Starting phenix.real_space_refine on Mon Apr 28 13:16:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xda_38271/04_2025/8xda_38271_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xda_38271/04_2025/8xda_38271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xda_38271/04_2025/8xda_38271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xda_38271/04_2025/8xda_38271.map" model { file = "/net/cci-nas-00/data/ceres_data/8xda_38271/04_2025/8xda_38271_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xda_38271/04_2025/8xda_38271_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.169 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 57 5.16 5 C 5100 2.51 5 N 1158 2.21 5 O 1305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7620 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2530 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2510 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 328, 2510 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2565 Chain: "B" Number of atoms: 2530 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2510 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 328, 2510 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2565 Chain: "C" Number of atoms: 2530 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2510 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 328, 2510 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2565 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 2, 8 Unusual residues: {'URE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 2, 8 Unusual residues: {'URE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 2, 8 Unusual residues: {'URE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N APHE A 120 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 120 " occ=0.50 residue: pdb=" N APHE B 120 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 120 " occ=0.50 residue: pdb=" N APHE C 120 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 120 " occ=0.50 residue: pdb=" C AURE A 401 " occ=0.25 ... (2 atoms not shown) pdb=" N2 AURE A 401 " occ=0.25 residue: pdb=" C AURE B 401 " occ=0.25 ... (2 atoms not shown) pdb=" N2 AURE B 401 " occ=0.25 residue: pdb=" C AURE C 401 " occ=0.25 ... (2 atoms not shown) pdb=" N2 AURE C 401 " occ=0.25 Time building chain proxies: 8.22, per 1000 atoms: 1.08 Number of scatterers: 7620 At special positions: 0 Unit cell: (94.76, 89.24, 71.76, 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 57 16.00 O 1305 8.00 N 1158 7.00 C 5100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.8 seconds 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 0 sheets defined 77.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 52 through 68 removed outlier: 3.867A pdb=" N VAL A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 removed outlier: 3.759A pdb=" N ASN A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 109 Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 122 through 135 removed outlier: 4.018A pdb=" N LEU A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 145 through 167 Proline residue: A 157 - end of helix removed outlier: 3.970A pdb=" N GLY A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.885A pdb=" N VAL A 216 " --> pdb=" O TRP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 removed outlier: 4.334A pdb=" N ILE A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 237 through 252 removed outlier: 3.642A pdb=" N SER A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 273 Processing helix chain 'A' and resid 276 through 283 removed outlier: 3.535A pdb=" N ILE A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 297 Processing helix chain 'A' and resid 304 through 330 Processing helix chain 'A' and resid 338 through 350 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 73 through 88 removed outlier: 3.759A pdb=" N ASN B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 109 Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 122 through 135 removed outlier: 4.018A pdb=" N LEU B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 145 through 167 Proline residue: B 157 - end of helix removed outlier: 3.969A pdb=" N GLY B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 212 through 216 removed outlier: 3.885A pdb=" N VAL B 216 " --> pdb=" O TRP B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 231 removed outlier: 4.334A pdb=" N ILE B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Proline residue: B 226 - end of helix Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 237 through 252 removed outlier: 3.643A pdb=" N SER B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 273 Processing helix chain 'B' and resid 276 through 283 removed outlier: 3.535A pdb=" N ILE B 280 " --> pdb=" O PRO B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 297 Processing helix chain 'B' and resid 304 through 330 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 368 through 379 Processing helix chain 'C' and resid 53 through 67 Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 73 through 88 removed outlier: 3.758A pdb=" N ASN C 88 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 122 through 135 removed outlier: 4.018A pdb=" N LEU C 127 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 145 through 167 Proline residue: C 157 - end of helix removed outlier: 3.969A pdb=" N GLY C 164 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 191 Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.885A pdb=" N VAL C 216 " --> pdb=" O TRP C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 231 removed outlier: 4.334A pdb=" N ILE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Proline residue: C 226 - end of helix Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 237 through 252 removed outlier: 3.642A pdb=" N SER C 251 " --> pdb=" O ALA C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 273 Processing helix chain 'C' and resid 276 through 283 removed outlier: 3.535A pdb=" N ILE C 280 " --> pdb=" O PRO C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 297 Processing helix chain 'C' and resid 304 through 330 Processing helix chain 'C' and resid 338 through 350 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 368 through 379 502 hydrogen bonds defined for protein. 1479 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1113 1.25 - 1.39: 2034 1.39 - 1.53: 4350 1.53 - 1.67: 273 1.67 - 1.81: 87 Bond restraints: 7857 Sorted by residual: bond pdb=" C URE A 402 " pdb=" O URE A 402 " ideal model delta sigma weight residual 1.225 1.115 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C URE C 402 " pdb=" O URE C 402 " ideal model delta sigma weight residual 1.225 1.115 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C URE B 402 " pdb=" O URE B 402 " ideal model delta sigma weight residual 1.225 1.115 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" CA SER C 168 " pdb=" C SER C 168 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.41e-02 5.03e+03 2.72e+01 bond pdb=" CA SER A 168 " pdb=" C SER A 168 " ideal model delta sigma weight residual 1.523 1.449 0.073 1.41e-02 5.03e+03 2.70e+01 ... (remaining 7852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 10560 2.60 - 5.20: 197 5.20 - 7.80: 22 7.80 - 10.40: 6 10.40 - 13.00: 6 Bond angle restraints: 10791 Sorted by residual: angle pdb=" N THR C 165 " pdb=" CA THR C 165 " pdb=" C THR C 165 " ideal model delta sigma weight residual 114.31 101.31 13.00 1.29e+00 6.01e-01 1.02e+02 angle pdb=" N THR B 165 " pdb=" CA THR B 165 " pdb=" C THR B 165 " ideal model delta sigma weight residual 114.31 101.33 12.98 1.29e+00 6.01e-01 1.01e+02 angle pdb=" N THR A 165 " pdb=" CA THR A 165 " pdb=" C THR A 165 " ideal model delta sigma weight residual 114.31 101.34 12.97 1.29e+00 6.01e-01 1.01e+02 angle pdb=" N TRP B 170 " pdb=" CA TRP B 170 " pdb=" C TRP B 170 " ideal model delta sigma weight residual 113.61 104.49 9.12 1.50e+00 4.44e-01 3.70e+01 angle pdb=" N TRP A 170 " pdb=" CA TRP A 170 " pdb=" C TRP A 170 " ideal model delta sigma weight residual 113.61 104.49 9.12 1.50e+00 4.44e-01 3.70e+01 ... (remaining 10786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.31: 3836 12.31 - 24.62: 442 24.62 - 36.92: 133 36.92 - 49.23: 29 49.23 - 61.54: 18 Dihedral angle restraints: 4458 sinusoidal: 1593 harmonic: 2865 Sorted by residual: dihedral pdb=" C THR A 338 " pdb=" N THR A 338 " pdb=" CA THR A 338 " pdb=" CB THR A 338 " ideal model delta harmonic sigma weight residual -122.00 -135.47 13.47 0 2.50e+00 1.60e-01 2.90e+01 dihedral pdb=" C THR B 338 " pdb=" N THR B 338 " pdb=" CA THR B 338 " pdb=" CB THR B 338 " ideal model delta harmonic sigma weight residual -122.00 -135.41 13.41 0 2.50e+00 1.60e-01 2.88e+01 dihedral pdb=" C THR C 338 " pdb=" N THR C 338 " pdb=" CA THR C 338 " pdb=" CB THR C 338 " ideal model delta harmonic sigma weight residual -122.00 -135.37 13.37 0 2.50e+00 1.60e-01 2.86e+01 ... (remaining 4455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1219 0.107 - 0.214: 48 0.214 - 0.321: 2 0.321 - 0.428: 0 0.428 - 0.534: 6 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA PHE C 70 " pdb=" N PHE C 70 " pdb=" C PHE C 70 " pdb=" CB PHE C 70 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.14e+00 chirality pdb=" CA PHE A 70 " pdb=" N PHE A 70 " pdb=" C PHE A 70 " pdb=" CB PHE A 70 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.10e+00 chirality pdb=" CA PHE B 70 " pdb=" N PHE B 70 " pdb=" C PHE B 70 " pdb=" CB PHE B 70 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.09e+00 ... (remaining 1272 not shown) Planarity restraints: 1314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 305 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C TRP A 305 " -0.034 2.00e-02 2.50e+03 pdb=" O TRP A 305 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A 306 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 305 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" C TRP B 305 " 0.034 2.00e-02 2.50e+03 pdb=" O TRP B 305 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN B 306 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 305 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C TRP C 305 " -0.033 2.00e-02 2.50e+03 pdb=" O TRP C 305 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN C 306 " 0.011 2.00e-02 2.50e+03 ... (remaining 1311 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2295 2.81 - 3.33: 7825 3.33 - 3.86: 13491 3.86 - 4.38: 16568 4.38 - 4.90: 27256 Nonbonded interactions: 67435 Sorted by model distance: nonbonded pdb=" ND2 ASN A 180 " pdb=" O CYS A 337 " model vdw 2.291 3.120 nonbonded pdb=" ND2 ASN B 180 " pdb=" O CYS B 337 " model vdw 2.291 3.120 nonbonded pdb=" ND2 ASN C 180 " pdb=" O CYS C 337 " model vdw 2.291 3.120 nonbonded pdb=" OG SER A 102 " pdb=" O HIS A 121 " model vdw 2.326 3.040 nonbonded pdb=" OG SER B 102 " pdb=" O HIS B 121 " model vdw 2.326 3.040 ... (remaining 67430 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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=0.25 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.770 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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:14.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 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 : 0.008 0.110 7857 Z= 0.434 Angle : 0.862 13.001 10791 Z= 0.495 Chirality : 0.061 0.534 1275 Planarity : 0.006 0.040 1314 Dihedral : 12.749 61.536 2628 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.98 % Allowed : 0.73 % Favored : 98.29 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.27), residues: 990 helix: 0.66 (0.19), residues: 693 sheet: None (None), residues: 0 loop : -0.04 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 305 HIS 0.004 0.002 HIS A 258 PHE 0.013 0.002 PHE B 287 TYR 0.014 0.002 TYR C 123 ARG 0.001 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.15194 ( 502) hydrogen bonds : angle 6.66378 ( 1479) covalent geometry : bond 0.00827 ( 7857) covalent geometry : angle 0.86158 (10791) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.819 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 57 average time/residue: 1.0553 time to fit residues: 65.0051 Evaluate side-chains 45 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN C 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.127874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111757 restraints weight = 29077.879| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.52 r_work: 0.3234 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7857 Z= 0.171 Angle : 0.605 7.478 10791 Z= 0.301 Chirality : 0.044 0.139 1275 Planarity : 0.005 0.038 1314 Dihedral : 4.631 19.158 1044 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.49 % Allowed : 5.13 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 990 helix: 0.85 (0.19), residues: 720 sheet: None (None), residues: 0 loop : 0.16 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS A 258 PHE 0.014 0.001 PHE A 287 TYR 0.010 0.001 TYR C 123 ARG 0.001 0.000 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 502) hydrogen bonds : angle 4.53040 ( 1479) covalent geometry : bond 0.00419 ( 7857) covalent geometry : angle 0.60499 (10791) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.708 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 1.0822 time to fit residues: 57.2558 Evaluate side-chains 48 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 160 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 28 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 86 optimal weight: 0.0770 chunk 95 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.126216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109951 restraints weight = 27633.275| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.48 r_work: 0.2998 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7857 Z= 0.134 Angle : 0.545 6.525 10791 Z= 0.272 Chirality : 0.041 0.131 1275 Planarity : 0.005 0.039 1314 Dihedral : 4.304 15.321 1044 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.37 % Allowed : 6.35 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.27), residues: 990 helix: 1.18 (0.19), residues: 723 sheet: None (None), residues: 0 loop : 0.32 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.002 0.001 HIS C 258 PHE 0.011 0.001 PHE A 287 TYR 0.008 0.001 TYR C 123 ARG 0.000 0.000 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 502) hydrogen bonds : angle 4.15483 ( 1479) covalent geometry : bond 0.00326 ( 7857) covalent geometry : angle 0.54497 (10791) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.724 Fit side-chains REVERT: A 84 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7670 (pt) REVERT: B 84 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7546 (pt) outliers start: 3 outliers final: 0 residues processed: 62 average time/residue: 0.8948 time to fit residues: 60.4457 Evaluate side-chains 51 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 84 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** 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 = 0.3379 r_free = 0.3379 target = 0.118157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.102767 restraints weight = 26368.388| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.30 r_work: 0.3111 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7857 Z= 0.175 Angle : 0.578 7.625 10791 Z= 0.285 Chirality : 0.043 0.119 1275 Planarity : 0.005 0.041 1314 Dihedral : 4.427 15.886 1044 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.98 % Allowed : 9.16 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.27), residues: 990 helix: 1.11 (0.19), residues: 723 sheet: None (None), residues: 0 loop : 0.36 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 170 HIS 0.004 0.001 HIS A 258 PHE 0.012 0.001 PHE A 287 TYR 0.011 0.001 TYR C 123 ARG 0.001 0.000 ARG C 373 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 502) hydrogen bonds : angle 4.22043 ( 1479) covalent geometry : bond 0.00446 ( 7857) covalent geometry : angle 0.57783 (10791) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.784 Fit side-chains REVERT: A 202 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8202 (mp) REVERT: A 273 ILE cc_start: 0.7565 (tp) cc_final: 0.7345 (tp) REVERT: B 84 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7932 (pt) REVERT: C 273 ILE cc_start: 0.7766 (tp) cc_final: 0.7530 (tp) outliers start: 8 outliers final: 5 residues processed: 68 average time/residue: 0.8903 time to fit residues: 66.0666 Evaluate side-chains 69 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain C residue 250 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** 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 = 0.3331 r_free = 0.3331 target = 0.115740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.100462 restraints weight = 26915.249| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.28 r_work: 0.3044 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7857 Z= 0.165 Angle : 0.566 7.306 10791 Z= 0.279 Chirality : 0.043 0.120 1275 Planarity : 0.005 0.042 1314 Dihedral : 4.395 15.373 1044 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.47 % Allowed : 9.40 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.26), residues: 990 helix: 1.16 (0.19), residues: 723 sheet: None (None), residues: 0 loop : 0.45 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 170 HIS 0.003 0.001 HIS A 258 PHE 0.012 0.001 PHE C 287 TYR 0.009 0.001 TYR C 123 ARG 0.000 0.000 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 502) hydrogen bonds : angle 4.18072 ( 1479) covalent geometry : bond 0.00415 ( 7857) covalent geometry : angle 0.56615 (10791) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.912 Fit side-chains REVERT: A 202 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8182 (mp) REVERT: A 236 ASP cc_start: 0.7748 (p0) cc_final: 0.7534 (p0) REVERT: A 273 ILE cc_start: 0.7709 (tp) cc_final: 0.7463 (tp) REVERT: B 84 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7932 (pt) REVERT: B 273 ILE cc_start: 0.7784 (tp) cc_final: 0.7518 (tp) REVERT: C 84 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8259 (pp) REVERT: C 273 ILE cc_start: 0.7876 (tp) cc_final: 0.7633 (tp) outliers start: 12 outliers final: 4 residues processed: 64 average time/residue: 0.9512 time to fit residues: 66.3629 Evaluate side-chains 66 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 250 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** 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 = 0.3333 r_free = 0.3333 target = 0.116002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.100395 restraints weight = 30255.284| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.42 r_work: 0.3042 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7857 Z= 0.152 Angle : 0.549 7.027 10791 Z= 0.270 Chirality : 0.042 0.120 1275 Planarity : 0.005 0.042 1314 Dihedral : 4.331 15.250 1044 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.32 % Allowed : 9.52 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.27), residues: 990 helix: 1.25 (0.19), residues: 723 sheet: None (None), residues: 0 loop : 0.55 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 170 HIS 0.003 0.001 HIS A 258 PHE 0.012 0.001 PHE C 287 TYR 0.009 0.001 TYR C 123 ARG 0.001 0.000 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 502) hydrogen bonds : angle 4.10869 ( 1479) covalent geometry : bond 0.00379 ( 7857) covalent geometry : angle 0.54896 (10791) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.834 Fit side-chains REVERT: A 202 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8180 (mp) REVERT: A 236 ASP cc_start: 0.7729 (p0) cc_final: 0.7503 (p0) REVERT: A 273 ILE cc_start: 0.7763 (tp) cc_final: 0.7489 (tp) REVERT: B 84 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7961 (pt) REVERT: B 168 SER cc_start: 0.8206 (t) cc_final: 0.7905 (p) REVERT: B 273 ILE cc_start: 0.7793 (tp) cc_final: 0.7490 (tp) REVERT: C 273 ILE cc_start: 0.7785 (tp) cc_final: 0.7507 (tp) outliers start: 19 outliers final: 9 residues processed: 71 average time/residue: 0.8464 time to fit residues: 65.7124 Evaluate side-chains 74 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 250 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 0.0670 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** 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 = 0.3344 r_free = 0.3344 target = 0.116754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.102555 restraints weight = 20686.560| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.90 r_work: 0.3090 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7857 Z= 0.144 Angle : 0.555 6.810 10791 Z= 0.276 Chirality : 0.042 0.120 1275 Planarity : 0.005 0.042 1314 Dihedral : 4.287 15.653 1044 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.83 % Allowed : 10.26 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.27), residues: 990 helix: 1.33 (0.19), residues: 723 sheet: None (None), residues: 0 loop : 0.62 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 339 HIS 0.003 0.001 HIS A 258 PHE 0.011 0.001 PHE C 287 TYR 0.009 0.001 TYR C 123 ARG 0.001 0.000 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 502) hydrogen bonds : angle 4.05927 ( 1479) covalent geometry : bond 0.00356 ( 7857) covalent geometry : angle 0.55527 (10791) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.814 Fit side-chains REVERT: A 84 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8126 (pt) REVERT: A 202 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8129 (mp) REVERT: A 236 ASP cc_start: 0.7704 (p0) cc_final: 0.7501 (p0) REVERT: A 273 ILE cc_start: 0.7666 (tp) cc_final: 0.7396 (tp) REVERT: B 84 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7970 (pt) REVERT: B 273 ILE cc_start: 0.7767 (tp) cc_final: 0.7466 (tp) REVERT: C 273 ILE cc_start: 0.7757 (tp) cc_final: 0.7476 (tp) outliers start: 15 outliers final: 9 residues processed: 65 average time/residue: 0.9445 time to fit residues: 66.7359 Evaluate side-chains 72 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 374 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** 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 = 0.3338 r_free = 0.3338 target = 0.116385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.100774 restraints weight = 30566.342| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.40 r_work: 0.3089 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7857 Z= 0.150 Angle : 0.560 7.155 10791 Z= 0.278 Chirality : 0.042 0.120 1275 Planarity : 0.005 0.043 1314 Dihedral : 4.291 16.253 1044 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.95 % Allowed : 10.13 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.27), residues: 990 helix: 1.35 (0.19), residues: 723 sheet: None (None), residues: 0 loop : 0.67 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.003 0.001 HIS A 258 PHE 0.011 0.001 PHE C 287 TYR 0.009 0.001 TYR C 123 ARG 0.001 0.000 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 502) hydrogen bonds : angle 4.07658 ( 1479) covalent geometry : bond 0.00374 ( 7857) covalent geometry : angle 0.56019 (10791) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.771 Fit side-chains REVERT: A 202 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8156 (mp) REVERT: A 273 ILE cc_start: 0.7717 (tp) cc_final: 0.7438 (tp) REVERT: B 84 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7933 (pt) REVERT: B 168 SER cc_start: 0.8179 (t) cc_final: 0.7870 (p) REVERT: B 273 ILE cc_start: 0.7801 (tp) cc_final: 0.7479 (tp) REVERT: C 84 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8244 (pp) REVERT: C 273 ILE cc_start: 0.7802 (tp) cc_final: 0.7520 (tp) outliers start: 16 outliers final: 10 residues processed: 66 average time/residue: 0.8599 time to fit residues: 61.9367 Evaluate side-chains 74 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 250 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 44 optimal weight: 0.0570 chunk 72 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** 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 = 0.3342 r_free = 0.3342 target = 0.116726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.101047 restraints weight = 31990.127| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.46 r_work: 0.3087 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7857 Z= 0.144 Angle : 0.553 6.875 10791 Z= 0.274 Chirality : 0.042 0.121 1275 Planarity : 0.005 0.043 1314 Dihedral : 4.256 16.145 1044 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.83 % Allowed : 10.50 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.27), residues: 990 helix: 1.39 (0.19), residues: 723 sheet: None (None), residues: 0 loop : 0.68 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 339 HIS 0.003 0.001 HIS A 258 PHE 0.011 0.001 PHE C 287 TYR 0.009 0.001 TYR B 123 ARG 0.001 0.000 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 502) hydrogen bonds : angle 4.04906 ( 1479) covalent geometry : bond 0.00357 ( 7857) covalent geometry : angle 0.55275 (10791) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.793 Fit side-chains REVERT: A 202 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8153 (mp) REVERT: A 273 ILE cc_start: 0.7702 (tp) cc_final: 0.7414 (tp) REVERT: B 84 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7927 (pt) REVERT: B 168 SER cc_start: 0.8194 (t) cc_final: 0.7881 (p) REVERT: B 273 ILE cc_start: 0.7820 (tp) cc_final: 0.7513 (tp) REVERT: C 273 ILE cc_start: 0.7813 (tp) cc_final: 0.7519 (tp) outliers start: 15 outliers final: 10 residues processed: 67 average time/residue: 0.9302 time to fit residues: 68.2632 Evaluate side-chains 72 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 250 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 74 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 12 optimal weight: 0.0670 chunk 38 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** 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 = 0.3345 r_free = 0.3345 target = 0.116877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.101808 restraints weight = 26896.987| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.21 r_work: 0.3110 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7857 Z= 0.140 Angle : 0.554 8.874 10791 Z= 0.274 Chirality : 0.042 0.120 1275 Planarity : 0.005 0.043 1314 Dihedral : 4.251 19.000 1044 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.47 % Allowed : 10.74 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.27), residues: 990 helix: 1.41 (0.19), residues: 723 sheet: None (None), residues: 0 loop : 0.68 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 339 HIS 0.003 0.001 HIS A 258 PHE 0.011 0.001 PHE C 287 TYR 0.009 0.001 TYR C 123 ARG 0.001 0.000 ARG C 63 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 502) hydrogen bonds : angle 4.03419 ( 1479) covalent geometry : bond 0.00346 ( 7857) covalent geometry : angle 0.55412 (10791) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.728 Fit side-chains REVERT: A 84 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8102 (pt) REVERT: A 202 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8141 (mp) REVERT: A 273 ILE cc_start: 0.7702 (tp) cc_final: 0.7406 (tp) REVERT: B 84 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7930 (pt) REVERT: B 168 SER cc_start: 0.8143 (t) cc_final: 0.7840 (p) REVERT: B 273 ILE cc_start: 0.7811 (tp) cc_final: 0.7494 (tp) REVERT: C 273 ILE cc_start: 0.7816 (tp) cc_final: 0.7513 (tp) outliers start: 12 outliers final: 10 residues processed: 63 average time/residue: 0.9756 time to fit residues: 66.5659 Evaluate side-chains 72 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 374 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** 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 = 0.3380 r_free = 0.3380 target = 0.118171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.102971 restraints weight = 26172.148| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.25 r_work: 0.3114 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7857 Z= 0.156 Angle : 0.568 8.513 10791 Z= 0.281 Chirality : 0.042 0.120 1275 Planarity : 0.005 0.043 1314 Dihedral : 4.306 19.709 1044 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.71 % Allowed : 10.74 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.27), residues: 990 helix: 1.38 (0.19), residues: 723 sheet: None (None), residues: 0 loop : 0.70 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 170 HIS 0.003 0.001 HIS A 258 PHE 0.012 0.001 PHE C 287 TYR 0.009 0.001 TYR C 123 ARG 0.001 0.000 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 502) hydrogen bonds : angle 4.10094 ( 1479) covalent geometry : bond 0.00392 ( 7857) covalent geometry : angle 0.56819 (10791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5019.39 seconds wall clock time: 86 minutes 36.27 seconds (5196.27 seconds total)