Starting phenix.real_space_refine on Thu Jul 2 09:01:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7spa_25370/07_2026/7spa_25370.cif Found real_map, /net/cci-nas-00/data/ceres_data/7spa_25370/07_2026/7spa_25370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7spa_25370/07_2026/7spa_25370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7spa_25370/07_2026/7spa_25370.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7spa_25370/07_2026/7spa_25370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7spa_25370/07_2026/7spa_25370.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7spa_25370/07_2026/7spa_25370.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7spa_25370/07_2026/7spa_25370.cif" } resolution = 2.8 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= -0.001 sd= 0.807 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1816 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 35 5.16 5 C 3898 2.51 5 N 985 2.21 5 O 1098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 6017 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 944 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "C" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 918 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain breaks: 2 Chain: "A" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4054 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 483} Chain breaks: 1 Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'3PE': 1, 'NAG': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.37, per 1000 atoms: 0.23 Number of scatterers: 6017 At special positions: 0 Unit cell: (70.2, 73.44, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 1 15.00 O 1098 8.00 N 985 7.00 C 3898 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 337.2 milliseconds 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1366 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 47.8% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.682A pdb=" N THR B 31 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.575A pdb=" N TYR B 111 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'A' and resid 39 through 74 removed outlier: 3.598A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.895A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.558A pdb=" N THR A 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 209 through 221 Proline residue: A 217 - end of helix removed outlier: 3.744A pdb=" N CYS A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 4.005A pdb=" N ARG A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 removed outlier: 5.261A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.802A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 358 Processing helix chain 'A' and resid 364 through 392 removed outlier: 4.388A pdb=" N ALA A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 420 removed outlier: 3.533A pdb=" N GLN A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.714A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 449 removed outlier: 3.873A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 476 through 497 Processing helix chain 'A' and resid 504 through 534 Processing helix chain 'A' and resid 539 through 552 removed outlier: 3.540A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 8 removed outlier: 3.503A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 20 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 5.794A pdb=" N GLY B 10 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 5.794A pdb=" N GLY B 10 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 97 " --> pdb=" O TYR B 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.629A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.757A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 34 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 97 " --> pdb=" O TYR C 115 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR C 115 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 142 through 143 removed outlier: 8.760A pdb=" N ILE A 168 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 116 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE A 170 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N CYS A 118 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLN A 172 " --> pdb=" O CYS A 118 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE A 120 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 84 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG A 115 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 90 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 121 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA A 85 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE A 200 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE A 87 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU A 272 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.395A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 10.587A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 885 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: 0.91 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1038 1.33 - 1.45: 1756 1.45 - 1.57: 3300 1.57 - 1.69: 19 1.69 - 1.81: 53 Bond restraints: 6166 Sorted by residual: bond pdb=" CBD Y01 A 902 " pdb=" CBG Y01 A 902 " ideal model delta sigma weight residual 1.520 1.642 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" CAV Y01 A 902 " pdb=" CAZ Y01 A 902 " ideal model delta sigma weight residual 1.507 1.612 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" CAV Y01 A 902 " pdb=" CBC Y01 A 902 " ideal model delta sigma weight residual 1.523 1.618 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" CBF Y01 A 902 " pdb=" CBH Y01 A 902 " ideal model delta sigma weight residual 1.550 1.644 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" CAY Y01 A 902 " pdb=" OAW Y01 A 902 " ideal model delta sigma weight residual 1.332 1.426 -0.094 2.00e-02 2.50e+03 2.21e+01 ... (remaining 6161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 8292 2.63 - 5.26: 46 5.26 - 7.89: 15 7.89 - 10.51: 1 10.51 - 13.14: 3 Bond angle restraints: 8357 Sorted by residual: angle pdb=" CAM Y01 A 902 " pdb=" CAY Y01 A 902 " pdb=" OAW Y01 A 902 " ideal model delta sigma weight residual 111.19 124.33 -13.14 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CAZ Y01 A 902 " pdb=" CAV Y01 A 902 " pdb=" CBC Y01 A 902 " ideal model delta sigma weight residual 111.19 123.54 -12.35 3.00e+00 1.11e-01 1.69e+01 angle pdb=" CAI Y01 A 902 " pdb=" CAZ Y01 A 902 " pdb=" CAV Y01 A 902 " ideal model delta sigma weight residual 120.03 131.77 -11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CAV Y01 A 902 " pdb=" CAZ Y01 A 902 " pdb=" CBH Y01 A 902 " ideal model delta sigma weight residual 116.96 108.50 8.46 3.00e+00 1.11e-01 7.96e+00 angle pdb=" OAG Y01 A 902 " pdb=" CAY Y01 A 902 " pdb=" OAW Y01 A 902 " ideal model delta sigma weight residual 123.38 115.56 7.82 3.00e+00 1.11e-01 6.80e+00 ... (remaining 8352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 3289 16.92 - 33.84: 227 33.84 - 50.76: 33 50.76 - 67.68: 9 67.68 - 84.60: 4 Dihedral angle restraints: 3562 sinusoidal: 1416 harmonic: 2146 Sorted by residual: dihedral pdb=" CA TYR A 248 " pdb=" CB TYR A 248 " pdb=" CG TYR A 248 " pdb=" CD1 TYR A 248 " ideal model delta sinusoidal sigma weight residual 90.00 35.42 54.58 2 2.00e+01 2.50e-03 7.97e+00 dihedral pdb=" N LYS A 359 " pdb=" CA LYS A 359 " pdb=" CB LYS A 359 " pdb=" CG LYS A 359 " ideal model delta sinusoidal sigma weight residual -60.00 -103.05 43.05 3 1.50e+01 4.44e-03 7.73e+00 dihedral pdb=" CB MET A 481 " pdb=" CG MET A 481 " pdb=" SD MET A 481 " pdb=" CE MET A 481 " ideal model delta sinusoidal sigma weight residual 60.00 102.32 -42.32 3 1.50e+01 4.44e-03 7.59e+00 ... (remaining 3559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 845 0.080 - 0.159: 55 0.159 - 0.239: 4 0.239 - 0.318: 1 0.318 - 0.398: 3 Chirality restraints: 908 Sorted by residual: chirality pdb=" CBG Y01 A 902 " pdb=" CAQ Y01 A 902 " pdb=" CBD Y01 A 902 " pdb=" CBI Y01 A 902 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CBE Y01 A 902 " pdb=" CAP Y01 A 902 " pdb=" CBB Y01 A 902 " pdb=" CBI Y01 A 902 " both_signs ideal model delta sigma weight residual False 2.57 2.92 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CBI Y01 A 902 " pdb=" CAU Y01 A 902 " pdb=" CBE Y01 A 902 " pdb=" CBG Y01 A 902 " both_signs ideal model delta sigma weight residual False 2.94 2.62 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 905 not shown) Planarity restraints: 1028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 345 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C SER A 345 " 0.039 2.00e-02 2.50e+03 pdb=" O SER A 345 " -0.015 2.00e-02 2.50e+03 pdb=" N TRP A 346 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 319 " -0.017 5.00e-02 4.00e+02 2.59e-02 1.07e+00 pdb=" N PRO A 320 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 172 " -0.015 5.00e-02 4.00e+02 2.29e-02 8.36e-01 pdb=" N PRO A 173 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.013 5.00e-02 4.00e+02 ... (remaining 1025 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1506 2.80 - 3.32: 5630 3.32 - 3.85: 9730 3.85 - 4.37: 11034 4.37 - 4.90: 19557 Nonbonded interactions: 47457 Sorted by model distance: nonbonded pdb=" OG SER A 343 " pdb=" NH1 ARG A 442 " model vdw 2.275 3.120 nonbonded pdb=" OG SER C 51 " pdb=" O GLY C 56 " model vdw 2.298 3.040 nonbonded pdb=" NZ LYS A 391 " pdb=" O ASP A 393 " model vdw 2.333 3.120 nonbonded pdb=" O ASN A 80 " pdb=" ND2 ASN A 112 " model vdw 2.349 3.120 nonbonded pdb=" O TRP A 71 " pdb=" OH TYR A 216 " model vdw 2.350 3.040 ... (remaining 47452 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=1.00 max=1.00 mean=1.00 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.820 Find NCS groups from input model: 0.020 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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 0.122 6167 Z= 0.227 Angle : 0.574 13.143 8359 Z= 0.264 Chirality : 0.046 0.398 908 Planarity : 0.002 0.026 1028 Dihedral : 11.963 84.599 2193 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.31), residues: 725 helix: 2.14 (0.30), residues: 320 sheet: 2.01 (0.44), residues: 140 loop : -0.72 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 247 TYR 0.008 0.001 TYR A 299 PHE 0.004 0.001 PHE A 252 TRP 0.005 0.000 TRP C 116 HIS 0.000 0.000 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.23 ( 6166) covalent geometry : angle 0.57433 / 0.26 ( 8357) SS BOND : bond 0.00240 / 0.13 ( 1) SS BOND : angle 0.29492 / 0.16 ( 2) hydrogen bonds : bond 0.18969 / 12.31 ( 315) hydrogen bonds : angle 6.67523 / 4.46 ( 885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.253 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.5512 time to fit residues: 74.5232 Evaluate side-chains 81 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0040 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 ASN A 78 ASN A 253 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 GLN A 537 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.116887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.100368 restraints weight = 13126.667| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.24 r_work: 0.3423 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6167 Z= 0.130 Angle : 0.510 5.757 8359 Z= 0.275 Chirality : 0.041 0.196 908 Planarity : 0.003 0.037 1028 Dihedral : 5.093 52.340 872 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.75 % Allowed : 11.31 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.31), residues: 725 helix: 2.21 (0.29), residues: 320 sheet: 1.79 (0.45), residues: 138 loop : -0.70 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 395 TYR 0.018 0.001 TYR A 377 PHE 0.019 0.001 PHE A 379 TRP 0.015 0.001 TRP A 262 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 6166) covalent geometry : angle 0.51032 / 0.27 ( 8357) SS BOND : bond 0.00313 / 0.16 ( 1) SS BOND : angle 0.15075 / 0.08 ( 2) hydrogen bonds : bond 0.04479 / 2.88 ( 315) hydrogen bonds : angle 4.33682 / 2.95 ( 885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.243 Fit side-chains REVERT: B 44 GLU cc_start: 0.6052 (tm-30) cc_final: 0.5795 (tm-30) REVERT: C 82 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.7033 (mpp) REVERT: A 311 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7599 (ptm) REVERT: A 382 MET cc_start: 0.8460 (mmm) cc_final: 0.8163 (mmm) REVERT: A 481 MET cc_start: 0.8225 (mmm) cc_final: 0.8021 (mmm) outliers start: 11 outliers final: 4 residues processed: 98 average time/residue: 0.5579 time to fit residues: 57.4428 Evaluate side-chains 83 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 351 TRP Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 551 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 81 GLN A 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.081757 restraints weight = 13140.313| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.20 r_work: 0.3081 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6167 Z= 0.224 Angle : 0.632 5.753 8359 Z= 0.347 Chirality : 0.046 0.189 908 Planarity : 0.005 0.050 1028 Dihedral : 6.162 46.663 872 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.93 % Favored : 97.93 % Rotamer: Outliers : 4.46 % Allowed : 12.58 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.31), residues: 725 helix: 1.85 (0.29), residues: 321 sheet: 1.45 (0.43), residues: 151 loop : -0.59 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 256 TYR 0.016 0.002 TYR C 115 PHE 0.026 0.002 PHE A 321 TRP 0.023 0.002 TRP C 116 HIS 0.004 0.002 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 ( 6166) covalent geometry : angle 0.63196 / 0.35 ( 8357) SS BOND : bond 0.00109 / 0.06 ( 1) SS BOND : angle 0.33281 / 0.19 ( 2) hydrogen bonds : bond 0.06253 / 4.11 ( 315) hydrogen bonds : angle 4.53659 / 3.16 ( 885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: B 18 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7611 (mt) REVERT: B 72 ASP cc_start: 0.7536 (t70) cc_final: 0.7320 (t0) REVERT: B 82 MET cc_start: 0.7736 (mtm) cc_final: 0.7280 (mtm) REVERT: A 253 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8052 (m110) REVERT: A 255 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: A 311 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8112 (mtm) REVERT: A 379 PHE cc_start: 0.7704 (t80) cc_final: 0.7319 (t80) REVERT: A 382 MET cc_start: 0.8848 (mmm) cc_final: 0.8590 (mmm) REVERT: A 446 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6615 (ppp) REVERT: A 481 MET cc_start: 0.8633 (mmm) cc_final: 0.8419 (mmm) outliers start: 28 outliers final: 8 residues processed: 109 average time/residue: 0.5776 time to fit residues: 66.0746 Evaluate side-chains 90 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 446 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 52 optimal weight: 0.0010 chunk 5 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.099856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.083183 restraints weight = 12850.552| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.12 r_work: 0.3128 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6167 Z= 0.148 Angle : 0.533 7.071 8359 Z= 0.290 Chirality : 0.042 0.179 908 Planarity : 0.003 0.030 1028 Dihedral : 5.805 47.657 872 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.52 % Rotamer: Outliers : 3.50 % Allowed : 15.13 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.31), residues: 725 helix: 1.93 (0.29), residues: 317 sheet: 1.56 (0.45), residues: 142 loop : -0.72 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 66 TYR 0.012 0.001 TYR A 414 PHE 0.022 0.002 PHE A 447 TRP 0.011 0.001 TRP A 262 HIS 0.003 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6166) covalent geometry : angle 0.53323 / 0.29 ( 8357) SS BOND : bond 0.00391 / 0.21 ( 1) SS BOND : angle 0.32074 / 0.17 ( 2) hydrogen bonds : bond 0.05082 / 3.32 ( 315) hydrogen bonds : angle 4.16164 / 2.89 ( 885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.249 Fit side-chains REVERT: B 72 ASP cc_start: 0.7739 (t70) cc_final: 0.7524 (t0) REVERT: C 46 GLU cc_start: 0.8143 (pm20) cc_final: 0.7822 (pm20) REVERT: A 253 ASN cc_start: 0.8519 (m110) cc_final: 0.8267 (m110) REVERT: A 254 VAL cc_start: 0.8911 (m) cc_final: 0.8572 (t) REVERT: A 311 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8034 (mtp) REVERT: A 382 MET cc_start: 0.8865 (mmm) cc_final: 0.8553 (mmm) REVERT: A 481 MET cc_start: 0.8534 (mmm) cc_final: 0.8322 (mmm) outliers start: 22 outliers final: 8 residues processed: 104 average time/residue: 0.5139 time to fit residues: 56.2999 Evaluate side-chains 96 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 387 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.097777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.081379 restraints weight = 13130.018| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.08 r_work: 0.3115 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6167 Z= 0.154 Angle : 0.551 6.707 8359 Z= 0.299 Chirality : 0.042 0.181 908 Planarity : 0.003 0.030 1028 Dihedral : 5.839 47.755 872 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.07 % Favored : 97.79 % Rotamer: Outliers : 3.50 % Allowed : 14.33 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.31), residues: 725 helix: 1.90 (0.29), residues: 317 sheet: 1.49 (0.44), residues: 143 loop : -0.67 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 108 TYR 0.013 0.001 TYR A 414 PHE 0.021 0.001 PHE A 447 TRP 0.012 0.001 TRP A 262 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 6166) covalent geometry : angle 0.55110 / 0.30 ( 8357) SS BOND : bond 0.00283 / 0.15 ( 1) SS BOND : angle 0.29196 / 0.17 ( 2) hydrogen bonds : bond 0.05109 / 3.37 ( 315) hydrogen bonds : angle 4.15995 / 2.90 ( 885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: B 18 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7634 (mt) REVERT: B 72 ASP cc_start: 0.7747 (t70) cc_final: 0.7473 (t0) REVERT: C 46 GLU cc_start: 0.8182 (pm20) cc_final: 0.7935 (pm20) REVERT: C 77 THR cc_start: 0.8630 (m) cc_final: 0.8253 (t) REVERT: A 254 VAL cc_start: 0.8942 (m) cc_final: 0.8590 (t) REVERT: A 266 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7559 (tp-100) REVERT: A 311 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8027 (mtp) REVERT: A 382 MET cc_start: 0.8921 (mmm) cc_final: 0.8677 (mmm) REVERT: A 481 MET cc_start: 0.8587 (mmm) cc_final: 0.8380 (mmm) outliers start: 22 outliers final: 11 residues processed: 103 average time/residue: 0.5360 time to fit residues: 58.1059 Evaluate side-chains 95 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 487 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 3 GLN A 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.096473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.080179 restraints weight = 12861.555| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.03 r_work: 0.3084 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6167 Z= 0.179 Angle : 0.574 7.255 8359 Z= 0.312 Chirality : 0.044 0.248 908 Planarity : 0.004 0.034 1028 Dihedral : 6.065 46.446 872 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.52 % Rotamer: Outliers : 3.34 % Allowed : 15.13 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.31), residues: 725 helix: 1.80 (0.29), residues: 317 sheet: 1.18 (0.43), residues: 152 loop : -0.66 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 303 TYR 0.013 0.002 TYR A 387 PHE 0.022 0.001 PHE A 447 TRP 0.012 0.001 TRP A 262 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 6166) covalent geometry : angle 0.57421 / 0.31 ( 8357) SS BOND : bond 0.00299 / 0.16 ( 1) SS BOND : angle 0.31923 / 0.17 ( 2) hydrogen bonds : bond 0.05361 / 3.53 ( 315) hydrogen bonds : angle 4.21437 / 2.95 ( 885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.240 Fit side-chains REVERT: B 58 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.8233 (m-80) REVERT: B 72 ASP cc_start: 0.7849 (t70) cc_final: 0.7604 (t0) REVERT: C 46 GLU cc_start: 0.8187 (pm20) cc_final: 0.7924 (pm20) REVERT: C 77 THR cc_start: 0.8763 (m) cc_final: 0.8322 (t) REVERT: A 46 TYR cc_start: 0.6165 (OUTLIER) cc_final: 0.4729 (t80) REVERT: A 254 VAL cc_start: 0.8975 (m) cc_final: 0.8630 (t) REVERT: A 266 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7592 (tp-100) REVERT: A 303 ARG cc_start: 0.7847 (tpp-160) cc_final: 0.7333 (ttm170) REVERT: A 311 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.7998 (mtp) REVERT: A 382 MET cc_start: 0.8909 (mmm) cc_final: 0.8676 (mmm) REVERT: A 446 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6758 (ppp) REVERT: A 481 MET cc_start: 0.8599 (mmm) cc_final: 0.8395 (mmm) outliers start: 21 outliers final: 11 residues processed: 98 average time/residue: 0.5243 time to fit residues: 54.0294 Evaluate side-chains 97 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 487 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.093479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.077329 restraints weight = 13135.050| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.01 r_work: 0.3034 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 6167 Z= 0.287 Angle : 0.670 7.494 8359 Z= 0.364 Chirality : 0.048 0.249 908 Planarity : 0.005 0.059 1028 Dihedral : 6.802 51.629 872 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.90 % Favored : 96.97 % Rotamer: Outliers : 4.46 % Allowed : 15.13 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.92 (0.31), residues: 725 helix: 1.47 (0.29), residues: 321 sheet: 0.86 (0.42), residues: 162 loop : -0.67 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 75 TYR 0.018 0.002 TYR A 430 PHE 0.025 0.002 PHE A 447 TRP 0.015 0.002 TRP A 262 HIS 0.003 0.002 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.29 ( 6166) covalent geometry : angle 0.67016 / 0.36 ( 8357) SS BOND : bond 0.00151 / 0.08 ( 1) SS BOND : angle 0.22392 / 0.13 ( 2) hydrogen bonds : bond 0.06386 / 4.25 ( 315) hydrogen bonds : angle 4.50919 / 3.16 ( 885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.226 Fit side-chains REVERT: B 72 ASP cc_start: 0.7910 (t70) cc_final: 0.7626 (t0) REVERT: B 86 LYS cc_start: 0.8474 (mtpm) cc_final: 0.8266 (mtmm) REVERT: C 46 GLU cc_start: 0.8275 (pm20) cc_final: 0.8013 (pm20) REVERT: A 46 TYR cc_start: 0.6018 (OUTLIER) cc_final: 0.4590 (t80) REVERT: A 230 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8475 (tt0) REVERT: A 254 VAL cc_start: 0.9133 (m) cc_final: 0.8829 (t) REVERT: A 266 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7571 (tp-100) REVERT: A 303 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7460 (ttm110) REVERT: A 382 MET cc_start: 0.8919 (mmm) cc_final: 0.8691 (mmm) REVERT: A 446 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6769 (ppp) outliers start: 28 outliers final: 12 residues processed: 100 average time/residue: 0.5567 time to fit residues: 58.3106 Evaluate side-chains 99 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 530 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.096767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.080762 restraints weight = 13056.230| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.03 r_work: 0.3101 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6167 Z= 0.130 Angle : 0.564 6.621 8359 Z= 0.306 Chirality : 0.042 0.223 908 Planarity : 0.004 0.064 1028 Dihedral : 6.305 53.929 872 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 2.55 % Allowed : 17.52 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.31), residues: 725 helix: 1.72 (0.30), residues: 318 sheet: 1.19 (0.44), residues: 147 loop : -0.83 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 75 TYR 0.014 0.001 TYR A 387 PHE 0.027 0.001 PHE A 447 TRP 0.010 0.001 TRP A 262 HIS 0.002 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 6166) covalent geometry : angle 0.56413 / 0.31 ( 8357) SS BOND : bond 0.00421 / 0.22 ( 1) SS BOND : angle 0.44479 / 0.24 ( 2) hydrogen bonds : bond 0.04944 / 3.22 ( 315) hydrogen bonds : angle 4.22044 / 2.93 ( 885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.238 Fit side-chains REVERT: B 3 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6886 (mm110) REVERT: B 46 GLU cc_start: 0.7288 (pm20) cc_final: 0.6907 (pp20) REVERT: B 72 ASP cc_start: 0.7897 (t70) cc_final: 0.7594 (t0) REVERT: C 46 GLU cc_start: 0.8217 (pm20) cc_final: 0.7967 (pm20) REVERT: C 77 THR cc_start: 0.8675 (m) cc_final: 0.8351 (t) REVERT: A 46 TYR cc_start: 0.5964 (OUTLIER) cc_final: 0.4542 (t80) REVERT: A 254 VAL cc_start: 0.9031 (m) cc_final: 0.8692 (t) REVERT: A 266 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7561 (tp-100) REVERT: A 303 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7354 (ttm110) REVERT: A 311 MET cc_start: 0.8506 (ptp) cc_final: 0.8112 (mtp) REVERT: A 382 MET cc_start: 0.8906 (mmm) cc_final: 0.8649 (mmm) outliers start: 16 outliers final: 6 residues processed: 98 average time/residue: 0.5437 time to fit residues: 55.8313 Evaluate side-chains 87 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 338 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 63 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.097635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.081377 restraints weight = 13202.219| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.08 r_work: 0.3104 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6167 Z= 0.128 Angle : 0.577 8.575 8359 Z= 0.308 Chirality : 0.042 0.214 908 Planarity : 0.004 0.060 1028 Dihedral : 6.152 53.906 872 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.76 % Favored : 97.10 % Rotamer: Outliers : 1.91 % Allowed : 18.63 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.31), residues: 725 helix: 1.72 (0.30), residues: 319 sheet: 1.24 (0.44), residues: 145 loop : -0.91 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 75 TYR 0.012 0.001 TYR A 414 PHE 0.028 0.001 PHE A 447 TRP 0.010 0.001 TRP A 262 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 6166) covalent geometry : angle 0.57711 / 0.31 ( 8357) SS BOND : bond 0.00375 / 0.20 ( 1) SS BOND : angle 0.41679 / 0.22 ( 2) hydrogen bonds : bond 0.04790 / 3.11 ( 315) hydrogen bonds : angle 4.20760 / 2.92 ( 885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.146 Fit side-chains REVERT: B 46 GLU cc_start: 0.7259 (pm20) cc_final: 0.6894 (pp20) REVERT: C 46 GLU cc_start: 0.8197 (pm20) cc_final: 0.7947 (pm20) REVERT: C 77 THR cc_start: 0.8627 (m) cc_final: 0.8343 (t) REVERT: A 46 TYR cc_start: 0.5951 (OUTLIER) cc_final: 0.4549 (t80) REVERT: A 254 VAL cc_start: 0.9016 (m) cc_final: 0.8675 (t) REVERT: A 266 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7578 (tp-100) REVERT: A 303 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7368 (ttm170) REVERT: A 311 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8090 (mtp) REVERT: A 382 MET cc_start: 0.8915 (mmm) cc_final: 0.8652 (mmm) outliers start: 12 outliers final: 7 residues processed: 87 average time/residue: 0.4655 time to fit residues: 42.6268 Evaluate side-chains 88 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 338 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.096971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.081137 restraints weight = 13012.456| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.99 r_work: 0.3105 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6167 Z= 0.137 Angle : 0.577 8.623 8359 Z= 0.307 Chirality : 0.042 0.212 908 Planarity : 0.004 0.062 1028 Dihedral : 6.095 54.688 872 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 2.39 % Allowed : 17.99 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.31), residues: 725 helix: 1.73 (0.30), residues: 318 sheet: 1.11 (0.44), residues: 147 loop : -0.86 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 75 TYR 0.015 0.001 TYR A 387 PHE 0.028 0.001 PHE A 447 TRP 0.011 0.001 TRP A 262 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 6166) covalent geometry : angle 0.57684 / 0.31 ( 8357) SS BOND : bond 0.00363 / 0.19 ( 1) SS BOND : angle 0.41904 / 0.22 ( 2) hydrogen bonds : bond 0.04859 / 3.17 ( 315) hydrogen bonds : angle 4.18363 / 2.90 ( 885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.246 Fit side-chains REVERT: B 46 GLU cc_start: 0.7240 (pm20) cc_final: 0.6906 (pp20) REVERT: B 58 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: C 77 THR cc_start: 0.8654 (m) cc_final: 0.8386 (t) REVERT: C 82 MET cc_start: 0.8012 (mpp) cc_final: 0.7805 (mtm) REVERT: A 46 TYR cc_start: 0.5947 (OUTLIER) cc_final: 0.4546 (t80) REVERT: A 254 VAL cc_start: 0.8996 (m) cc_final: 0.8660 (t) REVERT: A 266 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7538 (tp-100) REVERT: A 303 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7462 (ttm170) REVERT: A 311 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8076 (mtp) REVERT: A 382 MET cc_start: 0.8859 (mmm) cc_final: 0.8595 (mmm) outliers start: 15 outliers final: 6 residues processed: 90 average time/residue: 0.4843 time to fit residues: 45.8905 Evaluate side-chains 86 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 338 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.097598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.081607 restraints weight = 13050.293| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.05 r_work: 0.3116 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6167 Z= 0.127 Angle : 0.580 8.522 8359 Z= 0.308 Chirality : 0.042 0.205 908 Planarity : 0.004 0.058 1028 Dihedral : 5.988 56.378 872 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 1.75 % Allowed : 19.27 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.31), residues: 725 helix: 1.74 (0.30), residues: 319 sheet: 1.22 (0.44), residues: 145 loop : -0.89 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 75 TYR 0.012 0.001 TYR A 414 PHE 0.028 0.001 PHE A 447 TRP 0.010 0.001 TRP A 262 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 6166) covalent geometry : angle 0.58020 / 0.31 ( 8357) SS BOND : bond 0.00381 / 0.20 ( 1) SS BOND : angle 0.43568 / 0.23 ( 2) hydrogen bonds : bond 0.04640 / 3.01 ( 315) hydrogen bonds : angle 4.11039 / 2.86 ( 885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2075.76 seconds wall clock time: 36 minutes 7.33 seconds (2167.33 seconds total)