Starting phenix.real_space_refine on Tue Mar 3 15:01:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jna_22403/03_2026/7jna_22403.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jna_22403/03_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_22403/03_2026/7jna_22403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jna_22403/03_2026/7jna_22403.map" model { file = "/net/cci-nas-00/data/ceres_data/7jna_22403/03_2026/7jna_22403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jna_22403/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, J, O Time building chain proxies: 1.46, per 1000 atoms: 0.23 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: 0.61 Conformation dependent library (CDL) restraints added in 356.2 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: 0.21 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: 0.93 Time building geometry restraints manager: 0.81 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: 3581 15.44 - 30.87: 430 30.87 - 46.31: 57 46.31 - 61.74: 12 61.74 - 77.18: 6 Dihedral angle restraints: 4086 sinusoidal: 1617 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 4083 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: 0.470 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.710 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 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 : 12.954 77.175 2469 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 covalent geometry : bond 0.00485 ( 6594) covalent geometry : angle 0.71906 ( 8994) SS BOND : bond 0.00275 ( 3) SS BOND : angle 2.77092 ( 6) hydrogen bonds : bond 0.13361 ( 270) hydrogen bonds : angle 5.99911 ( 783) link_BETA1-4 : bond 0.00117 ( 3) link_BETA1-4 : angle 1.09008 ( 9) link_NAG-ASN : bond 0.00757 ( 12) link_NAG-ASN : angle 4.05923 ( 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 : 0.239 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: 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: 0.1044 time to fit residues: 27.4914 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 : 0.215 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3941 r_free = 0.3941 target = 0.164625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.134263 restraints weight = 9039.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136039 restraints weight = 6274.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138594 restraints weight = 4923.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138640 restraints weight = 4088.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139157 restraints weight = 3823.371| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6612 Z= 0.226 Angle : 0.851 12.309 9045 Z= 0.390 Chirality : 0.050 0.218 1062 Planarity : 0.005 0.042 1131 Dihedral : 8.518 54.135 1209 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.99 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: -2.47 (0.27), residues: 828 helix: 0.83 (0.30), residues: 267 sheet: -3.33 (0.25), residues: 249 loop : -2.21 (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 0.002 PHE A 236 TRP 0.005 0.001 TRP B 330 HIS 0.003 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 6594) covalent geometry : angle 0.77844 ( 8994) SS BOND : bond 0.00401 ( 3) SS BOND : angle 2.62377 ( 6) hydrogen bonds : bond 0.03636 ( 270) hydrogen bonds : angle 4.90450 ( 783) link_BETA1-4 : bond 0.00350 ( 3) link_BETA1-4 : angle 2.86414 ( 9) link_NAG-ASN : bond 0.00874 ( 12) link_NAG-ASN : angle 5.23439 ( 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 194 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.7770 (pm20) cc_final: 0.7170 (pp30) REVERT: A 242 MET cc_start: 0.8440 (ptp) cc_final: 0.8127 (ptp) REVERT: A 259 ARG cc_start: 0.7669 (mtm110) cc_final: 0.7395 (mtm110) REVERT: A 319 LYS cc_start: 0.7378 (ttpt) cc_final: 0.6985 (mptt) REVERT: B 260 GLN cc_start: 0.8415 (pp30) cc_final: 0.7597 (pp30) REVERT: B 309 LEU cc_start: 0.7927 (tp) cc_final: 0.7542 (tp) outliers start: 28 outliers final: 14 residues processed: 184 average time/residue: 0.0932 time to fit residues: 22.1145 Evaluate side-chains 145 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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: 0.9980 chunk 54 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3955 r_free = 0.3955 target = 0.165957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.134682 restraints weight = 9033.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137818 restraints weight = 6910.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139594 restraints weight = 4727.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140053 restraints weight = 3973.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140540 restraints weight = 3942.824| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6612 Z= 0.153 Angle : 0.722 11.915 9045 Z= 0.335 Chirality : 0.045 0.303 1062 Planarity : 0.004 0.036 1131 Dihedral : 6.995 42.530 1209 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.17 % Allowed : 27.69 % Favored : 69.14 % 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: -1.77 (0.29), residues: 828 helix: 1.47 (0.31), residues: 267 sheet: -2.95 (0.27), residues: 249 loop : -1.86 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 259 TYR 0.014 0.002 TYR A 111 PHE 0.019 0.002 PHE C 236 TRP 0.006 0.001 TRP A 287 HIS 0.003 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6594) covalent geometry : angle 0.62155 ( 8994) SS BOND : bond 0.00141 ( 3) SS BOND : angle 2.03637 ( 6) hydrogen bonds : bond 0.03469 ( 270) hydrogen bonds : angle 4.72258 ( 783) link_BETA1-4 : bond 0.00299 ( 3) link_BETA1-4 : angle 1.60028 ( 9) link_NAG-ASN : bond 0.00728 ( 12) link_NAG-ASN : angle 5.75173 ( 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 154 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.260 Fit side-chains 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: 0.7414 (pp30) REVERT: A 259 ARG cc_start: 0.7658 (mtm110) cc_final: 0.7297 (mtm110) REVERT: A 318 PHE cc_start: 0.7625 (t80) cc_final: 0.7185 (m-80) REVERT: A 319 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7296 (tppt) REVERT: B 147 MET cc_start: 0.7339 (mtp) cc_final: 0.7117 (mtt) REVERT: B 309 LEU cc_start: 0.8212 (tp) cc_final: 0.7888 (tp) REVERT: C 319 LYS cc_start: 0.7278 (tttt) cc_final: 0.6875 (tppt) REVERT: C 330 TRP cc_start: 0.7276 (t-100) cc_final: 0.6852 (t-100) outliers start: 18 outliers final: 13 residues processed: 147 average time/residue: 0.0851 time to fit residues: 16.6106 Evaluate side-chains 131 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 B residue 295 VAL 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: 0.9990 chunk 37 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3967 r_free = 0.3967 target = 0.166708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.134784 restraints weight = 9200.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138778 restraints weight = 6907.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140412 restraints weight = 4499.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141587 restraints weight = 3727.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141827 restraints weight = 3592.033| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6612 Z= 0.173 Angle : 0.713 12.585 9045 Z= 0.335 Chirality : 0.045 0.264 1062 Planarity : 0.004 0.032 1131 Dihedral : 6.604 42.150 1209 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 6.53 % Allowed : 26.63 % Favored : 66.84 % 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: -1.45 (0.30), residues: 828 helix: 1.77 (0.32), residues: 267 sheet: -2.65 (0.29), residues: 255 loop : -1.79 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 259 TYR 0.015 0.002 TYR C 156 PHE 0.021 0.002 PHE C 232 TRP 0.010 0.001 TRP C 287 HIS 0.002 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6594) covalent geometry : angle 0.61961 ( 8994) SS BOND : bond 0.00186 ( 3) SS BOND : angle 2.29243 ( 6) hydrogen bonds : bond 0.03373 ( 270) hydrogen bonds : angle 4.61593 ( 783) link_BETA1-4 : bond 0.00524 ( 3) link_BETA1-4 : angle 1.64020 ( 9) link_NAG-ASN : bond 0.00781 ( 12) link_NAG-ASN : angle 5.48964 ( 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 165 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 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: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8181 (ttp) REVERT: A 318 PHE cc_start: 0.7699 (t80) cc_final: 0.7176 (m-80) REVERT: A 319 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7384 (tppt) REVERT: B 172 GLN cc_start: 0.8689 (tt0) cc_final: 0.8462 (tp40) REVERT: B 238 THR cc_start: 0.9533 (OUTLIER) cc_final: 0.9298 (p) REVERT: C 254 GLU cc_start: 0.7911 (tt0) cc_final: 0.7686 (tt0) REVERT: C 257 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7614 (mt-10) REVERT: C 287 TRP cc_start: 0.9229 (m100) cc_final: 0.8905 (m100) REVERT: C 319 LYS cc_start: 0.7441 (tttt) cc_final: 0.6912 (tppt) REVERT: C 330 TRP cc_start: 0.7250 (t-100) cc_final: 0.6938 (t-100) outliers start: 37 outliers final: 24 residues processed: 154 average time/residue: 0.0695 time to fit residues: 14.7149 Evaluate side-chains 143 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET 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 225 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 297 ASP 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 238 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 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: 0.3980 chunk 4 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 73 optimal weight: 0.0070 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 65 optimal weight: 8.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3977 r_free = 0.3977 target = 0.168057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.136024 restraints weight = 9145.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138239 restraints weight = 7129.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139751 restraints weight = 5335.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140227 restraints weight = 4223.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143059 restraints weight = 4082.027| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4606 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= 0.133 Angle : 0.693 13.165 9045 Z= 0.322 Chirality : 0.043 0.246 1062 Planarity : 0.004 0.035 1131 Dihedral : 6.201 46.115 1209 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.64 % Allowed : 26.81 % Favored : 67.55 % 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: -1.30 (0.30), residues: 828 helix: 1.97 (0.32), residues: 267 sheet: -2.64 (0.27), residues: 282 loop : -1.53 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 259 TYR 0.020 0.002 TYR A 156 PHE 0.016 0.002 PHE C 232 TRP 0.007 0.001 TRP C 287 HIS 0.002 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6594) covalent geometry : angle 0.58493 ( 8994) SS BOND : bond 0.00096 ( 3) SS BOND : angle 2.12704 ( 6) hydrogen bonds : bond 0.03211 ( 270) hydrogen bonds : angle 4.44942 ( 783) link_BETA1-4 : bond 0.00426 ( 3) link_BETA1-4 : angle 1.42693 ( 9) link_NAG-ASN : bond 0.00863 ( 12) link_NAG-ASN : angle 5.81179 ( 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 163 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.231 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: 0.9022 (m100) cc_final: 0.8802 (m100) REVERT: A 305 ASN cc_start: 0.7512 (t0) cc_final: 0.7277 (t0) REVERT: A 318 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: A 319 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7418 (tppt) REVERT: B 296 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7365 (pt0) REVERT: C 253 ARG cc_start: 0.7247 (tpt170) cc_final: 0.6711 (tpt-90) REVERT: C 319 LYS cc_start: 0.7644 (tttt) cc_final: 0.7351 (tttt) outliers start: 32 outliers final: 24 residues processed: 150 average time/residue: 0.0761 time to fit residues: 15.4629 Evaluate side-chains 154 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 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 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 296 GLN Chi-restraints excluded: chain B residue 306 THR 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 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: 0.9990 chunk 10 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 9 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3983 r_free = 0.3983 target = 0.168256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134646 restraints weight = 9086.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138994 restraints weight = 5692.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.141853 restraints weight = 4284.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143799 restraints weight = 3574.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.145028 restraints weight = 3167.970| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6612 Z= 0.141 Angle : 0.721 14.114 9045 Z= 0.332 Chirality : 0.044 0.225 1062 Planarity : 0.004 0.031 1131 Dihedral : 6.037 47.100 1209 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 6.53 % Allowed : 27.69 % Favored : 65.78 % 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: -1.14 (0.30), residues: 828 helix: 2.08 (0.32), residues: 267 sheet: -2.59 (0.27), residues: 276 loop : -1.42 (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 0.016 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 covalent geometry : bond 0.00324 ( 6594) covalent geometry : angle 0.59908 ( 8994) SS BOND : bond 0.00046 ( 3) SS BOND : angle 2.33303 ( 6) hydrogen bonds : bond 0.03163 ( 270) hydrogen bonds : angle 4.39151 ( 783) link_BETA1-4 : bond 0.00324 ( 3) link_BETA1-4 : angle 1.26302 ( 9) link_NAG-ASN : bond 0.00992 ( 12) link_NAG-ASN : angle 6.29396 ( 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 182 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.254 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: 0.9059 (m100) cc_final: 0.8710 (m100) REVERT: A 305 ASN cc_start: 0.7649 (t0) cc_final: 0.7413 (t0) REVERT: A 318 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: A 319 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7263 (tppt) REVERT: B 287 TRP cc_start: 0.9212 (m100) cc_final: 0.8637 (m100) REVERT: B 330 TRP cc_start: 0.7159 (t-100) cc_final: 0.6794 (t-100) REVERT: C 105 TYR cc_start: 0.8618 (m-10) cc_final: 0.8352 (m-80) REVERT: C 253 ARG cc_start: 0.7054 (tpt170) cc_final: 0.6632 (tpt-90) REVERT: C 257 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7619 (mt-10) REVERT: C 259 ARG cc_start: 0.7553 (mtm110) cc_final: 0.7349 (mtm110) outliers start: 37 outliers final: 26 residues processed: 166 average time/residue: 0.0690 time to fit residues: 15.9529 Evaluate side-chains 158 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 74 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 78 optimal weight: 0.0870 chunk 35 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3964 r_free = 0.3964 target = 0.166458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136660 restraints weight = 8954.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.138176 restraints weight = 5851.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140078 restraints weight = 5065.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140723 restraints weight = 3977.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141714 restraints weight = 3702.156| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6612 Z= 0.172 Angle : 0.734 13.851 9045 Z= 0.349 Chirality : 0.045 0.222 1062 Planarity : 0.004 0.031 1131 Dihedral : 5.796 48.161 1209 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.82 % Allowed : 28.04 % Favored : 66.14 % 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: -0.98 (0.30), residues: 828 helix: 2.16 (0.32), residues: 267 sheet: -2.49 (0.29), residues: 255 loop : -1.41 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 259 TYR 0.019 0.002 TYR A 156 PHE 0.017 0.002 PHE A 236 TRP 0.004 0.001 TRP C 230 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 6594) covalent geometry : angle 0.64489 ( 8994) SS BOND : bond 0.00215 ( 3) SS BOND : angle 2.99859 ( 6) hydrogen bonds : bond 0.03269 ( 270) hydrogen bonds : angle 4.38952 ( 783) link_BETA1-4 : bond 0.00287 ( 3) link_BETA1-4 : angle 1.04022 ( 9) link_NAG-ASN : bond 0.00788 ( 12) link_NAG-ASN : angle 5.43369 ( 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 177 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 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: 0.9172 (m100) cc_final: 0.8759 (m100) REVERT: A 319 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7527 (tppt) REVERT: B 330 TRP cc_start: 0.6881 (t-100) cc_final: 0.6647 (t-100) REVERT: C 105 TYR cc_start: 0.8636 (m-10) cc_final: 0.8415 (m-80) REVERT: C 253 ARG cc_start: 0.7177 (tpt170) cc_final: 0.6673 (tpt-90) REVERT: C 287 TRP cc_start: 0.9218 (m100) cc_final: 0.8902 (m100) outliers start: 33 outliers final: 31 residues processed: 161 average time/residue: 0.0714 time to fit residues: 15.7781 Evaluate side-chains 165 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 257 GLU Chi-restraints excluded: chain A residue 268 ILE 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 230 TRP 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 10 optimal weight: 0.0670 chunk 18 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 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 = 0.3989 r_free = 0.3989 target = 0.169259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136725 restraints weight = 8962.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140032 restraints weight = 6931.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141327 restraints weight = 4741.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.142368 restraints weight = 4055.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.142654 restraints weight = 3682.146| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6612 Z= 0.137 Angle : 0.718 14.247 9045 Z= 0.339 Chirality : 0.045 0.202 1062 Planarity : 0.004 0.032 1131 Dihedral : 5.585 47.816 1209 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.47 % Allowed : 28.40 % Favored : 66.14 % 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: -0.82 (0.30), residues: 828 helix: 2.39 (0.32), residues: 261 sheet: -2.42 (0.29), residues: 255 loop : -1.31 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 93 TYR 0.020 0.002 TYR A 156 PHE 0.015 0.002 PHE C 232 TRP 0.007 0.001 TRP A 330 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6594) covalent geometry : angle 0.62510 ( 8994) SS BOND : bond 0.00152 ( 3) SS BOND : angle 2.35235 ( 6) hydrogen bonds : bond 0.03114 ( 270) hydrogen bonds : angle 4.32999 ( 783) link_BETA1-4 : bond 0.00402 ( 3) link_BETA1-4 : angle 0.96574 ( 9) link_NAG-ASN : bond 0.00940 ( 12) link_NAG-ASN : angle 5.55691 ( 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 170 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.222 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: 0.8582 (m-10) cc_final: 0.8382 (m-80) REVERT: A 287 TRP cc_start: 0.9096 (m100) cc_final: 0.8893 (m100) REVERT: A 319 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7498 (tppt) REVERT: B 287 TRP cc_start: 0.9306 (m100) cc_final: 0.8521 (m100) REVERT: B 296 GLN cc_start: 0.7753 (pt0) cc_final: 0.7525 (pt0) REVERT: C 253 ARG cc_start: 0.7128 (tpt170) cc_final: 0.6692 (tpt-90) REVERT: C 287 TRP cc_start: 0.9176 (m100) cc_final: 0.8898 (m100) outliers start: 31 outliers final: 28 residues processed: 157 average time/residue: 0.0736 time to fit residues: 15.9728 Evaluate side-chains 167 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 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 225 SER Chi-restraints excluded: chain B residue 230 TRP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 20 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3937 r_free = 0.3937 target = 0.164554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.133685 restraints weight = 9081.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136021 restraints weight = 5988.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.137947 restraints weight = 5412.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138403 restraints weight = 4086.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138744 restraints weight = 4215.025| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6612 Z= 0.224 Angle : 0.805 19.534 9045 Z= 0.379 Chirality : 0.052 0.640 1062 Planarity : 0.005 0.042 1131 Dihedral : 5.788 47.624 1209 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.82 % Allowed : 28.22 % Favored : 65.96 % 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: -1.00 (0.30), residues: 828 helix: 2.29 (0.32), residues: 261 sheet: -2.57 (0.28), residues: 261 loop : -1.40 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 259 TYR 0.021 0.002 TYR A 156 PHE 0.024 0.002 PHE C 236 TRP 0.011 0.002 TRP B 330 HIS 0.004 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 6594) covalent geometry : angle 0.67971 ( 8994) SS BOND : bond 0.00232 ( 3) SS BOND : angle 3.24216 ( 6) hydrogen bonds : bond 0.03234 ( 270) hydrogen bonds : angle 4.43920 ( 783) link_BETA1-4 : bond 0.00463 ( 3) link_BETA1-4 : angle 0.88880 ( 9) link_NAG-ASN : bond 0.00934 ( 12) link_NAG-ASN : angle 6.73180 ( 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 170 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.243 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: 0.8770 (pp30) cc_final: 0.7875 (pp30) REVERT: A 287 TRP cc_start: 0.9183 (m100) cc_final: 0.8940 (m100) REVERT: A 318 PHE cc_start: 0.6905 (m-10) cc_final: 0.6668 (m-10) REVERT: A 319 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7476 (tptt) REVERT: B 287 TRP cc_start: 0.9368 (m100) cc_final: 0.8556 (m100) REVERT: B 296 GLN cc_start: 0.7900 (pt0) cc_final: 0.7665 (pt0) REVERT: C 101 MET cc_start: 0.8762 (tmm) cc_final: 0.8555 (ttp) REVERT: C 253 ARG cc_start: 0.7133 (tpt170) cc_final: 0.6662 (tpt-90) outliers start: 33 outliers final: 31 residues processed: 152 average time/residue: 0.0739 time to fit residues: 15.4335 Evaluate side-chains 164 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 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 230 TRP 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 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: 0.7980 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 0.0170 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3981 r_free = 0.3981 target = 0.168870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134421 restraints weight = 8789.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138604 restraints weight = 5588.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141390 restraints weight = 4268.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.143219 restraints weight = 3597.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144088 restraints weight = 3220.467| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.6168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6612 Z= 0.138 Angle : 0.718 13.589 9045 Z= 0.338 Chirality : 0.045 0.309 1062 Planarity : 0.004 0.033 1131 Dihedral : 5.476 48.040 1209 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.94 % Allowed : 28.75 % Favored : 66.31 % 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: -0.91 (0.30), residues: 828 helix: 2.39 (0.32), residues: 261 sheet: -2.54 (0.27), residues: 261 loop : -1.34 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 259 TYR 0.021 0.002 TYR A 156 PHE 0.016 0.002 PHE B 232 TRP 0.030 0.002 TRP C 287 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6594) covalent geometry : angle 0.61577 ( 8994) SS BOND : bond 0.00225 ( 3) SS BOND : angle 2.44363 ( 6) hydrogen bonds : bond 0.03129 ( 270) hydrogen bonds : angle 4.31930 ( 783) link_BETA1-4 : bond 0.00406 ( 3) link_BETA1-4 : angle 0.80882 ( 9) link_NAG-ASN : bond 0.00658 ( 12) link_NAG-ASN : angle 5.79326 ( 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 165 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.8735 (pp30) cc_final: 0.7973 (pp30) REVERT: A 319 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7303 (tppt) REVERT: B 287 TRP cc_start: 0.9278 (m100) cc_final: 0.8554 (m100) REVERT: B 296 GLN cc_start: 0.7795 (pt0) cc_final: 0.7500 (pt0) REVERT: C 101 MET cc_start: 0.8662 (tmm) cc_final: 0.8416 (ttp) REVERT: C 314 PHE cc_start: 0.8290 (m-80) cc_final: 0.7887 (m-10) outliers start: 28 outliers final: 26 residues processed: 149 average time/residue: 0.0667 time to fit residues: 14.0924 Evaluate side-chains 159 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 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 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 230 TRP 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 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 53 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3980 r_free = 0.3980 target = 0.169020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138631 restraints weight = 8898.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140302 restraints weight = 6062.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.142027 restraints weight = 4823.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142557 restraints weight = 4033.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143418 restraints weight = 3782.888| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.6374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6612 Z= 0.146 Angle : 0.703 13.418 9045 Z= 0.336 Chirality : 0.045 0.302 1062 Planarity : 0.004 0.042 1131 Dihedral : 5.223 46.008 1209 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.29 % Allowed : 28.57 % Favored : 66.14 % 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: -0.89 (0.30), residues: 828 helix: 2.41 (0.32), residues: 261 sheet: -2.54 (0.28), residues: 261 loop : -1.33 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 259 TYR 0.021 0.002 TYR A 156 PHE 0.018 0.002 PHE A 236 TRP 0.055 0.002 TRP A 287 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6594) covalent geometry : angle 0.61615 ( 8994) SS BOND : bond 0.00169 ( 3) SS BOND : angle 2.25108 ( 6) hydrogen bonds : bond 0.03126 ( 270) hydrogen bonds : angle 4.31081 ( 783) link_BETA1-4 : bond 0.00501 ( 3) link_BETA1-4 : angle 1.08279 ( 9) link_NAG-ASN : bond 0.00683 ( 12) link_NAG-ASN : angle 5.31775 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1248.79 seconds wall clock time: 22 minutes 9.71 seconds (1329.71 seconds total)