Starting phenix.real_space_refine on Wed Sep 17 16:42:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6snh_10257/09_2025/6snh_10257.cif Found real_map, /net/cci-nas-00/data/ceres_data/6snh_10257/09_2025/6snh_10257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6snh_10257/09_2025/6snh_10257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6snh_10257/09_2025/6snh_10257.map" model { file = "/net/cci-nas-00/data/ceres_data/6snh_10257/09_2025/6snh_10257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6snh_10257/09_2025/6snh_10257.cif" } resolution = 3.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3122 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 31 5.16 5 C 4801 2.51 5 N 1156 2.21 5 O 1326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7315 Number of models: 1 Model: "" Number of chains: 4 Chain: "X" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3924 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 25, 'TRANS': 453} Chain breaks: 1 Chain: "H" Number of atoms: 1690 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} Conformer: "B" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} bond proxies already assigned to first conformer: 1721 Chain: "L" Number of atoms: 1659 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1654 Chain: "X" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'LMH': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.54, per 1000 atoms: 0.35 Number of scatterers: 7315 At special positions: 0 Unit cell: (110.04, 84.84, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 1 15.00 O 1326 8.00 N 1156 7.00 C 4801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS X 314 " - pdb=" SG CYS X 515 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.05 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: 0.67 Conformation dependent library (CDL) restraints added in 556.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1736 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 9 sheets defined 43.4% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'X' and resid 40 through 54 removed outlier: 4.335A pdb=" N VAL X 47 " --> pdb=" O PHE X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 68 through 81 removed outlier: 3.696A pdb=" N ALA X 72 " --> pdb=" O GLY X 68 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN X 81 " --> pdb=" O MET X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 88 removed outlier: 3.657A pdb=" N TRP X 88 " --> pdb=" O LEU X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 119 removed outlier: 3.824A pdb=" N ALA X 105 " --> pdb=" O PRO X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 120 through 124 removed outlier: 3.823A pdb=" N ALA X 124 " --> pdb=" O SER X 121 " (cutoff:3.500A) Processing helix chain 'X' and resid 138 through 154 Processing helix chain 'X' and resid 154 through 170 removed outlier: 3.521A pdb=" N VAL X 158 " --> pdb=" O TYR X 154 " (cutoff:3.500A) Processing helix chain 'X' and resid 172 through 185 removed outlier: 4.045A pdb=" N ILE X 183 " --> pdb=" O ALA X 179 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE X 185 " --> pdb=" O SER X 181 " (cutoff:3.500A) Processing helix chain 'X' and resid 186 through 194 Processing helix chain 'X' and resid 199 through 216 removed outlier: 4.272A pdb=" N MET X 203 " --> pdb=" O TYR X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 218 through 233 removed outlier: 3.818A pdb=" N VAL X 224 " --> pdb=" O ALA X 220 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS X 233 " --> pdb=" O SER X 229 " (cutoff:3.500A) Processing helix chain 'X' and resid 234 through 238 removed outlier: 3.862A pdb=" N TYR X 238 " --> pdb=" O MET X 235 " (cutoff:3.500A) Processing helix chain 'X' and resid 239 through 253 removed outlier: 4.157A pdb=" N ALA X 245 " --> pdb=" O PRO X 241 " (cutoff:3.500A) Processing helix chain 'X' and resid 259 through 282 removed outlier: 3.503A pdb=" N THR X 263 " --> pdb=" O ILE X 259 " (cutoff:3.500A) Proline residue: X 279 - end of helix Processing helix chain 'X' and resid 286 through 298 Processing helix chain 'X' and resid 312 through 321 removed outlier: 4.535A pdb=" N VAL X 318 " --> pdb=" O CYS X 314 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE X 319 " --> pdb=" O VAL X 315 " (cutoff:3.500A) Processing helix chain 'X' and resid 321 through 326 removed outlier: 3.741A pdb=" N ARG X 325 " --> pdb=" O LYS X 321 " (cutoff:3.500A) Processing helix chain 'X' and resid 328 through 353 removed outlier: 3.545A pdb=" N LEU X 336 " --> pdb=" O GLN X 332 " (cutoff:3.500A) Proline residue: X 345 - end of helix Processing helix chain 'X' and resid 355 through 357 No H-bonds generated for 'chain 'X' and resid 355 through 357' Processing helix chain 'X' and resid 358 through 374 removed outlier: 3.566A pdb=" N PHE X 373 " --> pdb=" O SER X 369 " (cutoff:3.500A) Processing helix chain 'X' and resid 382 through 391 Proline residue: X 388 - end of helix Processing helix chain 'X' and resid 397 through 415 removed outlier: 3.848A pdb=" N LEU X 401 " --> pdb=" O ASP X 397 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU X 415 " --> pdb=" O ALA X 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 415 through 421 Processing helix chain 'X' and resid 426 through 439 Processing helix chain 'X' and resid 476 through 499 removed outlier: 3.730A pdb=" N PHE X 495 " --> pdb=" O GLY X 491 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU X 496 " --> pdb=" O PHE X 492 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP X 497 " --> pdb=" O TYR X 493 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN X 498 " --> pdb=" O HIS X 494 " (cutoff:3.500A) Processing helix chain 'X' and resid 509 through 536 removed outlier: 3.742A pdb=" N PHE X 519 " --> pdb=" O CYS X 515 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE X 520 " --> pdb=" O ALA X 516 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS X 521 " --> pdb=" O VAL X 517 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 4.119A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 195 through 199 Processing helix chain 'L' and resid 125 through 130 removed outlier: 3.572A pdb=" N GLY L 130 " --> pdb=" O GLN L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 191 removed outlier: 3.700A pdb=" N HIS L 191 " --> pdb=" O ASP L 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.666A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 129 through 133 removed outlier: 4.278A pdb=" N SER H 188 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE H 175 " --> pdb=" O SER H 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 159 through 163 Processing sheet with id=AA5, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.367A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.367A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 116 through 120 removed outlier: 6.080A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 146 through 152 366 hydrogen bonds defined for protein. 1021 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1506 1.33 - 1.46: 2404 1.46 - 1.58: 3589 1.58 - 1.71: 2 1.71 - 1.84: 44 Bond restraints: 7545 Sorted by residual: bond pdb=" C SER L 10 " pdb=" O SER L 10 " ideal model delta sigma weight residual 1.235 1.344 -0.109 1.18e-02 7.18e+03 8.52e+01 bond pdb=" C31 LMH X 601 " pdb=" O32 LMH X 601 " ideal model delta sigma weight residual 1.418 1.500 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C SER L 10 " pdb=" CA ASER L 10 " ideal model delta sigma weight residual 1.520 1.558 -0.038 1.12e-02 7.97e+03 1.15e+01 bond pdb=" C SER L 10 " pdb=" CA BSER L 10 " ideal model delta sigma weight residual 1.520 1.558 -0.038 1.12e-02 7.97e+03 1.15e+01 bond pdb=" N VAL X 309 " pdb=" CA VAL X 309 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.11e-02 8.12e+03 1.14e+01 ... (remaining 7540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 10171 3.40 - 6.79: 100 6.79 - 10.19: 12 10.19 - 13.59: 4 13.59 - 16.99: 5 Bond angle restraints: 10292 Sorted by residual: angle pdb=" CA SER H 188 " pdb=" C SER H 188 " pdb=" O SER H 188 " ideal model delta sigma weight residual 120.89 131.05 -10.16 1.10e+00 8.26e-01 8.53e+01 angle pdb=" N SER L 10 " pdb=" CA ASER L 10 " pdb=" C SER L 10 " ideal model delta sigma weight residual 108.13 123.32 -15.19 1.72e+00 3.38e-01 7.80e+01 angle pdb=" N SER L 10 " pdb=" CA BSER L 10 " pdb=" C SER L 10 " ideal model delta sigma weight residual 108.13 123.32 -15.19 1.72e+00 3.38e-01 7.80e+01 angle pdb=" N SER H 188 " pdb=" CA SER H 188 " pdb=" C SER H 188 " ideal model delta sigma weight residual 108.76 122.69 -13.93 1.58e+00 4.01e-01 7.77e+01 angle pdb=" O SER L 10 " pdb=" C SER L 10 " pdb=" CA ASER L 10 " ideal model delta sigma weight residual 120.11 131.19 -11.08 1.37e+00 5.33e-01 6.54e+01 ... (remaining 10287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 3951 17.28 - 34.56: 371 34.56 - 51.84: 74 51.84 - 69.12: 21 69.12 - 86.40: 6 Dihedral angle restraints: 4423 sinusoidal: 1700 harmonic: 2723 Sorted by residual: dihedral pdb=" N HIS X 378 " pdb=" C HIS X 378 " pdb=" CA HIS X 378 " pdb=" CB HIS X 378 " ideal model delta harmonic sigma weight residual 122.80 149.53 -26.73 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" C HIS X 378 " pdb=" N HIS X 378 " pdb=" CA HIS X 378 " pdb=" CB HIS X 378 " ideal model delta harmonic sigma weight residual -122.60 -149.26 26.66 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" CB CYS X 314 " pdb=" SG CYS X 314 " pdb=" SG CYS X 515 " pdb=" CB CYS X 515 " ideal model delta sinusoidal sigma weight residual -86.00 -153.31 67.31 1 1.00e+01 1.00e-02 5.90e+01 ... (remaining 4420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.218: 1137 0.218 - 0.435: 1 0.435 - 0.653: 2 0.653 - 0.871: 0 0.871 - 1.088: 1 Chirality restraints: 1141 Sorted by residual: chirality pdb=" CA HIS X 378 " pdb=" N HIS X 378 " pdb=" C HIS X 378 " pdb=" CB HIS X 378 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA ASER L 10 " pdb=" N SER L 10 " pdb=" C SER L 10 " pdb=" CB ASER L 10 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA BSER L 10 " pdb=" N SER L 10 " pdb=" C SER L 10 " pdb=" CB BSER L 10 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 1138 not shown) Planarity restraints: 1267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE X 384 " 0.046 5.00e-02 4.00e+02 7.02e-02 7.90e+00 pdb=" N PRO X 385 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO X 385 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO X 385 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 165 " 0.013 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" C VAL L 165 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL L 165 " 0.016 2.00e-02 2.50e+03 pdb=" N THR L 166 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 160 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C THR H 160 " 0.042 2.00e-02 2.50e+03 pdb=" O THR H 160 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL H 161 " -0.014 2.00e-02 2.50e+03 ... (remaining 1264 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 648 2.72 - 3.27: 8096 3.27 - 3.81: 11907 3.81 - 4.36: 14169 4.36 - 4.90: 24151 Nonbonded interactions: 58971 Sorted by model distance: nonbonded pdb=" NH1 ARG L 110 " pdb=" O THR L 111 " model vdw 2.181 3.120 nonbonded pdb=" N VAL H 2 " pdb=" O SER H 25 " model vdw 2.212 3.120 nonbonded pdb=" O HIS L 191 " pdb=" NH1 ARG L 213 " model vdw 2.215 3.120 nonbonded pdb=" OH TYR H 59 " pdb=" N ILE H 69 " model vdw 2.230 3.120 nonbonded pdb=" O TYR L 188 " pdb=" OH TYR L 194 " model vdw 2.236 3.040 ... (remaining 58966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.30 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.980 Find NCS groups from input model: 0.040 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 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 0.109 7550 Z= 0.433 Angle : 0.995 16.985 10302 Z= 0.568 Chirality : 0.063 1.088 1141 Planarity : 0.005 0.070 1267 Dihedral : 14.505 86.399 2672 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.99 % Favored : 88.90 % Rotamer: Outliers : 1.49 % Allowed : 5.96 % Favored : 92.56 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.30 (0.23), residues: 918 helix: -1.92 (0.24), residues: 352 sheet: -2.67 (0.29), residues: 202 loop : -3.80 (0.26), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 66 TYR 0.021 0.002 TYR X 239 PHE 0.024 0.002 PHE X 197 TRP 0.020 0.002 TRP H 163 HIS 0.006 0.001 HIS X 194 Details of bonding type rmsd covalent geometry : bond 0.00815 ( 7545) covalent geometry : angle 0.99445 (10292) SS BOND : bond 0.00949 ( 5) SS BOND : angle 1.55663 ( 10) hydrogen bonds : bond 0.14030 ( 355) hydrogen bonds : angle 7.29690 ( 1021) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.287 Fit side-chains REVERT: X 189 LEU cc_start: 0.9340 (tp) cc_final: 0.9071 (tp) REVERT: X 190 MET cc_start: 0.8352 (ttm) cc_final: 0.7928 (ttm) REVERT: X 368 MET cc_start: 0.8839 (tpp) cc_final: 0.8632 (tpt) REVERT: X 490 MET cc_start: 0.8787 (mtm) cc_final: 0.8280 (mtm) REVERT: X 519 PHE cc_start: 0.8964 (t80) cc_final: 0.8626 (t80) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 0.0738 time to fit residues: 7.3445 Evaluate side-chains 44 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 380 LYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain H residue 138 LYS Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 166 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 82 HIS ** X 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 289 ASN X 291 HIS X 295 HIS X 408 ASN X 441 ASN H 13 GLN H 180 GLN L 37 GLN L 191 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.060870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.047172 restraints weight = 92669.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.049222 restraints weight = 34275.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.050639 restraints weight = 19127.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.051583 restraints weight = 13035.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.052317 restraints weight = 10124.566| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7550 Z= 0.136 Angle : 0.632 7.298 10302 Z= 0.325 Chirality : 0.043 0.172 1141 Planarity : 0.005 0.050 1267 Dihedral : 7.598 89.266 1071 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.12 % Allowed : 10.92 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.27), residues: 918 helix: 0.02 (0.28), residues: 356 sheet: -1.70 (0.34), residues: 177 loop : -2.74 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 110 TYR 0.014 0.001 TYR X 239 PHE 0.018 0.001 PHE X 432 TRP 0.011 0.001 TRP X 416 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7545) covalent geometry : angle 0.63135 (10292) SS BOND : bond 0.00730 ( 5) SS BOND : angle 1.14320 ( 10) hydrogen bonds : bond 0.04285 ( 355) hydrogen bonds : angle 5.65701 ( 1021) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: X 190 MET cc_start: 0.8795 (ttm) cc_final: 0.8439 (ttm) REVERT: X 193 ASP cc_start: 0.8635 (m-30) cc_final: 0.8294 (m-30) REVERT: X 490 MET cc_start: 0.8712 (mtm) cc_final: 0.8374 (mtm) REVERT: L 140 ASN cc_start: 0.9207 (m-40) cc_final: 0.8851 (m-40) REVERT: L 145 GLU cc_start: 0.9320 (tp30) cc_final: 0.9043 (tp30) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.0695 time to fit residues: 6.6445 Evaluate side-chains 51 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 138 LYS Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 196 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 73 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 63 optimal weight: 6.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 258 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 = 0.3268 r_free = 0.3268 target = 0.061341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.047138 restraints weight = 125636.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.049342 restraints weight = 39515.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.050888 restraints weight = 20575.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.052000 restraints weight = 13545.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.052570 restraints weight = 10091.274| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7550 Z= 0.126 Angle : 0.583 7.607 10302 Z= 0.298 Chirality : 0.042 0.174 1141 Planarity : 0.004 0.043 1267 Dihedral : 6.806 71.927 1064 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.86 % Allowed : 12.53 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.28), residues: 918 helix: 0.71 (0.29), residues: 356 sheet: -1.20 (0.34), residues: 177 loop : -2.36 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 110 TYR 0.012 0.001 TYR H 94 PHE 0.017 0.001 PHE X 343 TRP 0.012 0.001 TRP H 163 HIS 0.003 0.001 HIS X 75 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7545) covalent geometry : angle 0.58222 (10292) SS BOND : bond 0.00756 ( 5) SS BOND : angle 0.88554 ( 10) hydrogen bonds : bond 0.03807 ( 355) hydrogen bonds : angle 5.26061 ( 1021) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.298 Fit side-chains REVERT: X 189 LEU cc_start: 0.9332 (tp) cc_final: 0.8870 (tt) REVERT: X 190 MET cc_start: 0.8772 (ttm) cc_final: 0.8435 (ttm) REVERT: X 408 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8326 (t0) REVERT: X 490 MET cc_start: 0.8654 (mtm) cc_final: 0.8372 (mtm) REVERT: X 519 PHE cc_start: 0.9244 (t80) cc_final: 0.8900 (t80) REVERT: L 140 ASN cc_start: 0.9074 (m-40) cc_final: 0.8299 (m-40) REVERT: L 145 GLU cc_start: 0.9274 (tp30) cc_final: 0.9016 (tp30) outliers start: 14 outliers final: 7 residues processed: 60 average time/residue: 0.0656 time to fit residues: 6.1635 Evaluate side-chains 55 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 408 ASN Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 196 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 40 optimal weight: 0.0870 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 chunk 87 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 258 ASN X 409 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.062205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.048424 restraints weight = 103676.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.050567 restraints weight = 36035.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.052083 restraints weight = 19445.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.053087 restraints weight = 12998.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.053814 restraints weight = 9990.326| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7550 Z= 0.110 Angle : 0.566 7.171 10302 Z= 0.286 Chirality : 0.041 0.164 1141 Planarity : 0.004 0.044 1267 Dihedral : 6.431 67.083 1060 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.99 % Allowed : 14.39 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.28), residues: 918 helix: 1.00 (0.28), residues: 358 sheet: -0.64 (0.36), residues: 177 loop : -2.16 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 110 TYR 0.011 0.001 TYR H 94 PHE 0.018 0.001 PHE X 343 TRP 0.008 0.001 TRP X 416 HIS 0.003 0.001 HIS X 75 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7545) covalent geometry : angle 0.56402 (10292) SS BOND : bond 0.00634 ( 5) SS BOND : angle 1.45068 ( 10) hydrogen bonds : bond 0.03466 ( 355) hydrogen bonds : angle 5.04881 ( 1021) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.287 Fit side-chains REVERT: X 190 MET cc_start: 0.8782 (ttm) cc_final: 0.8519 (ttm) REVERT: X 408 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8329 (t0) REVERT: X 490 MET cc_start: 0.8586 (mtm) cc_final: 0.8366 (mtm) REVERT: L 140 ASN cc_start: 0.8993 (m-40) cc_final: 0.8233 (m-40) REVERT: L 145 GLU cc_start: 0.9285 (tp30) cc_final: 0.9017 (tp30) outliers start: 15 outliers final: 10 residues processed: 70 average time/residue: 0.0605 time to fit residues: 6.7081 Evaluate side-chains 66 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 408 ASN Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 196 CYS Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 13 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 409 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.062450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.048804 restraints weight = 102549.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.050968 restraints weight = 35230.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.052492 restraints weight = 18930.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.053444 restraints weight = 12597.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.054190 restraints weight = 9632.644| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7550 Z= 0.107 Angle : 0.566 7.046 10302 Z= 0.282 Chirality : 0.041 0.159 1141 Planarity : 0.004 0.044 1267 Dihedral : 6.215 61.102 1060 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.99 % Allowed : 15.51 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.28), residues: 918 helix: 1.21 (0.28), residues: 358 sheet: -0.21 (0.36), residues: 181 loop : -2.03 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 110 TYR 0.010 0.001 TYR L 49 PHE 0.018 0.001 PHE X 343 TRP 0.007 0.001 TRP H 163 HIS 0.003 0.001 HIS X 75 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 7545) covalent geometry : angle 0.56520 (10292) SS BOND : bond 0.00741 ( 5) SS BOND : angle 0.86006 ( 10) hydrogen bonds : bond 0.03469 ( 355) hydrogen bonds : angle 4.93418 ( 1021) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.314 Fit side-chains REVERT: X 77 MET cc_start: 0.8720 (mmm) cc_final: 0.8420 (mmm) REVERT: X 190 MET cc_start: 0.8838 (ttm) cc_final: 0.8529 (ttm) REVERT: X 408 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8337 (t0) REVERT: X 490 MET cc_start: 0.8505 (mtm) cc_final: 0.8230 (mtm) REVERT: X 519 PHE cc_start: 0.9212 (t80) cc_final: 0.8851 (t80) REVERT: L 140 ASN cc_start: 0.8920 (m-40) cc_final: 0.8180 (m-40) REVERT: L 145 GLU cc_start: 0.9264 (tp30) cc_final: 0.9031 (tp30) REVERT: L 163 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7688 (mm-30) outliers start: 15 outliers final: 12 residues processed: 73 average time/residue: 0.0613 time to fit residues: 7.1391 Evaluate side-chains 68 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 408 ASN Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 194 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.061509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.047820 restraints weight = 94353.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.049888 restraints weight = 34247.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.051299 restraints weight = 18836.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.052318 restraints weight = 12862.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.052923 restraints weight = 9881.869| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7550 Z= 0.143 Angle : 0.585 9.781 10302 Z= 0.293 Chirality : 0.041 0.178 1141 Planarity : 0.004 0.044 1267 Dihedral : 6.354 61.740 1060 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.85 % Allowed : 15.51 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.28), residues: 918 helix: 1.30 (0.29), residues: 357 sheet: -0.10 (0.38), residues: 181 loop : -1.99 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 261 TYR 0.013 0.001 TYR H 94 PHE 0.017 0.001 PHE X 343 TRP 0.012 0.001 TRP H 163 HIS 0.004 0.001 HIS X 194 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7545) covalent geometry : angle 0.58265 (10292) SS BOND : bond 0.00870 ( 5) SS BOND : angle 1.76767 ( 10) hydrogen bonds : bond 0.03552 ( 355) hydrogen bonds : angle 4.96009 ( 1021) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.322 Fit side-chains REVERT: X 77 MET cc_start: 0.8732 (mmm) cc_final: 0.8468 (mmm) REVERT: X 408 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8361 (t0) REVERT: X 490 MET cc_start: 0.8531 (mtm) cc_final: 0.8243 (mtm) REVERT: L 4 MET cc_start: 0.8388 (ttp) cc_final: 0.8158 (ttm) REVERT: L 140 ASN cc_start: 0.9021 (m-40) cc_final: 0.8347 (m-40) REVERT: L 145 GLU cc_start: 0.9303 (tp30) cc_final: 0.9067 (tp30) outliers start: 22 outliers final: 15 residues processed: 70 average time/residue: 0.0582 time to fit residues: 6.5132 Evaluate side-chains 68 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 235 MET Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 408 ASN Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 196 CYS Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 44 optimal weight: 0.0070 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- 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 = 0.3271 r_free = 0.3271 target = 0.061508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.047803 restraints weight = 95386.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049900 restraints weight = 33751.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.051394 restraints weight = 18477.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.052413 restraints weight = 12480.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.053042 restraints weight = 9606.184| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7550 Z= 0.156 Angle : 0.606 9.998 10302 Z= 0.303 Chirality : 0.042 0.171 1141 Planarity : 0.004 0.046 1267 Dihedral : 6.498 63.139 1060 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.23 % Allowed : 16.38 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.28), residues: 918 helix: 1.35 (0.29), residues: 354 sheet: -0.12 (0.38), residues: 175 loop : -2.01 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 261 TYR 0.015 0.001 TYR H 94 PHE 0.018 0.001 PHE X 343 TRP 0.013 0.001 TRP H 163 HIS 0.002 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7545) covalent geometry : angle 0.60192 (10292) SS BOND : bond 0.00896 ( 5) SS BOND : angle 2.24800 ( 10) hydrogen bonds : bond 0.03642 ( 355) hydrogen bonds : angle 5.00290 ( 1021) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.281 Fit side-chains REVERT: X 408 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8406 (t0) REVERT: X 490 MET cc_start: 0.8512 (mtm) cc_final: 0.8203 (mtm) REVERT: X 519 PHE cc_start: 0.9201 (t80) cc_final: 0.8854 (t80) REVERT: L 140 ASN cc_start: 0.9020 (m-40) cc_final: 0.8355 (m-40) REVERT: L 145 GLU cc_start: 0.9303 (tp30) cc_final: 0.9068 (tp30) outliers start: 17 outliers final: 15 residues processed: 67 average time/residue: 0.0602 time to fit residues: 6.4206 Evaluate side-chains 68 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 408 ASN Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 196 CYS Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 59 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 186 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 = 0.3306 r_free = 0.3306 target = 0.062802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.049046 restraints weight = 95299.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.051202 restraints weight = 33598.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.052702 restraints weight = 18285.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.053681 restraints weight = 12357.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.054407 restraints weight = 9597.830| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7550 Z= 0.110 Angle : 0.598 10.701 10302 Z= 0.295 Chirality : 0.042 0.175 1141 Planarity : 0.004 0.045 1267 Dihedral : 6.291 61.114 1060 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.11 % Allowed : 16.87 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.29), residues: 918 helix: 1.45 (0.29), residues: 355 sheet: 0.01 (0.38), residues: 175 loop : -1.89 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 74 TYR 0.011 0.001 TYR H 103 PHE 0.018 0.001 PHE X 343 TRP 0.008 0.001 TRP X 416 HIS 0.003 0.001 HIS X 75 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7545) covalent geometry : angle 0.59669 (10292) SS BOND : bond 0.00721 ( 5) SS BOND : angle 1.32024 ( 10) hydrogen bonds : bond 0.03411 ( 355) hydrogen bonds : angle 4.84984 ( 1021) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.314 Fit side-chains REVERT: X 408 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8407 (t0) REVERT: X 490 MET cc_start: 0.8422 (mtm) cc_final: 0.8148 (mtm) REVERT: X 519 PHE cc_start: 0.9208 (t80) cc_final: 0.8820 (t80) REVERT: L 140 ASN cc_start: 0.8924 (m-40) cc_final: 0.8211 (m-40) outliers start: 16 outliers final: 14 residues processed: 68 average time/residue: 0.0583 time to fit residues: 6.3565 Evaluate side-chains 65 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 408 ASN Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 196 CYS Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 85 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3229 r_free = 0.3229 target = 0.060052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.046399 restraints weight = 96950.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.048405 restraints weight = 34131.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.049862 restraints weight = 18686.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.050862 restraints weight = 12630.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.051454 restraints weight = 9713.722| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7550 Z= 0.243 Angle : 0.685 11.657 10302 Z= 0.347 Chirality : 0.044 0.170 1141 Planarity : 0.004 0.049 1267 Dihedral : 7.046 69.163 1060 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.74 % Allowed : 16.75 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.29), residues: 918 helix: 1.23 (0.29), residues: 353 sheet: -0.18 (0.36), residues: 196 loop : -1.98 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 302 TYR 0.020 0.002 TYR X 393 PHE 0.021 0.002 PHE X 343 TRP 0.023 0.001 TRP H 163 HIS 0.004 0.001 HIS X 378 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 7545) covalent geometry : angle 0.68165 (10292) SS BOND : bond 0.00920 ( 5) SS BOND : angle 2.32471 ( 10) hydrogen bonds : bond 0.04262 ( 355) hydrogen bonds : angle 5.23985 ( 1021) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.310 Fit side-chains REVERT: X 190 MET cc_start: 0.8940 (tpp) cc_final: 0.8566 (mmm) REVERT: X 490 MET cc_start: 0.8615 (mtm) cc_final: 0.8263 (mtm) REVERT: X 519 PHE cc_start: 0.9244 (t80) cc_final: 0.8913 (t80) REVERT: L 140 ASN cc_start: 0.9080 (m-40) cc_final: 0.8809 (m-40) outliers start: 13 outliers final: 12 residues processed: 59 average time/residue: 0.0599 time to fit residues: 5.7803 Evaluate side-chains 59 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 196 CYS Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3260 r_free = 0.3260 target = 0.061215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.047246 restraints weight = 117210.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.049430 restraints weight = 37430.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.050961 restraints weight = 19498.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.052045 restraints weight = 12897.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.052697 restraints weight = 9718.884| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7550 Z= 0.161 Angle : 0.635 11.830 10302 Z= 0.317 Chirality : 0.043 0.172 1141 Planarity : 0.004 0.044 1267 Dihedral : 6.819 67.692 1060 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.74 % Allowed : 16.50 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.29), residues: 918 helix: 1.30 (0.29), residues: 355 sheet: -0.09 (0.38), residues: 175 loop : -1.92 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 74 TYR 0.014 0.001 TYR H 94 PHE 0.019 0.001 PHE X 343 TRP 0.013 0.001 TRP H 163 HIS 0.002 0.001 HIS X 196 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 7545) covalent geometry : angle 0.63118 (10292) SS BOND : bond 0.00724 ( 5) SS BOND : angle 2.30987 ( 10) hydrogen bonds : bond 0.03824 ( 355) hydrogen bonds : angle 5.09819 ( 1021) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.289 Fit side-chains REVERT: X 490 MET cc_start: 0.8554 (mtm) cc_final: 0.8237 (mtm) REVERT: X 519 PHE cc_start: 0.9232 (t80) cc_final: 0.8889 (t80) REVERT: L 140 ASN cc_start: 0.9022 (m-40) cc_final: 0.8346 (m-40) outliers start: 13 outliers final: 11 residues processed: 60 average time/residue: 0.0601 time to fit residues: 5.7994 Evaluate side-chains 60 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 506 TYR Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 196 CYS Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 64 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 overall best weight: 0.7960 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.063160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.049479 restraints weight = 96247.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.051634 restraints weight = 34300.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053174 restraints weight = 18675.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.054124 restraints weight = 12543.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.054938 restraints weight = 9694.744| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7550 Z= 0.110 Angle : 0.609 11.127 10302 Z= 0.300 Chirality : 0.043 0.283 1141 Planarity : 0.004 0.045 1267 Dihedral : 6.412 61.707 1060 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.99 % Allowed : 16.38 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.29), residues: 918 helix: 1.51 (0.29), residues: 355 sheet: 0.18 (0.36), residues: 196 loop : -1.90 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 110 TYR 0.010 0.001 TYR H 103 PHE 0.017 0.001 PHE X 343 TRP 0.009 0.001 TRP X 416 HIS 0.003 0.001 HIS X 75 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7545) covalent geometry : angle 0.60638 (10292) SS BOND : bond 0.00527 ( 5) SS BOND : angle 1.85743 ( 10) hydrogen bonds : bond 0.03376 ( 355) hydrogen bonds : angle 4.89776 ( 1021) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1500.64 seconds wall clock time: 26 minutes 52.99 seconds (1612.99 seconds total)