Starting phenix.real_space_refine on Thu Jul 2 03:01:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b01_15775/07_2026/8b01_15775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b01_15775/07_2026/8b01_15775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b01_15775/07_2026/8b01_15775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b01_15775/07_2026/8b01_15775.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8b01_15775/07_2026/8b01_15775.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b01_15775/07_2026/8b01_15775.cif" model { file = "/net/cci-nas-00/data/ceres_data/8b01_15775/07_2026/8b01_15775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b01_15775/07_2026/8b01_15775.cif" } resolution = 3.03 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= 0.011 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 33 5.16 5 Na 2 4.78 5 C 3682 2.51 5 N 834 2.21 5 O 925 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5478 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1257 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 4, 'TRANS': 148} Chain: "B" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3208 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 404} Chain: "C" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 815 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 90 Unusual residues: {'D10': 1, 'OCT': 1, 'PTY': 1, 'TWT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 108 Unusual residues: {' NA': 2, 'D10': 1, 'HEX': 1, 'OCT': 5, 'PTY': 1, 'TRD': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" C1 OCT A 201 " occ=0.50 ... (6 atoms not shown) pdb=" C8 OCT A 201 " occ=0.50 residue: pdb=" C1 PTY A 202 " occ=0.50 ... (48 atoms not shown) pdb=" P1 PTY A 202 " occ=0.50 residue: pdb=" C1 TWT A 203 " occ=0.50 ... (20 atoms not shown) pdb=" C9 TWT A 203 " occ=0.50 residue: pdb=" C1 D10 A 204 " occ=0.50 ... (8 atoms not shown) pdb=" C9 D10 A 204 " occ=0.50 residue: pdb=" C1 OCT B 503 " occ=0.50 ... (6 atoms not shown) pdb=" C8 OCT B 503 " occ=0.50 residue: pdb=" C1 OCT B 504 " occ=0.50 ... (6 atoms not shown) pdb=" C8 OCT B 504 " occ=0.50 residue: pdb=" C1 OCT B 505 " occ=0.50 ... (6 atoms not shown) pdb=" C8 OCT B 505 " occ=0.50 residue: pdb=" C1 OCT B 506 " occ=0.50 ... (6 atoms not shown) pdb=" C8 OCT B 506 " occ=0.50 residue: pdb=" C1 OCT B 507 " occ=0.50 ... (6 atoms not shown) pdb=" C8 OCT B 507 " occ=0.50 residue: pdb=" C1 TRD B 508 " occ=0.50 ... (11 atoms not shown) pdb=" C9 TRD B 508 " occ=0.50 residue: pdb=" C1 D10 B 509 " occ=0.50 ... (8 atoms not shown) pdb=" C9 D10 B 509 " occ=0.50 residue: pdb=" C1 PTY B 510 " occ=0.50 ... (35 atoms not shown) pdb=" P1 PTY B 510 " occ=0.50 residue: pdb=" C1 HEX B 511 " occ=0.50 ... (4 atoms not shown) pdb=" C6 HEX B 511 " occ=0.50 Time building chain proxies: 1.03, per 1000 atoms: 0.19 Number of scatterers: 5478 At special positions: 0 Unit cell: (91.258, 77.082, 92.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 2 15.00 Na 2 11.00 O 925 8.00 N 834 7.00 C 3682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.04 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: 0.39 Conformation dependent library (CDL) restraints added in 200.2 milliseconds 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 3 sheets defined 74.0% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.527A pdb=" N ILE A 6 " --> pdb=" O PHE A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 35 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 41 through 64 removed outlier: 3.579A pdb=" N LEU A 45 " --> pdb=" O TRP A 41 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.723A pdb=" N LYS A 76 " --> pdb=" O PHE A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 111 removed outlier: 3.864A pdb=" N LEU A 85 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 128 through 152 removed outlier: 3.655A pdb=" N PHE A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.675A pdb=" N GLY B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 33 Processing helix chain 'B' and resid 35 through 39 removed outlier: 3.760A pdb=" N ILE B 38 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN B 39 " --> pdb=" O THR B 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 35 through 39' Processing helix chain 'B' and resid 40 through 50 removed outlier: 4.075A pdb=" N LEU B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 55 through 70 removed outlier: 4.046A pdb=" N PHE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 85 removed outlier: 4.205A pdb=" N ARG B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 104 Processing helix chain 'B' and resid 108 through 127 removed outlier: 3.594A pdb=" N ASP B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 removed outlier: 3.855A pdb=" N CYS B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 148 removed outlier: 4.023A pdb=" N LEU B 147 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 162 Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 172 through 195 removed outlier: 4.094A pdb=" N GLY B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 213 Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 230 removed outlier: 4.251A pdb=" N PHE B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 252 Processing helix chain 'B' and resid 258 through 292 removed outlier: 3.740A pdb=" N MET B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 307 removed outlier: 3.944A pdb=" N GLN B 298 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER B 307 " --> pdb=" O PHE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 325 Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 337 through 349 Proline residue: B 343 - end of helix removed outlier: 3.719A pdb=" N VAL B 348 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 367 Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 398 through 411 Processing helix chain 'B' and resid 412 through 423 removed outlier: 4.971A pdb=" N LEU B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.733A pdb=" N ILE A 121 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 17 through 22 removed outlier: 3.620A pdb=" N LEU C 20 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 78 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.350A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.57 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 847 1.32 - 1.45: 1431 1.45 - 1.57: 3249 1.57 - 1.69: 4 1.69 - 1.81: 57 Bond restraints: 5588 Sorted by residual: bond pdb=" C GLY B 231 " pdb=" N LYS B 232 " ideal model delta sigma weight residual 1.334 1.284 0.050 1.46e-02 4.69e+03 1.17e+01 bond pdb=" N VAL B 283 " pdb=" CA VAL B 283 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.33e+00 bond pdb=" N TYR C 107 " pdb=" CA TYR C 107 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.71e+00 bond pdb=" N SER B 106 " pdb=" CA SER B 106 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.17e-02 7.31e+03 7.48e+00 bond pdb=" CA TYR C 105 " pdb=" C TYR C 105 " ideal model delta sigma weight residual 1.524 1.557 -0.033 1.32e-02 5.74e+03 6.25e+00 ... (remaining 5583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 7288 1.47 - 2.94: 195 2.94 - 4.42: 35 4.42 - 5.89: 13 5.89 - 7.36: 3 Bond angle restraints: 7534 Sorted by residual: angle pdb=" N PRO C 104 " pdb=" CA PRO C 104 " pdb=" C PRO C 104 " ideal model delta sigma weight residual 113.40 106.04 7.36 1.34e+00 5.57e-01 3.02e+01 angle pdb=" N PHE B 102 " pdb=" CA PHE B 102 " pdb=" C PHE B 102 " ideal model delta sigma weight residual 112.54 107.68 4.86 1.22e+00 6.72e-01 1.59e+01 angle pdb=" N LEU B 321 " pdb=" CA LEU B 321 " pdb=" C LEU B 321 " ideal model delta sigma weight residual 111.14 106.89 4.25 1.08e+00 8.57e-01 1.55e+01 angle pdb=" N TYR A 128 " pdb=" CA TYR A 128 " pdb=" C TYR A 128 " ideal model delta sigma weight residual 113.15 108.69 4.46 1.19e+00 7.06e-01 1.41e+01 angle pdb=" CA TYR C 101 " pdb=" C TYR C 101 " pdb=" O TYR C 101 " ideal model delta sigma weight residual 121.49 117.51 3.98 1.16e+00 7.43e-01 1.18e+01 ... (remaining 7529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.60: 2893 14.60 - 29.19: 291 29.19 - 43.79: 86 43.79 - 58.39: 15 58.39 - 72.98: 5 Dihedral angle restraints: 3290 sinusoidal: 1334 harmonic: 1956 Sorted by residual: dihedral pdb=" CA PHE B 233 " pdb=" C PHE B 233 " pdb=" N THR B 234 " pdb=" CA THR B 234 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP B 131 " pdb=" CB ASP B 131 " pdb=" CG ASP B 131 " pdb=" OD1 ASP B 131 " ideal model delta sinusoidal sigma weight residual -30.00 -89.28 59.28 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CG ARG C 71 " pdb=" CD ARG C 71 " pdb=" NE ARG C 71 " pdb=" CZ ARG C 71 " ideal model delta sinusoidal sigma weight residual 90.00 134.72 -44.72 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 3287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 699 0.051 - 0.102: 151 0.102 - 0.153: 27 0.153 - 0.203: 3 0.203 - 0.254: 2 Chirality restraints: 882 Sorted by residual: chirality pdb=" CA LEU B 321 " pdb=" N LEU B 321 " pdb=" C LEU B 321 " pdb=" CB LEU B 321 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO C 104 " pdb=" N PRO C 104 " pdb=" C PRO C 104 " pdb=" CB PRO C 104 " both_signs ideal model delta sigma weight residual False 2.72 2.93 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LEU B 322 " pdb=" N LEU B 322 " pdb=" C LEU B 322 " pdb=" CB LEU B 322 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.23e-01 ... (remaining 879 not shown) Planarity restraints: 901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 105 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.57e+00 pdb=" C TYR C 105 " 0.041 2.00e-02 2.50e+03 pdb=" O TYR C 105 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR C 106 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 127 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C THR A 127 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 127 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR A 128 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 234 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO B 235 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 235 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 235 " 0.026 5.00e-02 4.00e+02 ... (remaining 898 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 821 2.75 - 3.29: 5229 3.29 - 3.83: 8542 3.83 - 4.36: 9479 4.36 - 4.90: 17735 Nonbonded interactions: 41806 Sorted by model distance: nonbonded pdb=" OD1 ASP B 351 " pdb=" OH TYR B 425 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O TYR C 98 " model vdw 2.228 3.040 nonbonded pdb=" O GLY B 145 " pdb="NA NA B 501 " model vdw 2.282 2.470 nonbonded pdb=" NH1 ARG A 32 " pdb=" OE2 GLU B 237 " model vdw 2.302 3.120 nonbonded pdb=" NE2 GLN C 39 " pdb=" O LYS C 43 " model vdw 2.311 3.120 ... (remaining 41801 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=0.00 max=1.00 mean=0.98 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: 1.890 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.240 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.004 0.050 5589 Z= 0.228 Angle : 0.598 7.359 7536 Z= 0.362 Chirality : 0.043 0.254 882 Planarity : 0.005 0.047 901 Dihedral : 13.046 72.985 2039 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.53 % Allowed : 0.53 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.33), residues: 678 helix: 2.35 (0.25), residues: 457 sheet: -0.48 (0.96), residues: 33 loop : -0.54 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 75 TYR 0.022 0.001 TYR A 128 PHE 0.011 0.001 PHE B 59 TRP 0.006 0.001 TRP A 27 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.23 ( 5588) covalent geometry : angle 0.59834 / 0.36 ( 7534) SS BOND : bond 0.00409 / 0.22 ( 1) SS BOND : angle 0.75101 / 0.44 ( 2) hydrogen bonds : bond 0.17056 / 11.30 ( 357) hydrogen bonds : angle 6.05612 / 4.24 ( 1056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7268 (mmm-85) cc_final: 0.6900 (mmm160) REVERT: A 4 LYS cc_start: 0.8466 (tppp) cc_final: 0.7601 (ptpt) REVERT: B 118 GLN cc_start: 0.7449 (tp40) cc_final: 0.7135 (tp-100) REVERT: B 122 LYS cc_start: 0.8294 (ttpt) cc_final: 0.7897 (tptp) REVERT: B 126 ASP cc_start: 0.9056 (m-30) cc_final: 0.8363 (m-30) REVERT: B 372 MET cc_start: 0.8171 (tmm) cc_final: 0.7735 (tmm) REVERT: B 392 ARG cc_start: 0.8307 (ttm170) cc_final: 0.7949 (ttp80) REVERT: C 34 MET cc_start: 0.8192 (tpp) cc_final: 0.7867 (tpp) REVERT: C 72 ASP cc_start: 0.8378 (t70) cc_final: 0.8036 (t0) REVERT: C 85 LEU cc_start: 0.8107 (mt) cc_final: 0.7861 (mt) REVERT: C 108 TRP cc_start: 0.7248 (m-10) cc_final: 0.6801 (m-10) outliers start: 3 outliers final: 0 residues processed: 111 average time/residue: 0.0735 time to fit residues: 10.1815 Evaluate side-chains 85 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.0000 chunk 27 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS B 354 HIS B 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.089519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.074839 restraints weight = 10648.275| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.62 r_work: 0.2899 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5589 Z= 0.126 Angle : 0.528 7.705 7536 Z= 0.271 Chirality : 0.039 0.149 882 Planarity : 0.005 0.049 901 Dihedral : 7.119 59.933 867 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.88 % Allowed : 6.14 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.33), residues: 678 helix: 2.56 (0.24), residues: 458 sheet: -0.81 (0.93), residues: 34 loop : -0.31 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.010 0.001 TYR B 425 PHE 0.027 0.001 PHE A 2 TRP 0.009 0.001 TRP B 8 HIS 0.002 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 5588) covalent geometry : angle 0.52810 / 0.27 ( 7534) SS BOND : bond 0.00382 / 0.20 ( 1) SS BOND : angle 1.32605 / 0.77 ( 2) hydrogen bonds : bond 0.05220 / 3.43 ( 357) hydrogen bonds : angle 4.36782 / 3.14 ( 1056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.123 Fit side-chains REVERT: A 4 LYS cc_start: 0.8407 (tppp) cc_final: 0.7805 (pttt) REVERT: B 105 MET cc_start: 0.7738 (mtt) cc_final: 0.7467 (mtt) REVERT: B 118 GLN cc_start: 0.7718 (tp40) cc_final: 0.7418 (tp-100) REVERT: B 126 ASP cc_start: 0.8860 (m-30) cc_final: 0.8406 (m-30) REVERT: B 392 ARG cc_start: 0.8547 (ttm170) cc_final: 0.8265 (ttp80) REVERT: C 34 MET cc_start: 0.8295 (tpp) cc_final: 0.7918 (tpp) REVERT: C 72 ASP cc_start: 0.8421 (t70) cc_final: 0.7996 (t0) outliers start: 5 outliers final: 3 residues processed: 90 average time/residue: 0.0632 time to fit residues: 7.3687 Evaluate side-chains 84 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain C residue 86 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 318 ASN B 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.087423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.073233 restraints weight = 10617.680| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.63 r_work: 0.2868 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5589 Z= 0.129 Angle : 0.504 7.446 7536 Z= 0.257 Chirality : 0.038 0.144 882 Planarity : 0.005 0.048 901 Dihedral : 7.046 59.870 867 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.05 % Allowed : 7.54 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.32), residues: 678 helix: 2.67 (0.24), residues: 456 sheet: -1.12 (0.88), residues: 34 loop : -0.35 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.011 0.001 TYR C 94 PHE 0.018 0.001 PHE A 2 TRP 0.006 0.001 TRP B 8 HIS 0.002 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 5588) covalent geometry : angle 0.50249 / 0.26 ( 7534) SS BOND : bond 0.00218 / 0.11 ( 1) SS BOND : angle 2.33641 / 1.34 ( 2) hydrogen bonds : bond 0.05019 / 3.29 ( 357) hydrogen bonds : angle 4.19080 / 3.00 ( 1056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.210 Fit side-chains REVERT: A 4 LYS cc_start: 0.8363 (tppp) cc_final: 0.7753 (pttt) REVERT: B 105 MET cc_start: 0.7885 (mtt) cc_final: 0.7620 (mtt) REVERT: B 118 GLN cc_start: 0.7712 (tp40) cc_final: 0.7425 (tp-100) REVERT: B 126 ASP cc_start: 0.8811 (m-30) cc_final: 0.8393 (m-30) REVERT: B 392 ARG cc_start: 0.8528 (ttm170) cc_final: 0.8237 (ttp80) REVERT: C 72 ASP cc_start: 0.8451 (t70) cc_final: 0.8039 (t0) REVERT: C 88 GLU cc_start: 0.8254 (mp0) cc_final: 0.7804 (mp0) outliers start: 6 outliers final: 5 residues processed: 88 average time/residue: 0.0679 time to fit residues: 7.7137 Evaluate side-chains 87 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.085781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.071516 restraints weight = 10885.294| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.59 r_work: 0.2871 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5589 Z= 0.143 Angle : 0.510 7.577 7536 Z= 0.260 Chirality : 0.038 0.143 882 Planarity : 0.004 0.049 901 Dihedral : 7.082 59.618 867 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.28 % Allowed : 9.12 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.33), residues: 678 helix: 2.66 (0.24), residues: 456 sheet: -1.29 (0.88), residues: 34 loop : -0.41 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.010 0.001 TYR C 94 PHE 0.014 0.001 PHE A 2 TRP 0.005 0.001 TRP A 27 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 5588) covalent geometry : angle 0.50901 / 0.26 ( 7534) SS BOND : bond 0.00496 / 0.26 ( 1) SS BOND : angle 2.04793 / 1.19 ( 2) hydrogen bonds : bond 0.05165 / 3.39 ( 357) hydrogen bonds : angle 4.14185 / 2.97 ( 1056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.118 Fit side-chains REVERT: A 4 LYS cc_start: 0.8399 (tppp) cc_final: 0.7779 (pttt) REVERT: B 105 MET cc_start: 0.8067 (mtt) cc_final: 0.7845 (mtt) REVERT: B 118 GLN cc_start: 0.7775 (tp40) cc_final: 0.7509 (tp-100) REVERT: B 126 ASP cc_start: 0.8757 (m-30) cc_final: 0.8376 (m-30) REVERT: B 392 ARG cc_start: 0.8560 (ttm170) cc_final: 0.8223 (ttp80) REVERT: C 43 LYS cc_start: 0.8778 (mmmm) cc_final: 0.8486 (mmmm) REVERT: C 72 ASP cc_start: 0.8505 (t70) cc_final: 0.8138 (t0) REVERT: C 88 GLU cc_start: 0.8291 (mp0) cc_final: 0.7819 (mp0) REVERT: C 103 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7226 (t0) outliers start: 13 outliers final: 9 residues processed: 90 average time/residue: 0.0565 time to fit residues: 6.5782 Evaluate side-chains 91 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 66 optimal weight: 0.0570 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 HIS B 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.074000 restraints weight = 11108.749| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.53 r_work: 0.2947 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5589 Z= 0.108 Angle : 0.473 6.893 7536 Z= 0.241 Chirality : 0.037 0.139 882 Planarity : 0.004 0.048 901 Dihedral : 6.831 58.588 867 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.11 % Allowed : 10.35 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.33), residues: 678 helix: 2.79 (0.24), residues: 455 sheet: -1.22 (0.90), residues: 34 loop : -0.30 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.008 0.001 TYR C 94 PHE 0.011 0.001 PHE A 2 TRP 0.006 0.001 TRP A 27 HIS 0.001 0.000 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 5588) covalent geometry : angle 0.47194 / 0.24 ( 7534) SS BOND : bond 0.00127 / 0.07 ( 1) SS BOND : angle 2.10670 / 1.22 ( 2) hydrogen bonds : bond 0.04349 / 2.84 ( 357) hydrogen bonds : angle 3.97052 / 2.85 ( 1056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.122 Fit side-chains REVERT: A 4 LYS cc_start: 0.8404 (tppp) cc_final: 0.7822 (pttt) REVERT: B 118 GLN cc_start: 0.7702 (tp40) cc_final: 0.7423 (tp-100) REVERT: B 126 ASP cc_start: 0.8775 (m-30) cc_final: 0.8399 (m-30) REVERT: B 392 ARG cc_start: 0.8526 (ttm170) cc_final: 0.8245 (ttp80) REVERT: C 72 ASP cc_start: 0.8533 (t70) cc_final: 0.8189 (t0) REVERT: C 103 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7383 (t0) outliers start: 12 outliers final: 10 residues processed: 89 average time/residue: 0.0578 time to fit residues: 6.6640 Evaluate side-chains 92 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.086898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.072576 restraints weight = 11031.679| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.62 r_work: 0.2888 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5589 Z= 0.118 Angle : 0.479 7.200 7536 Z= 0.244 Chirality : 0.037 0.136 882 Planarity : 0.004 0.048 901 Dihedral : 6.810 59.132 867 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.28 % Allowed : 11.23 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.33), residues: 678 helix: 2.82 (0.24), residues: 455 sheet: -1.20 (0.92), residues: 34 loop : -0.30 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.010 0.001 TYR C 94 PHE 0.010 0.001 PHE A 2 TRP 0.005 0.001 TRP A 27 HIS 0.002 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 5588) covalent geometry : angle 0.47797 / 0.24 ( 7534) SS BOND : bond 0.00017 / 0.01 ( 1) SS BOND : angle 2.10674 / 1.22 ( 2) hydrogen bonds : bond 0.04549 / 2.98 ( 357) hydrogen bonds : angle 3.95827 / 2.84 ( 1056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.122 Fit side-chains REVERT: A 4 LYS cc_start: 0.8376 (tppp) cc_final: 0.7786 (pttt) REVERT: B 118 GLN cc_start: 0.7668 (tp40) cc_final: 0.7417 (tp-100) REVERT: B 126 ASP cc_start: 0.8703 (m-30) cc_final: 0.8321 (m-30) REVERT: B 384 ASN cc_start: 0.9135 (OUTLIER) cc_final: 0.8866 (t0) REVERT: B 392 ARG cc_start: 0.8561 (ttm170) cc_final: 0.8269 (ttp80) REVERT: C 72 ASP cc_start: 0.8541 (t70) cc_final: 0.7898 (t0) REVERT: C 75 LYS cc_start: 0.9187 (mtmm) cc_final: 0.8447 (mtmm) REVERT: C 100 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6860 (pt) outliers start: 13 outliers final: 10 residues processed: 88 average time/residue: 0.0563 time to fit residues: 6.4013 Evaluate side-chains 92 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 384 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 47 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.085202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.070861 restraints weight = 11078.670| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.62 r_work: 0.2858 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5589 Z= 0.157 Angle : 0.514 7.585 7536 Z= 0.261 Chirality : 0.039 0.161 882 Planarity : 0.005 0.048 901 Dihedral : 6.974 59.915 867 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.46 % Allowed : 11.05 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.33), residues: 678 helix: 2.76 (0.24), residues: 455 sheet: -1.23 (0.91), residues: 34 loop : -0.45 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 75 TYR 0.010 0.001 TYR C 94 PHE 0.011 0.001 PHE B 248 TRP 0.005 0.001 TRP A 33 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 5588) covalent geometry : angle 0.51286 / 0.26 ( 7534) SS BOND : bond 0.00153 / 0.08 ( 1) SS BOND : angle 2.11902 / 1.22 ( 2) hydrogen bonds : bond 0.05083 / 3.34 ( 357) hydrogen bonds : angle 4.03887 / 2.90 ( 1056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.199 Fit side-chains REVERT: A 4 LYS cc_start: 0.8408 (tppp) cc_final: 0.7849 (pttt) REVERT: B 118 GLN cc_start: 0.7761 (tp40) cc_final: 0.7503 (tp-100) REVERT: B 126 ASP cc_start: 0.8693 (m-30) cc_final: 0.8303 (m-30) REVERT: B 392 ARG cc_start: 0.8564 (ttm170) cc_final: 0.8217 (ttp80) REVERT: C 72 ASP cc_start: 0.8547 (t70) cc_final: 0.8196 (t0) REVERT: C 100 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6901 (pt) REVERT: C 103 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7323 (t0) outliers start: 14 outliers final: 10 residues processed: 89 average time/residue: 0.0627 time to fit residues: 7.2372 Evaluate side-chains 89 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.086424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.072054 restraints weight = 10999.955| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.63 r_work: 0.2878 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5589 Z= 0.122 Angle : 0.491 7.264 7536 Z= 0.250 Chirality : 0.037 0.145 882 Planarity : 0.004 0.048 901 Dihedral : 6.849 58.521 867 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.28 % Allowed : 10.88 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.33), residues: 678 helix: 2.79 (0.24), residues: 456 sheet: -1.34 (0.90), residues: 34 loop : -0.38 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.010 0.001 TYR C 94 PHE 0.010 0.001 PHE A 2 TRP 0.006 0.001 TRP C 108 HIS 0.002 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 5588) covalent geometry : angle 0.48924 / 0.25 ( 7534) SS BOND : bond 0.00108 / 0.06 ( 1) SS BOND : angle 2.30562 / 1.32 ( 2) hydrogen bonds : bond 0.04643 / 3.04 ( 357) hydrogen bonds : angle 3.97164 / 2.85 ( 1056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.262 Fit side-chains REVERT: A 4 LYS cc_start: 0.8398 (tppp) cc_final: 0.7849 (pttt) REVERT: B 118 GLN cc_start: 0.7674 (tp40) cc_final: 0.7418 (tp-100) REVERT: B 126 ASP cc_start: 0.8698 (m-30) cc_final: 0.8310 (m-30) REVERT: B 392 ARG cc_start: 0.8573 (ttm170) cc_final: 0.8229 (ttp80) REVERT: C 46 GLU cc_start: 0.8200 (tt0) cc_final: 0.7895 (tt0) REVERT: C 72 ASP cc_start: 0.8531 (t70) cc_final: 0.8182 (t0) REVERT: C 100 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6875 (pt) REVERT: C 103 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7388 (t0) outliers start: 13 outliers final: 10 residues processed: 86 average time/residue: 0.0583 time to fit residues: 6.4559 Evaluate side-chains 89 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 384 ASN C 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.085186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.070996 restraints weight = 10935.931| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.57 r_work: 0.2845 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5589 Z= 0.160 Angle : 0.529 7.773 7536 Z= 0.268 Chirality : 0.039 0.145 882 Planarity : 0.005 0.047 901 Dihedral : 7.012 59.327 867 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.46 % Allowed : 10.88 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.33), residues: 678 helix: 2.73 (0.24), residues: 456 sheet: -1.39 (0.92), residues: 34 loop : -0.50 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 32 TYR 0.011 0.001 TYR C 94 PHE 0.010 0.001 PHE B 248 TRP 0.007 0.001 TRP C 108 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 5588) covalent geometry : angle 0.52762 / 0.27 ( 7534) SS BOND : bond 0.00144 / 0.08 ( 1) SS BOND : angle 2.77373 / 1.61 ( 2) hydrogen bonds : bond 0.05275 / 3.47 ( 357) hydrogen bonds : angle 4.08656 / 2.94 ( 1056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.224 Fit side-chains REVERT: A 4 LYS cc_start: 0.8411 (tppp) cc_final: 0.7875 (pttt) REVERT: B 83 MET cc_start: 0.8613 (tpp) cc_final: 0.8186 (tpp) REVERT: B 118 GLN cc_start: 0.7741 (tp40) cc_final: 0.7469 (tp-100) REVERT: B 126 ASP cc_start: 0.8668 (m-30) cc_final: 0.8248 (m-30) REVERT: B 392 ARG cc_start: 0.8562 (ttm170) cc_final: 0.8220 (ttp80) REVERT: C 72 ASP cc_start: 0.8550 (t70) cc_final: 0.8204 (t0) REVERT: C 100 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6924 (pt) REVERT: C 103 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7429 (t0) outliers start: 14 outliers final: 11 residues processed: 87 average time/residue: 0.0871 time to fit residues: 9.8544 Evaluate side-chains 89 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 53 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.087198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.072839 restraints weight = 10949.719| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.61 r_work: 0.2884 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5589 Z= 0.115 Angle : 0.499 7.084 7536 Z= 0.254 Chirality : 0.037 0.145 882 Planarity : 0.004 0.048 901 Dihedral : 6.726 57.742 867 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.11 % Allowed : 11.23 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.33), residues: 678 helix: 2.80 (0.24), residues: 456 sheet: -1.41 (0.92), residues: 34 loop : -0.41 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.009 0.001 TYR C 94 PHE 0.009 0.001 PHE A 2 TRP 0.007 0.001 TRP A 27 HIS 0.002 0.001 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 5588) covalent geometry : angle 0.49782 / 0.25 ( 7534) SS BOND : bond 0.00161 / 0.08 ( 1) SS BOND : angle 2.29621 / 1.32 ( 2) hydrogen bonds : bond 0.04499 / 2.95 ( 357) hydrogen bonds : angle 3.96059 / 2.85 ( 1056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.219 Fit side-chains REVERT: A 4 LYS cc_start: 0.8418 (tppp) cc_final: 0.7872 (pttt) REVERT: B 118 GLN cc_start: 0.7752 (tp40) cc_final: 0.7494 (tp-100) REVERT: B 126 ASP cc_start: 0.8687 (m-30) cc_final: 0.8311 (m-30) REVERT: B 392 ARG cc_start: 0.8532 (ttm170) cc_final: 0.8247 (ttp80) REVERT: C 46 GLU cc_start: 0.8270 (tt0) cc_final: 0.7967 (tt0) REVERT: C 72 ASP cc_start: 0.8540 (t70) cc_final: 0.8196 (t0) REVERT: C 100 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6873 (pt) REVERT: C 103 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7447 (t0) outliers start: 12 outliers final: 10 residues processed: 88 average time/residue: 0.0910 time to fit residues: 10.3285 Evaluate side-chains 90 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 6 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 0.0370 chunk 50 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.072703 restraints weight = 11025.894| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.65 r_work: 0.2888 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5589 Z= 0.116 Angle : 0.496 6.975 7536 Z= 0.254 Chirality : 0.037 0.144 882 Planarity : 0.004 0.047 901 Dihedral : 6.554 56.969 867 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.28 % Allowed : 11.23 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.33), residues: 678 helix: 2.84 (0.24), residues: 456 sheet: -1.40 (0.92), residues: 34 loop : -0.46 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.009 0.001 TYR C 94 PHE 0.009 0.001 PHE A 2 TRP 0.006 0.001 TRP C 108 HIS 0.002 0.000 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 5588) covalent geometry : angle 0.49530 / 0.25 ( 7534) SS BOND : bond 0.00124 / 0.07 ( 1) SS BOND : angle 2.15415 / 1.24 ( 2) hydrogen bonds : bond 0.04425 / 2.90 ( 357) hydrogen bonds : angle 3.93486 / 2.83 ( 1056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1050.39 seconds wall clock time: 18 minutes 46.95 seconds (1126.95 seconds total)