angle : 0.570 6.569 13271 Z= 0.287 Chirality : 0.041 0.180 1508 Planarity : 0.004 0.036 1646 Dihedral : 7.025 59.630 1708 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.24), residues: 1194 helix: 0.85 (0.33), residues: 246 sheet: 0.61 (0.33), residues: 252 loop : -1.53 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.040 0.002 TYR A 182 PHE 0.014 0.002 PHE H 29 TRP 0.013 0.001 TRP B 89 HIS 0.004 0.001 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9731) covalent geometry : angle 0.56924 (13253) SS BOND : bond 0.00383 ( 9) SS BOND : angle 0.89744 ( 18) hydrogen bonds : bond 0.04353 ( 274) hydrogen bonds : angle 4.93041 ( 768) Misc. bond : bond 0.00040 ( 3) *********************** 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 215 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8258 (ppp) cc_final: 0.7937 (ppp) REVERT: A 119 MET cc_start: 0.9054 (mmm) cc_final: 0.8844 (mmm) REVERT: A 137 ASP cc_start: 0.8739 (t70) cc_final: 0.8259 (p0) REVERT: A 194 LEU cc_start: 0.9210 (mm) cc_final: 0.8405 (mt) REVERT: D 175 LEU cc_start: 0.7904 (mt) cc_final: 0.7384 (mp) REVERT: D 181 LEU cc_start: 0.8505 (mm) cc_final: 0.8022 (pp) REVERT: H 16 ARG cc_start: 0.8296 (mmt-90) cc_final: 0.7919 (mmp80) REVERT: H 74 ASN cc_start: 0.8397 (t0) cc_final: 0.8071 (t0) REVERT: H 188 SER cc_start: 0.8818 (m) cc_final: 0.8441 (t) REVERT: L 181 LEU cc_start: 0.8543 (mm) cc_final: 0.8169 (pp) REVERT: L 194 CYS cc_start: 0.4422 (p) cc_final: 0.3996 (p) REVERT: B 181 GLN cc_start: 0.8878 (mt0) cc_final: 0.8455 (tt0) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.0815 time to fit residues: 25.9177 Evaluate side-chains 162 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 107 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN D 53 ASN D 93 ASN L 89 GLN B 63 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.157750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.127663 restraints weight = 29509.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.129405 restraints weight = 20550.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.131117 restraints weight = 14388.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.132368 restraints weight = 11787.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.132503 restraints weight = 9673.724| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9743 Z= 0.096 Angle : 0.565 6.882 13271 Z= 0.278 Chirality : 0.041 0.173 1508 Planarity : 0.004 0.067 1646 Dihedral : 6.755 58.433 1708 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.24), residues: 1194 helix: 0.93 (0.33), residues: 246 sheet: 0.54 (0.33), residues: 252 loop : -1.54 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 67 TYR 0.039 0.001 TYR A 182 PHE 0.013 0.001 PHE H 29 TRP 0.012 0.001 TRP B 89 HIS 0.007 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 9731) covalent geometry : angle 0.56485 (13253) SS BOND : bond 0.00379 ( 9) SS BOND : angle 0.75642 ( 18) hydrogen bonds : bond 0.03778 ( 274) hydrogen bonds : angle 4.69576 ( 768) Misc. bond : bond 0.00025 ( 3) *********************** 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 218 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.9055 (mmm) cc_final: 0.8833 (mmm) REVERT: A 137 ASP cc_start: 0.8553 (t70) cc_final: 0.8237 (p0) REVERT: A 194 LEU cc_start: 0.9213 (mm) cc_final: 0.8444 (mt) REVERT: D 175 LEU cc_start: 0.7763 (mt) cc_final: 0.7259 (mp) REVERT: D 181 LEU cc_start: 0.8518 (mm) cc_final: 0.8062 (pp) REVERT: H 16 ARG cc_start: 0.8201 (mmt-90) cc_final: 0.7854 (mmp80) REVERT: H 74 ASN cc_start: 0.8479 (t0) cc_final: 0.8152 (t0) REVERT: H 188 SER cc_start: 0.8803 (m) cc_final: 0.8468 (t) REVERT: H 203 TYR cc_start: 0.6411 (m-10) cc_final: 0.6196 (m-10) REVERT: L 181 LEU cc_start: 0.8517 (mm) cc_final: 0.8162 (pp) REVERT: L 194 CYS cc_start: 0.4728 (p) cc_final: 0.4413 (p) REVERT: B 181 GLN cc_start: 0.8844 (mt0) cc_final: 0.8353 (tt0) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.0766 time to fit residues: 25.3861 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 : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 66 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN L 89 GLN B 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.155345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.128305 restraints weight = 29391.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.128425 restraints weight = 19259.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.129619 restraints weight = 15726.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.130157 restraints weight = 12624.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.130382 restraints weight = 11884.993| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9743 Z= 0.107 Angle : 0.571 10.433 13271 Z= 0.284 Chirality : 0.041 0.149 1508 Planarity : 0.004 0.059 1646 Dihedral : 6.589 58.753 1708 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.25), residues: 1194 helix: 1.22 (0.33), residues: 230 sheet: 0.39 (0.34), residues: 234 loop : -1.37 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 67 TYR 0.036 0.001 TYR A 182 PHE 0.014 0.001 PHE C 29 TRP 0.021 0.002 TRP L 94 HIS 0.006 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9731) covalent geometry : angle 0.57026 (13253) SS BOND : bond 0.00334 ( 9) SS BOND : angle 0.75962 ( 18) hydrogen bonds : bond 0.03869 ( 274) hydrogen bonds : angle 4.64487 ( 768) Misc. bond : bond 0.00039 ( 3) *********************** 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 229 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8567 (t70) cc_final: 0.8297 (p0) REVERT: A 194 LEU cc_start: 0.9215 (mm) cc_final: 0.8404 (mt) REVERT: D 175 LEU cc_start: 0.7611 (mt) cc_final: 0.6945 (mp) REVERT: D 181 LEU cc_start: 0.8447 (mm) cc_final: 0.7999 (pp) REVERT: H 16 ARG cc_start: 0.8158 (mmt-90) cc_final: 0.7804 (mmp80) REVERT: H 188 SER cc_start: 0.8625 (m) cc_final: 0.8326 (t) REVERT: L 47 LEU cc_start: 0.8726 (tp) cc_final: 0.8525 (tp) REVERT: L 181 LEU cc_start: 0.8461 (mm) cc_final: 0.8112 (pp) REVERT: L 194 CYS cc_start: 0.3941 (p) cc_final: 0.3602 (p) REVERT: B 181 GLN cc_start: 0.8956 (mt0) cc_final: 0.8346 (tt0) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.0832 time to fit residues: 27.6353 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 : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 56 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 78 optimal weight: 0.0170 chunk 61 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN D 93 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN B 171 ASN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.144532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.116979 restraints weight = 29641.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116542 restraints weight = 20019.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.117356 restraints weight = 19092.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.118074 restraints weight = 13873.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.118400 restraints weight = 12235.000| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9743 Z= 0.210 Angle : 0.696 10.474 13271 Z= 0.356 Chirality : 0.044 0.179 1508 Planarity : 0.005 0.058 1646 Dihedral : 6.870 59.098 1708 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.10 % Allowed : 2.90 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.24), residues: 1194 helix: 1.07 (0.34), residues: 230 sheet: -0.16 (0.32), residues: 254 loop : -1.60 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 87 TYR 0.046 0.002 TYR A 182 PHE 0.020 0.002 PHE D 71 TRP 0.024 0.002 TRP H 36 HIS 0.006 0.001 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 9731) covalent geometry : angle 0.69559 (13253) SS BOND : bond 0.00365 ( 9) SS BOND : angle 1.11800 ( 18) hydrogen bonds : bond 0.05184 ( 274) hydrogen bonds : angle 5.10506 ( 768) Misc. bond : bond 0.00096 ( 3) *********************** 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 207 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8346 (mmm) cc_final: 0.8071 (tpp) REVERT: D 93 ASN cc_start: 0.8461 (m110) cc_final: 0.8168 (m-40) REVERT: D 181 LEU cc_start: 0.8480 (mm) cc_final: 0.8057 (pp) REVERT: C 16 ARG cc_start: 0.8175 (mmt-90) cc_final: 0.7948 (mmt-90) REVERT: H 203 TYR cc_start: 0.6334 (m-10) cc_final: 0.6132 (m-10) REVERT: H 213 ASN cc_start: 0.8662 (t0) cc_final: 0.8285 (t0) REVERT: L 118 PHE cc_start: 0.6115 (t80) cc_final: 0.5771 (t80) REVERT: L 175 LEU cc_start: 0.7976 (mt) cc_final: 0.7180 (mp) REVERT: L 181 LEU cc_start: 0.8550 (mm) cc_final: 0.8174 (pp) REVERT: L 194 CYS cc_start: 0.3807 (p) cc_final: 0.3491 (p) REVERT: B 148 LYS cc_start: 0.9474 (tmmt) cc_final: 0.8770 (ttpt) REVERT: B 181 GLN cc_start: 0.9233 (mt0) cc_final: 0.8593 (tt0) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.0797 time to fit residues: 24.4596 Evaluate side-chains 159 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 42 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS A 214 ASN C 30 ASN L 89 GLN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.140220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.112170 restraints weight = 29643.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.111755 restraints weight = 20321.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112626 restraints weight = 18690.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113022 restraints weight = 13512.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.113378 restraints weight = 12688.096| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9743 Z= 0.191 Angle : 0.685 9.506 13271 Z= 0.352 Chirality : 0.045 0.185 1508 Planarity : 0.005 0.069 1646 Dihedral : 6.793 56.683 1708 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.24), residues: 1194 helix: 0.96 (0.33), residues: 230 sheet: -0.44 (0.33), residues: 250 loop : -1.79 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 67 TYR 0.045 0.002 TYR A 182 PHE 0.021 0.002 PHE B 190 TRP 0.024 0.002 TRP H 36 HIS 0.006 0.001 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 9731) covalent geometry : angle 0.68400 (13253) SS BOND : bond 0.00460 ( 9) SS BOND : angle 1.23857 ( 18) hydrogen bonds : bond 0.05668 ( 274) hydrogen bonds : angle 5.11268 ( 768) Misc. bond : bond 0.00097 ( 3) *********************** 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 199 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8163 (pm20) REVERT: A 71 MET cc_start: 0.8500 (mmm) cc_final: 0.8251 (tpp) REVERT: A 181 GLN cc_start: 0.8043 (pp30) cc_final: 0.7472 (tm-30) REVERT: D 93 ASN cc_start: 0.8632 (m110) cc_final: 0.8367 (m-40) REVERT: D 181 LEU cc_start: 0.8391 (mm) cc_final: 0.7989 (pp) REVERT: H 16 ARG cc_start: 0.8470 (mmt-90) cc_final: 0.7966 (mmp80) REVERT: H 213 ASN cc_start: 0.8710 (t0) cc_final: 0.8327 (t0) REVERT: L 175 LEU cc_start: 0.7804 (mt) cc_final: 0.7514 (mt) REVERT: L 181 LEU cc_start: 0.8552 (mm) cc_final: 0.8191 (pp) REVERT: L 194 CYS cc_start: 0.3884 (p) cc_final: 0.3531 (p) REVERT: B 181 GLN cc_start: 0.9172 (mt0) cc_final: 0.8784 (tt0) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.0786 time to fit residues: 23.1014 Evaluate side-chains 152 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 37 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.137857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.109977 restraints weight = 29501.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.109432 restraints weight = 21463.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110071 restraints weight = 21408.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111016 restraints weight = 15247.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.111363 restraints weight = 13188.176| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9743 Z= 0.231 Angle : 0.741 10.434 13271 Z= 0.383 Chirality : 0.046 0.162 1508 Planarity : 0.006 0.075 1646 Dihedral : 7.006 56.858 1708 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.24), residues: 1194 helix: 0.69 (0.33), residues: 230 sheet: -0.75 (0.31), residues: 258 loop : -1.97 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 87 TYR 0.048 0.003 TYR A 182 PHE 0.028 0.003 PHE A 190 TRP 0.026 0.003 TRP C 36 HIS 0.004 0.001 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 9731) covalent geometry : angle 0.73948 (13253) SS BOND : bond 0.00539 ( 9) SS BOND : angle 1.36297 ( 18) hydrogen bonds : bond 0.06190 ( 274) hydrogen bonds : angle 5.52247 ( 768) Misc. bond : bond 0.00101 ( 3) *********************** 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 197 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8220 (pm20) REVERT: A 119 MET cc_start: 0.9112 (mmm) cc_final: 0.8817 (mmm) REVERT: A 149 MET cc_start: 0.8604 (mpp) cc_final: 0.8381 (mpp) REVERT: A 181 GLN cc_start: 0.8050 (pp30) cc_final: 0.7520 (tm-30) REVERT: D 118 PHE cc_start: 0.6326 (t80) cc_final: 0.5945 (t80) REVERT: D 181 LEU cc_start: 0.8406 (mm) cc_final: 0.7981 (pp) REVERT: C 16 ARG cc_start: 0.8353 (mmt-90) cc_final: 0.8096 (mmt-90) REVERT: H 87 ARG cc_start: 0.8564 (mmp-170) cc_final: 0.8330 (mmp-170) REVERT: H 203 TYR cc_start: 0.6545 (m-10) cc_final: 0.6326 (m-10) REVERT: H 213 ASN cc_start: 0.8832 (t0) cc_final: 0.8491 (t0) REVERT: L 181 LEU cc_start: 0.8475 (mm) cc_final: 0.8078 (pp) REVERT: L 194 CYS cc_start: 0.3948 (p) cc_final: 0.3642 (p) REVERT: B 71 MET cc_start: 0.8437 (tpp) cc_final: 0.7984 (tpp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.0778 time to fit residues: 22.2559 Evaluate side-chains 146 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 87 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 51 optimal weight: 0.0040 chunk 92 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN D 93 ASN C 30 ASN L 89 GLN L 93 ASN B 63 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.141980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.113905 restraints weight = 28538.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111815 restraints weight = 19681.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.112888 restraints weight = 17414.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113410 restraints weight = 13876.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.113652 restraints weight = 12796.148| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9743 Z= 0.123 Angle : 0.669 10.249 13271 Z= 0.333 Chirality : 0.043 0.162 1508 Planarity : 0.005 0.069 1646 Dihedral : 6.566 58.419 1708 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.10 % Allowed : 0.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.24), residues: 1194 helix: 1.15 (0.34), residues: 230 sheet: -0.64 (0.33), residues: 252 loop : -1.95 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 67 TYR 0.035 0.001 TYR A 182 PHE 0.013 0.001 PHE A 62 TRP 0.019 0.002 TRP B 89 HIS 0.005 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9731) covalent geometry : angle 0.66809 (13253) SS BOND : bond 0.00560 ( 9) SS BOND : angle 1.01678 ( 18) hydrogen bonds : bond 0.05203 ( 274) hydrogen bonds : angle 4.99443 ( 768) Misc. bond : bond 0.00046 ( 3) *********************** 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 212 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8307 (pm20) REVERT: A 71 MET cc_start: 0.8160 (tpp) cc_final: 0.7684 (tpp) REVERT: A 119 MET cc_start: 0.9036 (mmm) cc_final: 0.8726 (mmm) REVERT: A 197 MET cc_start: 0.8137 (tpt) cc_final: 0.7694 (tpt) REVERT: D 118 PHE cc_start: 0.6520 (t80) cc_final: 0.5912 (t80) REVERT: D 148 TRP cc_start: 0.6917 (m-10) cc_final: 0.5709 (m-10) REVERT: D 181 LEU cc_start: 0.8447 (mm) cc_final: 0.8011 (pp) REVERT: H 13 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8143 (tm-30) REVERT: H 16 ARG cc_start: 0.8278 (mmt-90) cc_final: 0.7718 (mmt-90) REVERT: H 203 TYR cc_start: 0.6528 (m-10) cc_final: 0.6320 (m-10) REVERT: H 213 ASN cc_start: 0.8766 (t0) cc_final: 0.8428 (t0) REVERT: L 93 ASN cc_start: 0.8686 (m-40) cc_final: 0.8368 (m-40) REVERT: L 148 TRP cc_start: 0.7094 (m-10) cc_final: 0.5808 (m-10) REVERT: L 175 LEU cc_start: 0.7686 (mt) cc_final: 0.7003 (mp) REVERT: L 181 LEU cc_start: 0.8549 (mm) cc_final: 0.8160 (pp) REVERT: B 148 LYS cc_start: 0.9437 (tmmt) cc_final: 0.8765 (pttt) REVERT: B 181 GLN cc_start: 0.9161 (mt0) cc_final: 0.8861 (tt0) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.0859 time to fit residues: 26.1635 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 : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 115 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 13 optimal weight: 0.0010 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN C 30 ASN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN B 63 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.142973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.114030 restraints weight = 29235.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.114691 restraints weight = 19874.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.115612 restraints weight = 15608.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.115947 restraints weight = 12441.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.116021 restraints weight = 11916.140| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9743 Z= 0.125 Angle : 0.677 10.089 13271 Z= 0.336 Chirality : 0.043 0.192 1508 Planarity : 0.005 0.068 1646 Dihedral : 6.381 59.810 1708 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.24), residues: 1194 helix: 1.14 (0.34), residues: 230 sheet: -0.59 (0.34), residues: 252 loop : -1.99 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.037 0.001 TYR A 182 PHE 0.032 0.001 PHE D 71 TRP 0.038 0.002 TRP C 47 HIS 0.005 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9731) covalent geometry : angle 0.67534 (13253) SS BOND : bond 0.00365 ( 9) SS BOND : angle 1.57394 ( 18) hydrogen bonds : bond 0.04816 ( 274) hydrogen bonds : angle 4.90068 ( 768) Misc. bond : bond 0.00045 ( 3) ********************** 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 212 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8125 (tpp) cc_final: 0.7683 (tpp) REVERT: A 119 MET cc_start: 0.9089 (mmm) cc_final: 0.8761 (mmm) REVERT: A 194 LEU cc_start: 0.9314 (mm) cc_final: 0.9081 (mm) REVERT: H 16 ARG cc_start: 0.8215 (mmt-90) cc_final: 0.7622 (mmp80) REVERT: H 203 TYR cc_start: 0.6372 (m-10) cc_final: 0.6148 (m-10) REVERT: H 213 ASN cc_start: 0.8752 (t0) cc_final: 0.8406 (t0) REVERT: L 93 ASN cc_start: 0.8798 (m-40) cc_final: 0.8529 (m-40) REVERT: L 181 LEU cc_start: 0.8423 (mm) cc_final: 0.8094 (pp) REVERT: B 148 LYS cc_start: 0.9457 (tmmt) cc_final: 0.8804 (pttt) REVERT: B 181 GLN cc_start: 0.9184 (mt0) cc_final: 0.8797 (tt0) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.0862 time to fit residues: 26.5098 Evaluate side-chains 160 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 92 optimal weight: 0.0670 chunk 108 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 55 optimal weight: 0.0270 chunk 79 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS A 214 ASN C 30 ASN L 89 GLN B 63 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.143430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.114902 restraints weight = 28307.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.113533 restraints weight = 19194.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.114760 restraints weight = 15857.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115194 restraints weight = 13142.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115373 restraints weight = 12427.678| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9743 Z= 0.118 Angle : 0.680 10.840 13271 Z= 0.334 Chirality : 0.043 0.185 1508 Planarity : 0.005 0.067 1646 Dihedral : 6.200 58.834 1708 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.24), residues: 1194 helix: 1.18 (0.34), residues: 230 sheet: -0.63 (0.34), residues: 252 loop : -2.00 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.035 0.001 TYR A 182 PHE 0.032 0.001 PHE D 71 TRP 0.028 0.002 TRP C 47 HIS 0.006 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9731) covalent geometry : angle 0.67858 (13253) SS BOND : bond 0.00389 ( 9) SS BOND : angle 1.43075 ( 18) hydrogen bonds : bond 0.04520 ( 274) hydrogen bonds : angle 4.84223 ( 768) Misc. bond : bond 0.00043 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1485.58 seconds wall clock time: 26 minutes 29.79 seconds (1589.79 seconds total)