Starting phenix.real_space_refine on Fri Dec 27 17:26:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b01_15775/12_2024/8b01_15775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b01_15775/12_2024/8b01_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_15775/12_2024/8b01_15775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b01_15775/12_2024/8b01_15775.map" model { file = "/net/cci-nas-00/data/ceres_data/8b01_15775/12_2024/8b01_15775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b01_15775/12_2024/8b01_15775.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 4.31, per 1000 atoms: 0.79 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: 1.86 Conformation dependent library (CDL) restraints added in 801.8 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: 0.60 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: 1.63 Time building geometry restraints manager: 1.90 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 - 17.16: 2984 17.16 - 34.32: 246 34.32 - 51.48: 57 51.48 - 68.64: 12 68.64 - 85.80: 3 Dihedral angle restraints: 3302 sinusoidal: 1346 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 3299 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: 0.010 Normalize map: mean=0, sd=1: 1.100 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.720 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 5588 Z= 0.262 Angle : 0.598 7.359 7534 Z= 0.362 Chirality : 0.043 0.254 882 Planarity : 0.005 0.047 901 Dihedral : 13.526 85.796 2051 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.006 0.001 TRP A 27 HIS 0.003 0.001 HIS B 86 PHE 0.011 0.001 PHE B 59 TYR 0.022 0.001 TYR A 128 ARG 0.002 0.000 ARG B 75 *********************** 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 : 0.606 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: 0.7247 (m-10) cc_final: 0.6801 (m-10) outliers start: 3 outliers final: 0 residues processed: 111 average time/residue: 0.2445 time to fit residues: 33.0048 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 : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 20 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS B 354 HIS B 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5588 Z= 0.189 Angle : 0.538 7.917 7534 Z= 0.275 Chirality : 0.039 0.147 882 Planarity : 0.005 0.049 901 Dihedral : 8.992 87.212 879 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.05 % Allowed : 5.79 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.33), residues: 678 helix: 2.55 (0.24), residues: 458 sheet: -0.79 (0.93), residues: 34 loop : -0.32 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 8 HIS 0.002 0.001 HIS B 354 PHE 0.024 0.001 PHE A 2 TYR 0.011 0.001 TYR B 425 ARG 0.003 0.000 ARG A 32 *********************** 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: 6 poor density : 87 time to evaluate : 0.661 Fit side-chains REVERT: A 4 LYS cc_start: 0.8270 (tppp) cc_final: 0.7643 (pttt) REVERT: B 105 MET cc_start: 0.7219 (mtt) cc_final: 0.6986 (mtt) REVERT: B 118 GLN cc_start: 0.7482 (tp40) cc_final: 0.7192 (tp-100) REVERT: B 126 ASP cc_start: 0.8792 (m-30) cc_final: 0.8299 (m-30) REVERT: B 392 ARG cc_start: 0.8322 (ttm170) cc_final: 0.7965 (ttp80) REVERT: C 34 MET cc_start: 0.8265 (tpp) cc_final: 0.7921 (tpp) REVERT: C 72 ASP cc_start: 0.8016 (t70) cc_final: 0.7550 (t0) REVERT: C 108 TRP cc_start: 0.7263 (m-10) cc_final: 0.6954 (m-10) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 0.2058 time to fit residues: 23.5928 Evaluate side-chains 85 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 48 optimal weight: 0.0970 chunk 45 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS B 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5588 Z= 0.170 Angle : 0.496 7.405 7534 Z= 0.253 Chirality : 0.038 0.144 882 Planarity : 0.005 0.048 901 Dihedral : 8.849 88.258 879 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.70 % Allowed : 8.07 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.32), residues: 678 helix: 2.68 (0.24), residues: 456 sheet: -1.07 (0.90), residues: 34 loop : -0.38 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 8 HIS 0.002 0.001 HIS B 86 PHE 0.018 0.001 PHE A 2 TYR 0.011 0.001 TYR C 94 ARG 0.004 0.000 ARG A 32 *********************** 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 88 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.675 Fit side-chains REVERT: A 4 LYS cc_start: 0.8201 (tppp) cc_final: 0.7599 (pttt) REVERT: B 105 MET cc_start: 0.7376 (mtt) cc_final: 0.7153 (mtt) REVERT: B 118 GLN cc_start: 0.7486 (tp40) cc_final: 0.7199 (tp-100) REVERT: B 126 ASP cc_start: 0.8740 (m-30) cc_final: 0.8292 (m-30) REVERT: B 392 ARG cc_start: 0.8317 (ttm170) cc_final: 0.8010 (ttp80) REVERT: C 72 ASP cc_start: 0.8035 (t70) cc_final: 0.7576 (t0) REVERT: C 88 GLU cc_start: 0.8105 (mp0) cc_final: 0.7630 (mp0) outliers start: 4 outliers final: 4 residues processed: 86 average time/residue: 0.2017 time to fit residues: 22.1975 Evaluate side-chains 86 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5588 Z= 0.184 Angle : 0.497 7.385 7534 Z= 0.254 Chirality : 0.038 0.143 882 Planarity : 0.004 0.048 901 Dihedral : 8.779 88.796 879 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.28 % Allowed : 8.95 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.33), residues: 678 helix: 2.73 (0.24), residues: 456 sheet: -1.23 (0.89), residues: 34 loop : -0.39 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 108 HIS 0.002 0.001 HIS B 86 PHE 0.013 0.001 PHE A 2 TYR 0.010 0.001 TYR C 94 ARG 0.004 0.000 ARG A 32 *********************** 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 95 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.643 Fit side-chains REVERT: A 4 LYS cc_start: 0.8200 (tppp) cc_final: 0.7587 (pttt) REVERT: B 118 GLN cc_start: 0.7477 (tp40) cc_final: 0.7206 (tp-100) REVERT: B 126 ASP cc_start: 0.8704 (m-30) cc_final: 0.8260 (m-30) REVERT: B 392 ARG cc_start: 0.8307 (ttm170) cc_final: 0.7998 (ttp80) REVERT: C 43 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8368 (mmmm) REVERT: C 72 ASP cc_start: 0.8074 (t70) cc_final: 0.7634 (t0) REVERT: C 88 GLU cc_start: 0.8111 (mp0) cc_final: 0.7640 (mp0) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.2011 time to fit residues: 23.4045 Evaluate side-chains 91 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 78 VAL Chi-restraints excluded: chain C residue 86 LYS 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 48 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5588 Z= 0.217 Angle : 0.507 7.529 7534 Z= 0.257 Chirality : 0.038 0.140 882 Planarity : 0.004 0.048 901 Dihedral : 8.793 89.151 879 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.28 % Allowed : 10.00 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.33), residues: 678 helix: 2.71 (0.24), residues: 456 sheet: -1.25 (0.91), residues: 34 loop : -0.43 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 27 HIS 0.002 0.001 HIS B 86 PHE 0.012 0.001 PHE A 2 TYR 0.010 0.001 TYR C 94 ARG 0.004 0.000 ARG A 32 *********************** 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 91 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.698 Fit side-chains REVERT: A 4 LYS cc_start: 0.8228 (tppp) cc_final: 0.7611 (pttt) REVERT: B 118 GLN cc_start: 0.7495 (tp40) cc_final: 0.7228 (tp-100) REVERT: B 126 ASP cc_start: 0.8709 (m-30) cc_final: 0.8282 (m-30) REVERT: B 392 ARG cc_start: 0.8307 (ttm170) cc_final: 0.7939 (ttp80) REVERT: C 72 ASP cc_start: 0.8091 (t70) cc_final: 0.7666 (t0) REVERT: C 88 GLU cc_start: 0.8129 (mp0) cc_final: 0.7688 (mp0) REVERT: C 100 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6799 (pt) outliers start: 13 outliers final: 9 residues processed: 87 average time/residue: 0.1946 time to fit residues: 21.8637 Evaluate side-chains 87 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 0.0060 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5588 Z= 0.153 Angle : 0.476 7.017 7534 Z= 0.243 Chirality : 0.037 0.147 882 Planarity : 0.004 0.048 901 Dihedral : 8.631 89.961 879 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.40 % Allowed : 11.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.33), residues: 678 helix: 2.82 (0.24), residues: 455 sheet: -1.32 (0.91), residues: 34 loop : -0.31 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 27 HIS 0.001 0.000 HIS B 86 PHE 0.010 0.001 PHE A 2 TYR 0.009 0.001 TYR C 94 ARG 0.003 0.000 ARG A 32 *********************** 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 89 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.598 Fit side-chains REVERT: A 4 LYS cc_start: 0.8204 (tppp) cc_final: 0.7620 (pttt) REVERT: B 118 GLN cc_start: 0.7405 (tp40) cc_final: 0.7140 (tp-100) REVERT: B 126 ASP cc_start: 0.8626 (m-30) cc_final: 0.8176 (m-30) REVERT: B 384 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8743 (t0) REVERT: B 392 ARG cc_start: 0.8308 (ttm170) cc_final: 0.8001 (ttp80) REVERT: C 72 ASP cc_start: 0.8122 (t70) cc_final: 0.7703 (t0) outliers start: 8 outliers final: 7 residues processed: 86 average time/residue: 0.2332 time to fit residues: 25.3424 Evaluate side-chains 88 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 384 ASN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 86 LYS 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 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 ASN C 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5588 Z= 0.269 Angle : 0.528 7.773 7534 Z= 0.269 Chirality : 0.039 0.157 882 Planarity : 0.005 0.048 901 Dihedral : 8.787 89.044 879 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.93 % Allowed : 11.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.33), residues: 678 helix: 2.69 (0.24), residues: 456 sheet: -1.35 (0.91), residues: 34 loop : -0.47 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 33 HIS 0.004 0.001 HIS B 86 PHE 0.011 0.001 PHE B 248 TYR 0.011 0.001 TYR C 94 ARG 0.002 0.000 ARG B 75 *********************** 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 88 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.664 Fit side-chains REVERT: A 4 LYS cc_start: 0.8235 (tppp) cc_final: 0.7711 (pttt) REVERT: B 118 GLN cc_start: 0.7493 (tp40) cc_final: 0.7217 (tp-100) REVERT: B 126 ASP cc_start: 0.8681 (m-30) cc_final: 0.8248 (m-30) REVERT: B 392 ARG cc_start: 0.8305 (ttm170) cc_final: 0.7943 (ttp80) REVERT: C 72 ASP cc_start: 0.8143 (t70) cc_final: 0.7723 (t0) REVERT: C 100 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6812 (pt) outliers start: 11 outliers final: 9 residues processed: 84 average time/residue: 0.1970 time to fit residues: 21.2945 Evaluate side-chains 86 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 0.0050 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 0.029 5588 Z= 0.173 Angle : 0.486 7.147 7534 Z= 0.248 Chirality : 0.037 0.144 882 Planarity : 0.004 0.048 901 Dihedral : 8.622 89.922 879 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.58 % Allowed : 11.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.33), residues: 678 helix: 2.79 (0.24), residues: 456 sheet: -1.38 (0.92), residues: 34 loop : -0.48 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 27 HIS 0.002 0.000 HIS B 86 PHE 0.010 0.001 PHE A 2 TYR 0.010 0.001 TYR C 94 ARG 0.003 0.000 ARG A 32 *********************** 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 89 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.680 Fit side-chains REVERT: A 4 LYS cc_start: 0.8223 (tppp) cc_final: 0.7683 (pttt) REVERT: B 118 GLN cc_start: 0.7428 (tp40) cc_final: 0.7162 (tp-100) REVERT: B 126 ASP cc_start: 0.8607 (m-30) cc_final: 0.8163 (m-30) REVERT: B 392 ARG cc_start: 0.8290 (ttm170) cc_final: 0.7927 (ttp80) REVERT: C 46 GLU cc_start: 0.8141 (tt0) cc_final: 0.7704 (tt0) REVERT: C 72 ASP cc_start: 0.8127 (t70) cc_final: 0.7713 (t0) outliers start: 9 outliers final: 8 residues processed: 86 average time/residue: 0.2089 time to fit residues: 22.9299 Evaluate side-chains 87 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 C residue 56 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 86 LYS 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 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5588 Z= 0.159 Angle : 0.489 7.030 7534 Z= 0.248 Chirality : 0.037 0.144 882 Planarity : 0.004 0.048 901 Dihedral : 8.381 88.956 879 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.93 % Allowed : 11.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.33), residues: 678 helix: 2.85 (0.24), residues: 456 sheet: -1.43 (0.93), residues: 34 loop : -0.42 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 108 HIS 0.001 0.000 HIS B 388 PHE 0.009 0.001 PHE A 2 TYR 0.009 0.001 TYR C 94 ARG 0.003 0.000 ARG A 32 *********************** 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 89 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.623 Fit side-chains REVERT: A 4 LYS cc_start: 0.8222 (tppp) cc_final: 0.7677 (pttt) REVERT: B 118 GLN cc_start: 0.7414 (tp40) cc_final: 0.7157 (tp-100) REVERT: B 126 ASP cc_start: 0.8627 (m-30) cc_final: 0.8191 (m-30) REVERT: B 392 ARG cc_start: 0.8298 (ttm170) cc_final: 0.7989 (ttp80) REVERT: C 46 GLU cc_start: 0.8241 (tt0) cc_final: 0.7830 (tt0) REVERT: C 72 ASP cc_start: 0.8174 (t70) cc_final: 0.7763 (t0) REVERT: C 100 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6724 (pt) outliers start: 11 outliers final: 9 residues processed: 86 average time/residue: 0.2083 time to fit residues: 22.9741 Evaluate side-chains 87 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.0010 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.002 0.030 5588 Z= 0.150 Angle : 0.487 6.929 7534 Z= 0.248 Chirality : 0.037 0.142 882 Planarity : 0.004 0.048 901 Dihedral : 8.199 88.158 879 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.93 % Allowed : 11.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.33), residues: 678 helix: 2.83 (0.24), residues: 459 sheet: -1.43 (0.93), residues: 34 loop : -0.50 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 27 HIS 0.001 0.000 HIS B 86 PHE 0.009 0.001 PHE A 2 TYR 0.009 0.001 TYR C 94 ARG 0.003 0.000 ARG A 32 ********************** 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 89 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.649 Fit side-chains REVERT: A 4 LYS cc_start: 0.8217 (tppp) cc_final: 0.7669 (pttt) REVERT: B 118 GLN cc_start: 0.7415 (tp40) cc_final: 0.7175 (tp-100) REVERT: B 126 ASP cc_start: 0.8620 (m-30) cc_final: 0.8183 (m-30) REVERT: B 392 ARG cc_start: 0.8300 (ttm170) cc_final: 0.7987 (ttp80) REVERT: C 46 GLU cc_start: 0.8224 (tt0) cc_final: 0.7838 (tt0) REVERT: C 72 ASP cc_start: 0.8183 (t70) cc_final: 0.7782 (t0) REVERT: C 100 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6735 (pt) outliers start: 11 outliers final: 9 residues processed: 87 average time/residue: 0.2056 time to fit residues: 22.8682 Evaluate side-chains 88 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.089811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.074887 restraints weight = 10709.545| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.64 r_work: 0.2932 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 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 = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5588 Z= 0.166 Angle : 0.495 7.024 7534 Z= 0.252 Chirality : 0.037 0.142 882 Planarity : 0.004 0.047 901 Dihedral : 8.127 87.937 879 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.75 % Allowed : 11.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.33), residues: 678 helix: 2.82 (0.24), residues: 459 sheet: -1.45 (0.91), residues: 34 loop : -0.50 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 27 HIS 0.001 0.000 HIS B 388 PHE 0.009 0.001 PHE A 2 TYR 0.009 0.001 TYR C 94 ARG 0.003 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1454.35 seconds wall clock time: 29 minutes 19.51 seconds (1759.51 seconds total)