Starting phenix.real_space_refine on Thu Jul 2 03:46:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jna_22403/07_2026/7jna_22403.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jna_22403/07_2026/7jna_22403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jna_22403/07_2026/7jna_22403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jna_22403/07_2026/7jna_22403.map" model { file = "/net/cci-nas-00/data/ceres_data/7jna_22403/07_2026/7jna_22403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jna_22403/07_2026/7jna_22403.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jna_22403/07_2026/7jna_22403.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jna_22403/07_2026/7jna_22403.cif" } resolution = 3.6 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4176 2.51 5 N 1071 2.21 5 O 1161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6432 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2074 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 13, 'TRANS': 264} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 3, 'ASP:plan': 5, 'GLN:plan1': 6, 'GLU:plan': 3, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, J, O Time building chain proxies: 1.35, per 1000 atoms: 0.21 Number of scatterers: 6432 At special positions: 0 Unit cell: (83.106, 82.08, 127.224, 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 24 16.00 O 1161 8.00 N 1071 7.00 C 4176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 149 " 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=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG J 1 " - " NAG J 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 148 " " NAG A 402 " - " ASN A 162 " " NAG A 403 " - " ASN A 190 " " NAG B 401 " - " ASN B 148 " " NAG B 402 " - " ASN B 162 " " NAG B 403 " - " ASN B 190 " " NAG C 401 " - " ASN C 148 " " NAG C 402 " - " ASN C 162 " " NAG C 403 " - " ASN C 190 " " NAG E 1 " - " ASN A 155 " " NAG J 1 " - " ASN B 155 " " NAG O 1 " - " ASN C 155 " Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 379.6 milliseconds 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1608 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 15 sheets defined 32.7% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 62 through 98 removed outlier: 3.535A pdb=" N PHE A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 removed outlier: 3.523A pdb=" N PHE A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.984A pdb=" N GLN A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 338 Processing helix chain 'B' and resid 62 through 98 removed outlier: 3.535A pdb=" N PHE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 213 removed outlier: 3.523A pdb=" N PHE B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 removed outlier: 3.984A pdb=" N GLN B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 338 Processing helix chain 'C' and resid 62 through 98 removed outlier: 3.535A pdb=" N PHE C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.524A pdb=" N PHE C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 227 removed outlier: 3.984A pdb=" N GLN C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 338 Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 130 removed outlier: 6.450A pdb=" N GLN A 186 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS A 128 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE A 184 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N HIS A 130 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU A 182 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 283 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N PHE A 236 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL A 284 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR A 238 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU A 286 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 240 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 247 Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AA7, first strand: chain 'B' and resid 169 through 172 Processing sheet with id=AA8, first strand: chain 'B' and resid 125 through 130 removed outlier: 6.450A pdb=" N GLN B 186 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS B 128 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE B 184 " --> pdb=" O CYS B 128 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS B 130 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU B 182 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 283 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N PHE B 236 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL B 284 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR B 238 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLU B 286 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 240 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 200 Processing sheet with id=AB1, first strand: chain 'B' and resid 244 through 247 Processing sheet with id=AB2, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 172 Processing sheet with id=AB4, first strand: chain 'C' and resid 125 through 130 removed outlier: 6.450A pdb=" N GLN C 186 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS C 128 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE C 184 " --> pdb=" O CYS C 128 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N HIS C 130 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU C 182 " --> pdb=" O HIS C 130 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 283 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N PHE C 236 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL C 284 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR C 238 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLU C 286 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL C 240 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 198 through 200 Processing sheet with id=AB6, first strand: chain 'C' and resid 244 through 247 270 hydrogen bonds defined for protein. 783 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: 0.87 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1990 1.34 - 1.45: 1037 1.45 - 1.57: 3531 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 6594 Sorted by residual: bond pdb=" N ILE B 89 " pdb=" CA ILE B 89 " ideal model delta sigma weight residual 1.461 1.495 -0.033 1.17e-02 7.31e+03 8.16e+00 bond pdb=" N ILE A 89 " pdb=" CA ILE A 89 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.78e+00 bond pdb=" N ILE C 89 " pdb=" CA ILE C 89 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.64e+00 bond pdb=" N LYS A 319 " pdb=" CA LYS A 319 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.19e+00 bond pdb=" N LYS B 319 " pdb=" CA LYS B 319 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.10e+00 ... (remaining 6589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 7951 1.01 - 2.02: 805 2.02 - 3.03: 164 3.03 - 4.04: 50 4.04 - 5.05: 24 Bond angle restraints: 8994 Sorted by residual: angle pdb=" C SER B 206 " pdb=" N PHE B 207 " pdb=" CA PHE B 207 " ideal model delta sigma weight residual 120.29 124.94 -4.65 1.42e+00 4.96e-01 1.07e+01 angle pdb=" C SER C 206 " pdb=" N PHE C 207 " pdb=" CA PHE C 207 " ideal model delta sigma weight residual 120.29 124.89 -4.60 1.42e+00 4.96e-01 1.05e+01 angle pdb=" C SER A 206 " pdb=" N PHE A 207 " pdb=" CA PHE A 207 " ideal model delta sigma weight residual 120.29 124.88 -4.59 1.42e+00 4.96e-01 1.05e+01 angle pdb=" CA ILE B 89 " pdb=" C ILE B 89 " pdb=" O ILE B 89 " ideal model delta sigma weight residual 121.17 117.90 3.27 1.06e+00 8.90e-01 9.53e+00 angle pdb=" CA ILE A 89 " pdb=" C ILE A 89 " pdb=" O ILE A 89 " ideal model delta sigma weight residual 121.17 117.91 3.26 1.06e+00 8.90e-01 9.48e+00 ... (remaining 8989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.44: 3290 15.44 - 30.87: 406 30.87 - 46.31: 57 46.31 - 61.74: 12 61.74 - 77.18: 6 Dihedral angle restraints: 3771 sinusoidal: 1302 harmonic: 2469 Sorted by residual: dihedral pdb=" CA ASN B 190 " pdb=" C ASN B 190 " pdb=" N LYS B 191 " pdb=" CA LYS B 191 " ideal model delta harmonic sigma weight residual -180.00 -155.58 -24.42 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ASN A 190 " pdb=" C ASN A 190 " pdb=" N LYS A 191 " pdb=" CA LYS A 191 " ideal model delta harmonic sigma weight residual 180.00 -155.64 -24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ASN C 190 " pdb=" C ASN C 190 " pdb=" N LYS C 191 " pdb=" CA LYS C 191 " ideal model delta harmonic sigma weight residual -180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 3768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 722 0.039 - 0.079: 228 0.079 - 0.118: 97 0.118 - 0.158: 9 0.158 - 0.197: 6 Chirality restraints: 1062 Sorted by residual: chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 162 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" C1 NAG C 402 " pdb=" ND2 ASN C 162 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" C1 NAG A 402 " pdb=" ND2 ASN A 162 " pdb=" C2 NAG A 402 " pdb=" O5 NAG A 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 1059 not shown) Planarity restraints: 1143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG E 2 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.527 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG J 2 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.527 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " -0.340 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG O 2 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " -0.114 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " -0.151 2.00e-02 2.50e+03 ... (remaining 1140 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 841 2.75 - 3.29: 6563 3.29 - 3.83: 10337 3.83 - 4.36: 11863 4.36 - 4.90: 20118 Nonbonded interactions: 49722 Sorted by model distance: nonbonded pdb=" OH TYR B 156 " pdb=" OE1 GLU B 224 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR A 156 " pdb=" OE1 GLU A 224 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR C 156 " pdb=" OE1 GLU C 224 " model vdw 2.215 3.040 nonbonded pdb=" ND1 HIS C 130 " pdb=" OE2 GLU C 181 " model vdw 2.262 3.120 nonbonded pdb=" ND1 HIS A 130 " pdb=" OE2 GLU A 181 " model vdw 2.262 3.120 ... (remaining 49717 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'O' } 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.830 Find NCS groups from input model: 0.030 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 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 : 0.005 0.036 6612 Z= 0.252 Angle : 0.766 10.453 9045 Z= 0.416 Chirality : 0.045 0.197 1062 Planarity : 0.025 0.295 1131 Dihedral : 13.483 77.175 2154 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.83 (0.24), residues: 828 helix: -0.91 (0.27), residues: 267 sheet: -3.40 (0.25), residues: 255 loop : -3.02 (0.29), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.007 0.001 TYR C 156 PHE 0.015 0.002 PHE C 204 TRP 0.009 0.002 TRP B 330 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.25 ( 6594) covalent geometry : angle 0.71906 / 0.41 ( 8994) SS BOND : bond 0.00275 / 0.14 ( 3) SS BOND : angle 2.77092 / 1.43 ( 6) hydrogen bonds : bond 0.13361 / 9.08 ( 270) hydrogen bonds : angle 5.99911 / 4.15 ( 783) link_BETA1-4 : bond 0.00117 / 0.06 ( 3) link_BETA1-4 : angle 1.09008 / 0.62 ( 9) link_NAG-ASN : bond 0.00757 / 0.51 ( 12) link_NAG-ASN : angle 4.05923 / 3.50 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 309 LEU cc_start: 0.7550 (tp) cc_final: 0.7307 (tp) REVERT: C 242 MET cc_start: 0.7600 (mtm) cc_final: 0.6999 (ptp) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.0769 time to fit residues: 20.4001 Evaluate side-chains 130 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN B 172 GLN C 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.164433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134140 restraints weight = 9028.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135831 restraints weight = 6260.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138328 restraints weight = 4914.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138399 restraints weight = 4107.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139011 restraints weight = 3826.495| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6612 Z= 0.233 Angle : 0.868 12.103 9045 Z= 0.394 Chirality : 0.051 0.241 1062 Planarity : 0.005 0.043 1131 Dihedral : 5.174 26.604 894 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.94 % Allowed : 22.75 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.49 (0.27), residues: 828 helix: 0.81 (0.30), residues: 267 sheet: -3.33 (0.25), residues: 249 loop : -2.22 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 259 TYR 0.018 0.002 TYR A 201 PHE 0.026 0.003 PHE A 236 TRP 0.005 0.001 TRP B 330 HIS 0.003 0.001 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 ( 6594) covalent geometry : angle 0.79782 / 0.38 ( 8994) SS BOND : bond 0.00517 / 0.26 ( 3) SS BOND : angle 2.65310 / 1.38 ( 6) hydrogen bonds : bond 0.03666 / 2.64 ( 270) hydrogen bonds : angle 4.90695 / 3.49 ( 783) link_BETA1-4 : bond 0.00552 / 0.28 ( 3) link_BETA1-4 : angle 3.27170 / 1.94 ( 9) link_NAG-ASN : bond 0.01264 / 0.86 ( 12) link_NAG-ASN : angle 5.15284 / 4.24 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.7762 (pm20) cc_final: 0.7164 (pp30) REVERT: A 259 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7409 (mtm110) REVERT: A 319 LYS cc_start: 0.7384 (ttpt) cc_final: 0.6919 (mptt) REVERT: B 260 GLN cc_start: 0.8411 (pp30) cc_final: 0.7602 (pp30) REVERT: B 309 LEU cc_start: 0.7927 (tp) cc_final: 0.7532 (tp) REVERT: B 319 LYS cc_start: 0.7473 (ttpt) cc_final: 0.7185 (tppt) outliers start: 28 outliers final: 14 residues processed: 181 average time/residue: 0.0711 time to fit residues: 16.7605 Evaluate side-chains 143 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 298 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 75 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.166458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135390 restraints weight = 9039.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138480 restraints weight = 6764.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139673 restraints weight = 4657.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139991 restraints weight = 4230.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142776 restraints weight = 3827.937| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6612 Z= 0.145 Angle : 0.725 11.375 9045 Z= 0.335 Chirality : 0.044 0.239 1062 Planarity : 0.004 0.036 1131 Dihedral : 4.904 26.857 894 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.53 % Allowed : 26.81 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.71 (0.29), residues: 828 helix: 1.55 (0.31), residues: 267 sheet: -2.89 (0.27), residues: 255 loop : -1.83 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 259 TYR 0.014 0.002 TYR A 111 PHE 0.019 0.002 PHE B 236 TRP 0.006 0.001 TRP B 330 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 6594) covalent geometry : angle 0.63372 / 0.31 ( 8994) SS BOND : bond 0.00198 / 0.10 ( 3) SS BOND : angle 1.99653 / 1.02 ( 6) hydrogen bonds : bond 0.03443 / 2.41 ( 270) hydrogen bonds : angle 4.72162 / 3.36 ( 783) link_BETA1-4 : bond 0.00373 / 0.19 ( 3) link_BETA1-4 : angle 1.51400 / 0.87 ( 9) link_NAG-ASN : bond 0.00691 / 0.48 ( 12) link_NAG-ASN : angle 5.52850 / 4.56 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.7935 (pm20) cc_final: 0.7265 (pp30) REVERT: A 230 TRP cc_start: 0.8410 (p90) cc_final: 0.8201 (p90) REVERT: A 259 ARG cc_start: 0.7646 (mtm110) cc_final: 0.7287 (mtm110) REVERT: A 318 PHE cc_start: 0.7541 (t80) cc_final: 0.7108 (m-80) REVERT: A 319 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7347 (tppt) REVERT: B 309 LEU cc_start: 0.8220 (tp) cc_final: 0.7906 (tp) REVERT: B 319 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7380 (tppt) REVERT: C 318 PHE cc_start: 0.7127 (m-80) cc_final: 0.6581 (m-10) REVERT: C 319 LYS cc_start: 0.7329 (tttt) cc_final: 0.6889 (tppt) REVERT: C 330 TRP cc_start: 0.7219 (t-100) cc_final: 0.6809 (t-100) outliers start: 20 outliers final: 12 residues processed: 148 average time/residue: 0.0635 time to fit residues: 12.5472 Evaluate side-chains 132 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 295 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN ** C 124 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 = 0.3957 r_free = 0.3957 target = 0.165495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133235 restraints weight = 9126.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135691 restraints weight = 7608.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137766 restraints weight = 5179.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139943 restraints weight = 4021.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.140015 restraints weight = 3629.323| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6612 Z= 0.184 Angle : 0.728 12.283 9045 Z= 0.341 Chirality : 0.045 0.264 1062 Planarity : 0.004 0.032 1131 Dihedral : 4.841 28.188 894 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.70 % Allowed : 25.57 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.30), residues: 828 helix: 1.81 (0.31), residues: 267 sheet: -2.66 (0.29), residues: 255 loop : -1.76 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 259 TYR 0.017 0.002 TYR C 156 PHE 0.023 0.002 PHE A 232 TRP 0.011 0.001 TRP C 287 HIS 0.002 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 ( 6594) covalent geometry : angle 0.63910 / 0.32 ( 8994) SS BOND : bond 0.00217 / 0.11 ( 3) SS BOND : angle 2.59385 / 1.34 ( 6) hydrogen bonds : bond 0.03358 / 2.37 ( 270) hydrogen bonds : angle 4.63032 / 3.30 ( 783) link_BETA1-4 : bond 0.00186 / 0.09 ( 3) link_BETA1-4 : angle 1.62709 / 0.93 ( 9) link_NAG-ASN : bond 0.00589 / 0.40 ( 12) link_NAG-ASN : angle 5.43021 / 4.47 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8209 (ttp) REVERT: A 287 TRP cc_start: 0.9118 (m100) cc_final: 0.8859 (m100) REVERT: A 318 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: A 319 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7291 (tptt) REVERT: B 319 LYS cc_start: 0.7898 (ttpt) cc_final: 0.7421 (tppt) REVERT: C 287 TRP cc_start: 0.9199 (m100) cc_final: 0.8967 (m100) REVERT: C 318 PHE cc_start: 0.7176 (m-80) cc_final: 0.6654 (m-10) REVERT: C 319 LYS cc_start: 0.7554 (tttt) cc_final: 0.7134 (tptt) REVERT: C 330 TRP cc_start: 0.7200 (t-100) cc_final: 0.6927 (t-100) outliers start: 38 outliers final: 23 residues processed: 149 average time/residue: 0.0569 time to fit residues: 11.7854 Evaluate side-chains 144 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 268 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 46 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN ** C 124 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 = 0.3972 r_free = 0.3972 target = 0.167232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135611 restraints weight = 9160.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138786 restraints weight = 6828.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139996 restraints weight = 4674.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140289 restraints weight = 4245.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142972 restraints weight = 3835.876| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6612 Z= 0.137 Angle : 0.697 13.804 9045 Z= 0.321 Chirality : 0.043 0.233 1062 Planarity : 0.004 0.035 1131 Dihedral : 4.785 30.862 894 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.47 % Allowed : 26.81 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.20 (0.30), residues: 828 helix: 1.95 (0.32), residues: 267 sheet: -2.56 (0.29), residues: 255 loop : -1.57 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 259 TYR 0.020 0.002 TYR A 156 PHE 0.016 0.002 PHE C 232 TRP 0.006 0.001 TRP B 330 HIS 0.002 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6594) covalent geometry : angle 0.59076 / 0.30 ( 8994) SS BOND : bond 0.00055 / 0.03 ( 3) SS BOND : angle 2.13928 / 1.05 ( 6) hydrogen bonds : bond 0.03253 / 2.29 ( 270) hydrogen bonds : angle 4.45740 / 3.16 ( 783) link_BETA1-4 : bond 0.00259 / 0.13 ( 3) link_BETA1-4 : angle 1.57319 / 0.90 ( 9) link_NAG-ASN : bond 0.00781 / 0.55 ( 12) link_NAG-ASN : angle 5.79348 / 4.70 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 TRP cc_start: 0.9069 (m100) cc_final: 0.8849 (m100) REVERT: A 305 ASN cc_start: 0.7443 (t0) cc_final: 0.7202 (t0) REVERT: A 318 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: A 319 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7164 (mptt) REVERT: B 319 LYS cc_start: 0.7780 (ttpt) cc_final: 0.7412 (tppt) REVERT: C 253 ARG cc_start: 0.7181 (tpt170) cc_final: 0.6656 (tpt-90) REVERT: C 287 TRP cc_start: 0.9180 (m100) cc_final: 0.8926 (m100) REVERT: C 318 PHE cc_start: 0.7126 (m-80) cc_final: 0.6632 (m-10) REVERT: C 319 LYS cc_start: 0.7520 (tttt) cc_final: 0.7195 (tptt) outliers start: 31 outliers final: 24 residues processed: 155 average time/residue: 0.0615 time to fit residues: 13.0397 Evaluate side-chains 154 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 230 TRP Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 268 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 66 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 74 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 9 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 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 = 0.3984 r_free = 0.3984 target = 0.168301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134393 restraints weight = 9105.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138731 restraints weight = 5746.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141609 restraints weight = 4334.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143493 restraints weight = 3617.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144775 restraints weight = 3210.831| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6612 Z= 0.134 Angle : 0.722 14.321 9045 Z= 0.334 Chirality : 0.045 0.221 1062 Planarity : 0.004 0.031 1131 Dihedral : 4.759 34.796 894 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.47 % Allowed : 28.22 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.17 (0.30), residues: 828 helix: 2.07 (0.32), residues: 267 sheet: -2.61 (0.27), residues: 276 loop : -1.45 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 259 TYR 0.019 0.002 TYR A 156 PHE 0.015 0.002 PHE C 232 TRP 0.008 0.001 TRP C 330 HIS 0.002 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 6594) covalent geometry : angle 0.61117 / 0.31 ( 8994) SS BOND : bond 0.00041 / 0.02 ( 3) SS BOND : angle 2.23084 / 1.15 ( 6) hydrogen bonds : bond 0.03199 / 2.25 ( 270) hydrogen bonds : angle 4.40060 / 3.11 ( 783) link_BETA1-4 : bond 0.00238 / 0.12 ( 3) link_BETA1-4 : angle 1.54996 / 0.89 ( 9) link_NAG-ASN : bond 0.00729 / 0.50 ( 12) link_NAG-ASN : angle 6.02691 / 4.86 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 TRP cc_start: 0.9037 (m100) cc_final: 0.8767 (m100) REVERT: A 318 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.7183 (m-80) REVERT: A 319 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7030 (tptt) REVERT: B 319 LYS cc_start: 0.7573 (ttpt) cc_final: 0.7187 (tppt) REVERT: B 330 TRP cc_start: 0.7138 (t-100) cc_final: 0.6785 (t-100) REVERT: C 105 TYR cc_start: 0.8617 (m-10) cc_final: 0.8364 (m-80) REVERT: C 253 ARG cc_start: 0.7062 (tpt170) cc_final: 0.6631 (tpt-90) REVERT: C 279 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6852 (tt0) REVERT: C 318 PHE cc_start: 0.7248 (m-80) cc_final: 0.6728 (m-10) REVERT: C 319 LYS cc_start: 0.7434 (tttt) cc_final: 0.7118 (tppt) outliers start: 31 outliers final: 21 residues processed: 164 average time/residue: 0.0476 time to fit residues: 10.9163 Evaluate side-chains 154 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 230 TRP Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 279 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 74 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 78 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 64 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.166713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.134275 restraints weight = 8913.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137693 restraints weight = 6795.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139200 restraints weight = 4668.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139560 restraints weight = 3964.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140464 restraints weight = 3673.843| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6612 Z= 0.165 Angle : 0.761 14.044 9045 Z= 0.356 Chirality : 0.045 0.207 1062 Planarity : 0.004 0.033 1131 Dihedral : 4.771 30.836 894 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.64 % Allowed : 28.75 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.96 (0.30), residues: 828 helix: 2.17 (0.31), residues: 267 sheet: -2.48 (0.28), residues: 255 loop : -1.39 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 259 TYR 0.020 0.002 TYR A 156 PHE 0.017 0.002 PHE A 236 TRP 0.005 0.001 TRP C 330 HIS 0.002 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 6594) covalent geometry : angle 0.65939 / 0.33 ( 8994) SS BOND : bond 0.00273 / 0.14 ( 3) SS BOND : angle 3.01935 / 1.51 ( 6) hydrogen bonds : bond 0.03262 / 2.29 ( 270) hydrogen bonds : angle 4.33345 / 3.07 ( 783) link_BETA1-4 : bond 0.00275 / 0.14 ( 3) link_BETA1-4 : angle 1.31264 / 0.75 ( 9) link_NAG-ASN : bond 0.00960 / 0.71 ( 12) link_NAG-ASN : angle 5.92569 / 4.80 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 TRP cc_start: 0.9136 (m100) cc_final: 0.8733 (m100) REVERT: A 318 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7187 (m-80) REVERT: A 319 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7126 (mptt) REVERT: B 319 LYS cc_start: 0.7814 (ttpt) cc_final: 0.7376 (tppt) REVERT: B 330 TRP cc_start: 0.6944 (t-100) cc_final: 0.6705 (t-100) REVERT: C 105 TYR cc_start: 0.8645 (m-10) cc_final: 0.8431 (m-80) REVERT: C 253 ARG cc_start: 0.7226 (tpt170) cc_final: 0.6711 (tpt-90) REVERT: C 287 TRP cc_start: 0.9232 (m100) cc_final: 0.8912 (m100) REVERT: C 318 PHE cc_start: 0.7161 (m-80) cc_final: 0.6690 (m-10) REVERT: C 319 LYS cc_start: 0.7642 (tttt) cc_final: 0.7322 (tptt) outliers start: 32 outliers final: 29 residues processed: 161 average time/residue: 0.0561 time to fit residues: 12.3419 Evaluate side-chains 167 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 230 TRP Chi-restraints excluded: chain C residue 247 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.168090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136171 restraints weight = 8971.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139114 restraints weight = 6810.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.140310 restraints weight = 4759.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140687 restraints weight = 4275.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142832 restraints weight = 3892.945| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6612 Z= 0.141 Angle : 0.737 15.767 9045 Z= 0.341 Chirality : 0.046 0.418 1062 Planarity : 0.004 0.035 1131 Dihedral : 4.777 37.897 894 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.11 % Allowed : 29.10 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.79 (0.30), residues: 828 helix: 2.43 (0.32), residues: 261 sheet: -2.46 (0.28), residues: 255 loop : -1.25 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 93 TYR 0.019 0.002 TYR A 156 PHE 0.017 0.002 PHE B 232 TRP 0.005 0.001 TRP C 330 HIS 0.002 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 6594) covalent geometry : angle 0.62059 / 0.31 ( 8994) SS BOND : bond 0.00176 / 0.09 ( 3) SS BOND : angle 2.85866 / 1.46 ( 6) hydrogen bonds : bond 0.03150 / 2.22 ( 270) hydrogen bonds : angle 4.29223 / 3.04 ( 783) link_BETA1-4 : bond 0.00357 / 0.18 ( 3) link_BETA1-4 : angle 1.15632 / 0.67 ( 9) link_NAG-ASN : bond 0.00611 / 0.42 ( 12) link_NAG-ASN : angle 6.19725 / 4.63 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8597 (m-10) cc_final: 0.8389 (m-80) REVERT: A 287 TRP cc_start: 0.9101 (m100) cc_final: 0.8891 (m100) REVERT: A 318 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: A 319 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7281 (tptt) REVERT: B 287 TRP cc_start: 0.9308 (m100) cc_final: 0.8538 (m100) REVERT: B 319 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7552 (tppp) REVERT: C 253 ARG cc_start: 0.7173 (tpt170) cc_final: 0.6694 (tpt-90) REVERT: C 287 TRP cc_start: 0.9212 (m100) cc_final: 0.8940 (m100) REVERT: C 318 PHE cc_start: 0.7203 (m-80) cc_final: 0.6763 (m-10) REVERT: C 319 LYS cc_start: 0.7670 (tttt) cc_final: 0.7390 (tppt) outliers start: 29 outliers final: 25 residues processed: 161 average time/residue: 0.0591 time to fit residues: 13.0116 Evaluate side-chains 164 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 230 TRP Chi-restraints excluded: chain C residue 247 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 20 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.166874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135794 restraints weight = 9001.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136845 restraints weight = 6170.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139499 restraints weight = 5088.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139547 restraints weight = 4212.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140190 restraints weight = 3943.507| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6612 Z= 0.178 Angle : 0.761 14.323 9045 Z= 0.355 Chirality : 0.046 0.381 1062 Planarity : 0.004 0.037 1131 Dihedral : 4.907 36.353 894 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.82 % Allowed : 28.22 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -0.88 (0.30), residues: 828 helix: 2.37 (0.32), residues: 261 sheet: -2.52 (0.28), residues: 261 loop : -1.28 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 93 TYR 0.021 0.002 TYR A 156 PHE 0.020 0.002 PHE B 232 TRP 0.014 0.001 TRP B 330 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 6594) covalent geometry : angle 0.65585 / 0.33 ( 8994) SS BOND : bond 0.00042 / 0.02 ( 3) SS BOND : angle 2.42963 / 1.27 ( 6) hydrogen bonds : bond 0.03173 / 2.26 ( 270) hydrogen bonds : angle 4.34694 / 3.08 ( 783) link_BETA1-4 : bond 0.00249 / 0.12 ( 3) link_BETA1-4 : angle 0.90034 / 0.52 ( 9) link_NAG-ASN : bond 0.00885 / 0.67 ( 12) link_NAG-ASN : angle 6.07957 / 4.64 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.8715 (pp30) cc_final: 0.7842 (pp30) REVERT: A 287 TRP cc_start: 0.9121 (m100) cc_final: 0.8892 (m100) REVERT: A 318 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: A 319 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7419 (tppt) REVERT: B 260 GLN cc_start: 0.8416 (pp30) cc_final: 0.7540 (pp30) REVERT: B 287 TRP cc_start: 0.9299 (m100) cc_final: 0.8746 (m100) REVERT: B 319 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7635 (tppt) REVERT: C 253 ARG cc_start: 0.7161 (tpt170) cc_final: 0.6704 (tpt-90) REVERT: C 318 PHE cc_start: 0.7249 (m-80) cc_final: 0.6813 (m-10) REVERT: C 319 LYS cc_start: 0.7919 (tttt) cc_final: 0.7605 (tppt) outliers start: 33 outliers final: 31 residues processed: 157 average time/residue: 0.0626 time to fit residues: 13.4434 Evaluate side-chains 167 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 230 TRP Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 69 optimal weight: 0.0060 chunk 42 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 60 optimal weight: 0.0370 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.5274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.170682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137164 restraints weight = 8886.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140282 restraints weight = 6888.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141810 restraints weight = 4815.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142647 restraints weight = 4043.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142950 restraints weight = 3730.201| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6612 Z= 0.132 Angle : 0.771 17.790 9045 Z= 0.355 Chirality : 0.049 0.507 1062 Planarity : 0.004 0.038 1131 Dihedral : 4.987 33.963 894 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.94 % Allowed : 29.63 % Favored : 65.43 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -0.81 (0.30), residues: 828 helix: 2.42 (0.32), residues: 261 sheet: -2.44 (0.28), residues: 261 loop : -1.28 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 259 TYR 0.021 0.002 TYR A 156 PHE 0.016 0.002 PHE B 232 TRP 0.034 0.002 TRP C 287 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 6594) covalent geometry : angle 0.63474 / 0.32 ( 8994) SS BOND : bond 0.00205 / 0.10 ( 3) SS BOND : angle 2.53192 / 1.33 ( 6) hydrogen bonds : bond 0.03116 / 2.20 ( 270) hydrogen bonds : angle 4.25678 / 3.02 ( 783) link_BETA1-4 : bond 0.00346 / 0.17 ( 3) link_BETA1-4 : angle 1.01824 / 0.58 ( 9) link_NAG-ASN : bond 0.00603 / 0.42 ( 12) link_NAG-ASN : angle 6.88167 / 5.26 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.8688 (pp30) cc_final: 0.7991 (pp30) REVERT: A 318 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: A 319 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7371 (tppt) REVERT: B 260 GLN cc_start: 0.8410 (pp30) cc_final: 0.7596 (pp30) REVERT: B 287 TRP cc_start: 0.9277 (m100) cc_final: 0.8558 (m100) REVERT: B 319 LYS cc_start: 0.7977 (ttpt) cc_final: 0.7564 (tppt) REVERT: C 253 ARG cc_start: 0.7146 (tpt170) cc_final: 0.6689 (tpt-90) REVERT: C 318 PHE cc_start: 0.7252 (m-80) cc_final: 0.6848 (m-10) REVERT: C 319 LYS cc_start: 0.7763 (tttt) cc_final: 0.7470 (tppt) outliers start: 28 outliers final: 24 residues processed: 159 average time/residue: 0.0576 time to fit residues: 12.7347 Evaluate side-chains 166 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 230 TRP Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 53 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 0.0270 chunk 61 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.167264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.133974 restraints weight = 8967.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137176 restraints weight = 6942.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138636 restraints weight = 4728.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139335 restraints weight = 4000.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139750 restraints weight = 3709.694| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.6411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6612 Z= 0.187 Angle : 0.744 13.424 9045 Z= 0.353 Chirality : 0.047 0.306 1062 Planarity : 0.005 0.044 1131 Dihedral : 5.021 33.102 894 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 6.00 % Allowed : 28.40 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -0.97 (0.30), residues: 828 helix: 2.34 (0.31), residues: 261 sheet: -2.53 (0.27), residues: 279 loop : -1.31 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 110 TYR 0.022 0.002 TYR A 156 PHE 0.022 0.002 PHE A 236 TRP 0.046 0.002 TRP A 287 HIS 0.004 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 6594) covalent geometry : angle 0.65158 / 0.33 ( 8994) SS BOND : bond 0.00123 / 0.06 ( 3) SS BOND : angle 2.66528 / 1.45 ( 6) hydrogen bonds : bond 0.03164 / 2.27 ( 270) hydrogen bonds : angle 4.34931 / 3.09 ( 783) link_BETA1-4 : bond 0.00316 / 0.16 ( 3) link_BETA1-4 : angle 0.94470 / 0.55 ( 9) link_NAG-ASN : bond 0.00580 / 0.40 ( 12) link_NAG-ASN : angle 5.61742 / 4.34 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1056.74 seconds wall clock time: 18 minutes 54.44 seconds (1134.44 seconds total)