Starting phenix.real_space_refine on Sat Sep 12 08:52:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6y92_10732/09_2026/6y92_10732.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y92_10732/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6y92_10732/09_2026/6y92_10732.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6y92_10732/09_2026/6y92_10732.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y92_10732/09_2026/6y92_10732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y92_10732/09_2026/6y92_10732.map" model { file = "/net/cci-nas-00/data/ceres_data/6y92_10732/09_2026/6y92_10732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y92_10732/09_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-2.2.1-6174/lib/python3.11/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: 11 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: 2.36, per 1000 atoms: 0.25 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: 0.78 Conformation dependent library (CDL) restraints added in 375.1 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: 0.28 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: 1.30 Time building geometry restraints manager: 1.02 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: 5241 19.18 - 38.36: 423 38.36 - 57.54: 63 57.54 - 76.72: 24 76.72 - 95.91: 4 Dihedral angle restraints: 5755 sinusoidal: 2257 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 5752 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: 1.200 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.610 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 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 : 14.069 95.906 3488 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/Z covalent geometry : bond 0.00579 / 0.29 ( 9731) covalent geometry : angle 0.77368 / 0.36 (13253) SS BOND : bond 0.00228 / 0.13 ( 9) SS BOND : angle 0.64407 / 0.36 ( 18) hydrogen bonds : bond 0.20760 / 14.16 ( 274) hydrogen bonds : angle 7.76820 / 5.93 ( 768) Misc. bond : bond 0.00058 / 0.03 ( 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 : 0.401 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: 0.0831 time to fit residues: 29.9202 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 : 0.384 ------------------------------------------------------------------------------- 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... 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 = 0.4158 r_free = 0.4158 target = 0.159630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.129608 restraints weight = 28556.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.132400 restraints weight = 18275.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.134343 restraints weight = 13099.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.135618 restraints weight = 10257.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.136370 restraints weight = 8642.113| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9743 Z= 0.108 Angle : 0.571 7.132 13271 Z= 0.285 Chirality : 0.040 0.133 1508 Planarity : 0.004 0.034 1646 Dihedral : 5.776 59.466 1366 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % 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: -0.60 (0.25), residues: 1194 helix: 1.02 (0.34), residues: 234 sheet: 1.01 (0.36), residues: 234 loop : -1.45 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 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 0.007 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 9731) covalent geometry : angle 0.57032 / 0.28 (13253) SS BOND : bond 0.00297 / 0.17 ( 9) SS BOND : angle 0.81598 / 0.47 ( 18) hydrogen bonds : bond 0.03982 / 2.58 ( 274) hydrogen bonds : angle 5.67080 / 4.30 ( 768) Misc. bond : bond 0.00050 / 0.03 ( 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 214 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8303 (ppp) cc_final: 0.8084 (ppp) REVERT: A 137 ASP cc_start: 0.8693 (t70) cc_final: 0.8393 (p0) REVERT: A 194 LEU cc_start: 0.9179 (mm) cc_final: 0.8521 (mm) REVERT: D 181 LEU cc_start: 0.8374 (mm) cc_final: 0.7959 (pp) REVERT: D 192 TYR cc_start: 0.4900 (m-10) cc_final: 0.4614 (m-80) REVERT: H 16 ARG cc_start: 0.8220 (mmt-90) cc_final: 0.7949 (mmp80) REVERT: H 74 ASN cc_start: 0.8252 (t0) cc_final: 0.7934 (t0) REVERT: L 181 LEU cc_start: 0.8512 (mm) cc_final: 0.8160 (pp) REVERT: L 194 CYS cc_start: 0.3819 (p) cc_final: 0.3419 (p) REVERT: B 137 ASP cc_start: 0.8434 (t0) cc_final: 0.8101 (p0) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.0739 time to fit residues: 23.9921 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 : 0.364 ------------------------------------------------------------------------------- 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: 8.9990 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 12 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4107 r_free = 0.4107 target = 0.154524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.126596 restraints weight = 29284.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.126943 restraints weight = 18805.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.128338 restraints weight = 14798.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.128772 restraints weight = 11861.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.128905 restraints weight = 11122.127| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9743 Z= 0.133 Angle : 0.596 6.641 13271 Z= 0.299 Chirality : 0.042 0.185 1508 Planarity : 0.004 0.039 1646 Dihedral : 5.535 57.977 1366 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % 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: -0.76 (0.25), residues: 1194 helix: 0.94 (0.33), residues: 234 sheet: 0.51 (0.33), residues: 252 loop : -1.47 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 87 TYR 0.044 0.002 TYR A 182 PHE 0.013 0.002 PHE L 71 TRP 0.014 0.002 TRP B 89 HIS 0.004 0.001 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 9731) covalent geometry : angle 0.59530 / 0.30 (13253) SS BOND : bond 0.00256 / 0.15 ( 9) SS BOND : angle 0.99949 / 0.63 ( 18) hydrogen bonds : bond 0.04599 / 2.94 ( 274) hydrogen bonds : angle 4.90179 / 3.64 ( 768) Misc. bond : bond 0.00027 / 0.01 ( 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 218 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8751 (t70) cc_final: 0.8272 (p0) REVERT: A 194 LEU cc_start: 0.9212 (mm) cc_final: 0.8383 (mt) REVERT: D 175 LEU cc_start: 0.7809 (mt) cc_final: 0.7179 (mp) REVERT: D 181 LEU cc_start: 0.8449 (mm) cc_final: 0.7998 (pp) REVERT: H 16 ARG cc_start: 0.8319 (mmt-90) cc_final: 0.7945 (mmp80) REVERT: H 74 ASN cc_start: 0.8494 (t0) cc_final: 0.8136 (t0) REVERT: H 188 SER cc_start: 0.8722 (m) cc_final: 0.8370 (t) REVERT: L 181 LEU cc_start: 0.8542 (mm) cc_final: 0.8140 (pp) REVERT: L 194 CYS cc_start: 0.3908 (p) cc_final: 0.3561 (p) REVERT: B 181 GLN cc_start: 0.9030 (mt0) cc_final: 0.8530 (tt0) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.0836 time to fit residues: 26.6206 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 : 0.358 ------------------------------------------------------------------------------- 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: 4.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN D 93 ASN 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 = 0.4008 r_free = 0.4008 target = 0.150923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123570 restraints weight = 24612.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.122767 restraints weight = 20051.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.124007 restraints weight = 18217.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.124521 restraints weight = 13696.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.124772 restraints weight = 12522.295| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2856 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= 0.120 Angle : 0.583 6.450 13271 Z= 0.293 Chirality : 0.041 0.173 1508 Planarity : 0.004 0.065 1646 Dihedral : 5.632 59.855 1366 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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: -0.80 (0.24), residues: 1194 helix: 0.95 (0.33), residues: 244 sheet: 0.63 (0.32), residues: 256 loop : -1.62 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 67 TYR 0.045 0.001 TYR A 182 PHE 0.013 0.001 PHE C 27 TRP 0.015 0.002 TRP H 36 HIS 0.004 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9731) covalent geometry : angle 0.58238 / 0.29 (13253) SS BOND : bond 0.00409 / 0.23 ( 9) SS BOND : angle 0.90570 / 0.53 ( 18) hydrogen bonds : bond 0.04182 / 2.70 ( 274) hydrogen bonds : angle 4.74015 / 3.53 ( 768) Misc. bond : bond 0.00031 / 0.02 ( 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 223 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8745 (t70) cc_final: 0.8433 (p0) REVERT: A 194 LEU cc_start: 0.9162 (mm) cc_final: 0.8327 (mm) REVERT: D 175 LEU cc_start: 0.7535 (mt) cc_final: 0.6817 (mp) REVERT: D 181 LEU cc_start: 0.8397 (mm) cc_final: 0.7962 (pp) REVERT: H 16 ARG cc_start: 0.8106 (mmt-90) cc_final: 0.7780 (mmp80) REVERT: H 188 SER cc_start: 0.8471 (m) cc_final: 0.8207 (t) REVERT: L 47 LEU cc_start: 0.8717 (tp) cc_final: 0.8503 (tp) REVERT: L 181 LEU cc_start: 0.8363 (mm) cc_final: 0.8054 (pp) REVERT: L 194 CYS cc_start: 0.3394 (p) cc_final: 0.3152 (p) REVERT: B 181 GLN cc_start: 0.9048 (mt0) cc_final: 0.8435 (tt0) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.0857 time to fit residues: 28.0797 Evaluate side-chains 164 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 2.9990 chunk 3 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 107 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN L 89 GLN L 93 ASN B 63 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.149197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.121819 restraints weight = 24064.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.121291 restraints weight = 19254.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.122380 restraints weight = 17597.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.122809 restraints weight = 13436.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.123076 restraints weight = 12213.010| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9743 Z= 0.123 Angle : 0.592 8.516 13271 Z= 0.299 Chirality : 0.041 0.160 1508 Planarity : 0.004 0.061 1646 Dihedral : 5.599 58.616 1366 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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: -0.86 (0.24), residues: 1194 helix: 1.27 (0.34), residues: 230 sheet: 0.16 (0.33), residues: 252 loop : -1.55 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 67 TYR 0.042 0.001 TYR A 182 PHE 0.014 0.001 PHE H 29 TRP 0.016 0.002 TRP B 89 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9731) covalent geometry : angle 0.59150 / 0.30 (13253) SS BOND : bond 0.00593 / 0.42 ( 9) SS BOND : angle 0.95031 / 0.57 ( 18) hydrogen bonds : bond 0.04376 / 2.81 ( 274) hydrogen bonds : angle 4.70260 / 3.48 ( 768) Misc. bond : bond 0.00029 / 0.01 ( 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 225 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 175 LEU cc_start: 0.7386 (mt) cc_final: 0.7103 (mt) REVERT: D 181 LEU cc_start: 0.8250 (mm) cc_final: 0.7875 (pp) REVERT: C 16 ARG cc_start: 0.8131 (mmt-90) cc_final: 0.7774 (mmp80) REVERT: H 16 ARG cc_start: 0.7985 (mmt-90) cc_final: 0.7707 (mmp80) REVERT: H 188 SER cc_start: 0.8364 (m) cc_final: 0.8134 (t) REVERT: L 118 PHE cc_start: 0.5377 (t80) cc_final: 0.5019 (t80) REVERT: L 181 LEU cc_start: 0.8337 (mm) cc_final: 0.8012 (pp) REVERT: L 194 CYS cc_start: 0.2902 (p) cc_final: 0.2598 (p) REVERT: B 181 GLN cc_start: 0.9073 (mt0) cc_final: 0.8353 (tt0) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.0793 time to fit residues: 26.4876 Evaluate side-chains 168 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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: 10.0000 chunk 75 optimal weight: 20.0000 chunk 78 optimal weight: 0.0020 chunk 61 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 0.0870 chunk 73 optimal weight: 6.9990 overall best weight: 2.6172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN D 93 ASN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN 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 = 0.3922 r_free = 0.3922 target = 0.140869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.111039 restraints weight = 28973.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113149 restraints weight = 20022.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113210 restraints weight = 15221.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.113618 restraints weight = 11875.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113765 restraints weight = 11323.243| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9743 Z= 0.180 Angle : 0.672 8.612 13271 Z= 0.341 Chirality : 0.043 0.191 1508 Planarity : 0.005 0.065 1646 Dihedral : 5.901 58.072 1366 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.10 % Allowed : 3.29 % Favored : 96.62 % 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: -1.13 (0.24), residues: 1194 helix: 1.16 (0.34), residues: 230 sheet: -0.12 (0.32), residues: 252 loop : -1.73 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 67 TYR 0.045 0.002 TYR A 182 PHE 0.017 0.002 PHE L 71 TRP 0.019 0.002 TRP C 36 HIS 0.003 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 9731) covalent geometry : angle 0.67111 / 0.34 (13253) SS BOND : bond 0.00365 / 0.20 ( 9) SS BOND : angle 1.07025 / 0.65 ( 18) hydrogen bonds : bond 0.05147 / 3.34 ( 274) hydrogen bonds : angle 4.95976 / 3.66 ( 768) Misc. bond : bond 0.00072 / 0.04 ( 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 205 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8183 (pm20) REVERT: D 181 LEU cc_start: 0.8432 (mm) cc_final: 0.8017 (pp) REVERT: H 16 ARG cc_start: 0.8259 (mmt-90) cc_final: 0.8034 (mmt-90) REVERT: L 118 PHE cc_start: 0.6216 (t80) cc_final: 0.5849 (t80) REVERT: L 175 LEU cc_start: 0.7909 (mt) cc_final: 0.7271 (mp) REVERT: L 181 LEU cc_start: 0.8503 (mm) cc_final: 0.8168 (pp) REVERT: L 194 CYS cc_start: 0.3999 (p) cc_final: 0.3647 (p) REVERT: B 71 MET cc_start: 0.8534 (tpp) cc_final: 0.8095 (tpp) REVERT: B 148 LYS cc_start: 0.9486 (tmmt) cc_final: 0.8772 (ttpt) REVERT: B 181 GLN cc_start: 0.9077 (mt0) cc_final: 0.8521 (tt0) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.0829 time to fit residues: 24.8592 Evaluate side-chains 158 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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: 0.6980 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN D 93 ASN C 30 ASN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN L 93 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 = 0.3935 r_free = 0.3935 target = 0.141849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.113359 restraints weight = 29521.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.113808 restraints weight = 21099.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.114705 restraints weight = 18061.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.114754 restraints weight = 13386.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.115110 restraints weight = 12328.539| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9743 Z= 0.158 Angle : 0.640 7.371 13271 Z= 0.325 Chirality : 0.043 0.173 1508 Planarity : 0.005 0.066 1646 Dihedral : 5.890 54.774 1366 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.10 % Allowed : 1.55 % 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: -1.26 (0.24), residues: 1194 helix: 1.17 (0.34), residues: 230 sheet: -0.27 (0.31), residues: 272 loop : -1.87 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.043 0.002 TYR A 182 PHE 0.033 0.002 PHE D 71 TRP 0.021 0.002 TRP H 47 HIS 0.003 0.001 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 9731) covalent geometry : angle 0.63940 / 0.32 (13253) SS BOND : bond 0.00389 / 0.22 ( 9) SS BOND : angle 1.08082 / 0.64 ( 18) hydrogen bonds : bond 0.05265 / 3.42 ( 274) hydrogen bonds : angle 4.92505 / 3.64 ( 768) Misc. bond : bond 0.00045 / 0.02 ( 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 214 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8189 (pm20) REVERT: A 137 ASP cc_start: 0.8486 (t0) cc_final: 0.8187 (p0) REVERT: A 194 LEU cc_start: 0.9314 (mm) cc_final: 0.9077 (mt) REVERT: D 181 LEU cc_start: 0.8382 (mm) cc_final: 0.7955 (pp) REVERT: C 16 ARG cc_start: 0.8264 (mmt-90) cc_final: 0.7792 (mmp80) REVERT: L 175 LEU cc_start: 0.7632 (mt) cc_final: 0.7415 (mt) REVERT: L 181 LEU cc_start: 0.8497 (mm) cc_final: 0.8151 (pp) REVERT: L 194 CYS cc_start: 0.3831 (p) cc_final: 0.3482 (p) REVERT: B 168 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8816 (tp30) REVERT: B 181 GLN cc_start: 0.8935 (mt0) cc_final: 0.8537 (tt0) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.0821 time to fit residues: 25.9300 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 : 0.370 ------------------------------------------------------------------------------- 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: 0.9980 chunk 96 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN C 30 ASN H 180 GLN 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 = 0.3989 r_free = 0.3989 target = 0.145786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.116641 restraints weight = 29052.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.117090 restraints weight = 18759.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118033 restraints weight = 15039.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.118460 restraints weight = 12452.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.119333 restraints weight = 12145.183| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9743 Z= 0.112 Angle : 0.629 7.960 13271 Z= 0.310 Chirality : 0.042 0.175 1508 Planarity : 0.004 0.061 1646 Dihedral : 5.651 55.518 1366 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.19 % Allowed : 1.84 % Favored : 97.97 % 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: -1.19 (0.24), residues: 1194 helix: 1.33 (0.34), residues: 230 sheet: -0.26 (0.32), residues: 274 loop : -1.85 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 67 TYR 0.034 0.001 TYR A 182 PHE 0.012 0.001 PHE D 71 TRP 0.014 0.002 TRP B 89 HIS 0.005 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9731) covalent geometry : angle 0.62909 / 0.31 (13253) SS BOND : bond 0.00413 / 0.23 ( 9) SS BOND : angle 0.86329 / 0.51 ( 18) hydrogen bonds : bond 0.04630 / 3.01 ( 274) hydrogen bonds : angle 4.75020 / 3.50 ( 768) Misc. bond : bond 0.00022 / 0.01 ( 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 230 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 228 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8077 (pm20) REVERT: A 119 MET cc_start: 0.9105 (mmm) cc_final: 0.8898 (mmm) REVERT: A 137 ASP cc_start: 0.8270 (t0) cc_final: 0.8036 (p0) REVERT: A 194 LEU cc_start: 0.9297 (mm) cc_final: 0.9026 (mt) REVERT: D 1 GLU cc_start: 0.7517 (pt0) cc_final: 0.6976 (mp0) REVERT: D 93 ASN cc_start: 0.8786 (m-40) cc_final: 0.8270 (m-40) REVERT: C 16 ARG cc_start: 0.8169 (mmt-90) cc_final: 0.7736 (mmp80) REVERT: H 13 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8210 (tm-30) REVERT: H 213 ASN cc_start: 0.8667 (t0) cc_final: 0.8293 (t0) REVERT: L 93 ASN cc_start: 0.8569 (m-40) cc_final: 0.8250 (m-40) REVERT: L 175 LEU cc_start: 0.7596 (mt) cc_final: 0.7045 (mp) REVERT: B 148 LYS cc_start: 0.9477 (tmmt) cc_final: 0.8888 (pttt) REVERT: B 181 GLN cc_start: 0.8861 (mt0) cc_final: 0.8423 (tt0) outliers start: 2 outliers final: 0 residues processed: 230 average time/residue: 0.0861 time to fit residues: 28.7871 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 : 0.309 ------------------------------------------------------------------------------- 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: 5.9990 chunk 38 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 0.0570 chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 78 optimal weight: 0.0010 chunk 4 optimal weight: 0.9980 overall best weight: 0.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN C 30 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN B 63 HIS B 181 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.147294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.118114 restraints weight = 23690.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.118918 restraints weight = 14940.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118782 restraints weight = 11414.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.119100 restraints weight = 11079.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119320 restraints weight = 10752.520| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9743 Z= 0.109 Angle : 0.627 7.547 13271 Z= 0.307 Chirality : 0.042 0.167 1508 Planarity : 0.004 0.059 1646 Dihedral : 5.499 57.237 1366 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % 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: -1.21 (0.24), residues: 1194 helix: 1.34 (0.34), residues: 230 sheet: -0.08 (0.33), residues: 254 loop : -1.92 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 156 TYR 0.034 0.001 TYR A 182 PHE 0.013 0.001 PHE A 62 TRP 0.015 0.001 TRP L 94 HIS 0.007 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 9731) covalent geometry : angle 0.62671 / 0.31 (13253) SS BOND : bond 0.00432 / 0.27 ( 9) SS BOND : angle 0.68803 / 0.40 ( 18) hydrogen bonds : bond 0.04117 / 2.69 ( 274) hydrogen bonds : angle 4.57814 / 3.37 ( 768) Misc. bond : bond 0.00004 / 0.00 ( 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 230 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8343 (mmm) cc_final: 0.8137 (tpp) REVERT: A 119 MET cc_start: 0.9042 (mmm) cc_final: 0.8818 (mmm) REVERT: A 137 ASP cc_start: 0.8401 (t0) cc_final: 0.8166 (p0) REVERT: D 1 GLU cc_start: 0.7378 (pt0) cc_final: 0.6752 (mp0) REVERT: D 93 ASN cc_start: 0.8707 (m-40) cc_final: 0.8260 (m-40) REVERT: C 13 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8221 (tm-30) REVERT: H 13 GLN cc_start: 0.8362 (tm-30) cc_final: 0.8120 (tm-30) REVERT: H 16 ARG cc_start: 0.8019 (mmt-90) cc_final: 0.7560 (mmt-90) REVERT: H 213 ASN cc_start: 0.8591 (t0) cc_final: 0.8187 (t0) REVERT: L 93 ASN cc_start: 0.8720 (m-40) cc_final: 0.8437 (m-40) REVERT: L 148 TRP cc_start: 0.6804 (m-10) cc_final: 0.5620 (m-10) REVERT: L 175 LEU cc_start: 0.7508 (mt) cc_final: 0.6796 (mp) REVERT: L 181 LEU cc_start: 0.8356 (mm) cc_final: 0.7830 (tp) REVERT: B 62 PHE cc_start: 0.8628 (t80) cc_final: 0.8209 (t80) REVERT: B 181 GLN cc_start: 0.8911 (mt0) cc_final: 0.8480 (tt0) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.0890 time to fit residues: 29.4069 Evaluate side-chains 173 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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: 2.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 0.0370 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 50 optimal weight: 0.0870 chunk 114 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN 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 = 0.3948 r_free = 0.3948 target = 0.146635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117611 restraints weight = 23995.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117893 restraints weight = 18082.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119159 restraints weight = 14272.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119463 restraints weight = 10795.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.119549 restraints weight = 10551.623| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9743 Z= 0.109 Angle : 0.637 7.637 13271 Z= 0.312 Chirality : 0.042 0.176 1508 Planarity : 0.004 0.059 1646 Dihedral : 5.449 58.101 1366 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % 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 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: -1.23 (0.24), residues: 1194 helix: 1.22 (0.34), residues: 242 sheet: -0.23 (0.32), residues: 274 loop : -1.93 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 156 TYR 0.033 0.001 TYR A 182 PHE 0.028 0.001 PHE A 62 TRP 0.015 0.001 TRP L 94 HIS 0.007 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9731) covalent geometry : angle 0.63679 / 0.31 (13253) SS BOND : bond 0.00380 / 0.21 ( 9) SS BOND : angle 0.81042 / 0.47 ( 18) hydrogen bonds : bond 0.04027 / 2.63 ( 274) hydrogen bonds : angle 4.52773 / 3.33 ( 768) Misc. bond : bond 0.00026 / 0.01 ( 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 : 0.362 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.9052 (mmm) cc_final: 0.8807 (mmm) REVERT: D 1 GLU cc_start: 0.7239 (pt0) cc_final: 0.6611 (mp0) REVERT: D 93 ASN cc_start: 0.8785 (m-40) cc_final: 0.8343 (m-40) REVERT: D 148 TRP cc_start: 0.5797 (m-10) cc_final: 0.5470 (m-10) REVERT: C 16 ARG cc_start: 0.8184 (mmt-90) cc_final: 0.7750 (mmp80) REVERT: H 16 ARG cc_start: 0.7974 (mmt-90) cc_final: 0.7655 (mmp80) REVERT: H 213 ASN cc_start: 0.8596 (t0) cc_final: 0.8202 (t0) REVERT: L 1 GLU cc_start: 0.7545 (pt0) cc_final: 0.7110 (mp0) REVERT: L 93 ASN cc_start: 0.8855 (m-40) cc_final: 0.8351 (m-40) REVERT: L 181 LEU cc_start: 0.8386 (mm) cc_final: 0.7874 (tp) REVERT: B 148 LYS cc_start: 0.9445 (tmmt) cc_final: 0.8718 (pttt) REVERT: B 181 GLN cc_start: 0.8921 (mt0) cc_final: 0.8420 (tt0) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.0796 time to fit residues: 24.6906 Evaluate side-chains 166 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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: 0.6980 chunk 78 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 63 optimal weight: 0.1980 chunk 55 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.0070 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN B 181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.145247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.112605 restraints weight = 26241.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.114219 restraints weight = 15644.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.115448 restraints weight = 11208.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.116205 restraints weight = 9435.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.116417 restraints weight = 8416.523| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9743 Z= 0.147 Angle : 0.662 8.175 13271 Z= 0.333 Chirality : 0.042 0.184 1508 Planarity : 0.005 0.060 1646 Dihedral : 5.645 57.039 1366 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % 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 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: -1.42 (0.24), residues: 1194 helix: 1.10 (0.34), residues: 242 sheet: -0.44 (0.33), residues: 252 loop : -1.98 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 156 TYR 0.038 0.002 TYR A 182 PHE 0.015 0.002 PHE L 71 TRP 0.014 0.002 TRP D 148 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 9731) covalent geometry : angle 0.66169 / 0.33 (13253) SS BOND : bond 0.00411 / 0.23 ( 9) SS BOND : angle 0.89859 / 0.55 ( 18) hydrogen bonds : bond 0.04706 / 3.08 ( 274) hydrogen bonds : angle 4.73288 / 3.46 ( 768) Misc. bond : bond 0.00067 / 0.04 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1537.33 seconds wall clock time: 27 minutes 27.84 seconds (1647.84 seconds total)