Starting phenix.real_space_refine on Tue Mar 3 18:31:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7spa_25370/03_2026/7spa_25370.cif Found real_map, /net/cci-nas-00/data/ceres_data/7spa_25370/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7spa_25370/03_2026/7spa_25370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7spa_25370/03_2026/7spa_25370.map" model { file = "/net/cci-nas-00/data/ceres_data/7spa_25370/03_2026/7spa_25370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7spa_25370/03_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-5986/lib/python3.9/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: 1.80, per 1000 atoms: 0.30 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: 0.66 Conformation dependent library (CDL) restraints added in 228.2 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: 0.20 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: 1.01 Time building geometry restraints manager: 0.83 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: 3367 16.92 - 33.84: 236 33.84 - 50.76: 37 50.76 - 67.68: 11 67.68 - 84.60: 5 Dihedral angle restraints: 3656 sinusoidal: 1510 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 3653 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: 1.450 Set stop_for_unknowns flag: 0.010 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.010 Find NCS groups from input model: 0.030 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:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 12.248 84.599 2287 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 covalent geometry : bond 0.00447 ( 6166) covalent geometry : angle 0.57433 ( 8357) SS BOND : bond 0.00240 ( 1) SS BOND : angle 0.29492 ( 2) hydrogen bonds : bond 0.18969 ( 315) hydrogen bonds : angle 6.67523 ( 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 : 0.227 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.6072 time to fit residues: 81.7888 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 : 0.213 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 76 ASN A 78 ASN A 253 ASN 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 = 0.3812 r_free = 0.3812 target = 0.117913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.101481 restraints weight = 13145.546| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.24 r_work: 0.3439 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2175 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= 0.131 Angle : 0.510 5.750 8359 Z= 0.276 Chirality : 0.041 0.190 908 Planarity : 0.004 0.049 1028 Dihedral : 6.246 71.561 966 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.27 % Allowed : 11.46 % Favored : 87.26 % 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: 1.71 (0.31), residues: 725 helix: 2.25 (0.29), residues: 320 sheet: 1.87 (0.46), residues: 137 loop : -0.70 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 256 TYR 0.017 0.001 TYR A 377 PHE 0.020 0.001 PHE A 379 TRP 0.013 0.001 TRP A 262 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6166) covalent geometry : angle 0.51035 ( 8357) SS BOND : bond 0.00317 ( 1) SS BOND : angle 0.13842 ( 2) hydrogen bonds : bond 0.04397 ( 315) hydrogen bonds : angle 4.38252 ( 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 102 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.244 Fit side-chains REVERT: B 44 GLU cc_start: 0.6130 (tm-30) cc_final: 0.5876 (tm-30) REVERT: C 75 ARG cc_start: 0.7997 (mpp80) cc_final: 0.7659 (mpp80) REVERT: C 82 MET cc_start: 0.7224 (mpt) cc_final: 0.6965 (mpp) REVERT: A 230 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7991 (tm-30) outliers start: 8 outliers final: 3 residues processed: 99 average time/residue: 0.5777 time to fit residues: 59.8530 Evaluate side-chains 80 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 351 TRP Chi-restraints excluded: chain A residue 387 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 0.7980 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: 0.7980 chunk 4 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3507 r_free = 0.3507 target = 0.098933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.081809 restraints weight = 13160.021| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.23 r_work: 0.3083 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6167 Z= 0.233 Angle : 0.635 5.711 8359 Z= 0.349 Chirality : 0.046 0.181 908 Planarity : 0.005 0.049 1028 Dihedral : 7.185 73.021 966 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.79 % Favored : 98.07 % Rotamer: Outliers : 4.30 % Allowed : 13.06 % Favored : 82.64 % 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: 1.43 (0.31), residues: 725 helix: 1.86 (0.29), residues: 321 sheet: 1.44 (0.44), residues: 153 loop : -0.57 (0.35), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 303 TYR 0.016 0.002 TYR A 377 PHE 0.026 0.002 PHE A 321 TRP 0.024 0.002 TRP C 116 HIS 0.004 0.002 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 6166) covalent geometry : angle 0.63493 ( 8357) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.26479 ( 2) hydrogen bonds : bond 0.06217 ( 315) hydrogen bonds : angle 4.52830 ( 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 119 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: B 3 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7320 (mp10) REVERT: B 72 ASP cc_start: 0.7498 (t70) cc_final: 0.7253 (t0) REVERT: B 81 GLN cc_start: 0.8664 (tp-100) cc_final: 0.8456 (tp-100) REVERT: B 82 MET cc_start: 0.7636 (mtm) cc_final: 0.7283 (mtm) REVERT: C 2 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8760 (p) REVERT: A 230 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: A 253 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8016 (m110) REVERT: A 255 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8386 (mp0) REVERT: A 311 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8162 (mtp) REVERT: A 379 PHE cc_start: 0.7706 (t80) cc_final: 0.7313 (t80) REVERT: A 382 MET cc_start: 0.8831 (mmm) cc_final: 0.8552 (mmm) REVERT: A 446 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6628 (ppp) outliers start: 27 outliers final: 8 residues processed: 109 average time/residue: 0.6115 time to fit residues: 69.7346 Evaluate side-chains 91 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL 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 230 GLU 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: 4.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 52 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.0570 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.100307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083579 restraints weight = 12935.665| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.11 r_work: 0.3153 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6167 Z= 0.136 Angle : 0.522 6.922 8359 Z= 0.284 Chirality : 0.042 0.191 908 Planarity : 0.003 0.034 1028 Dihedral : 6.688 69.291 966 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.21 % Favored : 97.66 % Rotamer: Outliers : 4.30 % Allowed : 14.81 % Favored : 80.89 % 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: 1.44 (0.31), residues: 725 helix: 2.01 (0.29), residues: 315 sheet: 1.52 (0.45), residues: 143 loop : -0.67 (0.33), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 303 TYR 0.012 0.001 TYR A 377 PHE 0.021 0.001 PHE A 447 TRP 0.011 0.001 TRP A 262 HIS 0.003 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6166) covalent geometry : angle 0.52243 ( 8357) SS BOND : bond 0.00401 ( 1) SS BOND : angle 0.36177 ( 2) hydrogen bonds : bond 0.04945 ( 315) hydrogen bonds : angle 4.14274 ( 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: 27 poor density : 83 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: B 18 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7355 (mt) REVERT: B 58 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: B 72 ASP cc_start: 0.7582 (t70) cc_final: 0.7376 (t70) REVERT: C 46 GLU cc_start: 0.8107 (pm20) cc_final: 0.7779 (mp0) REVERT: A 253 ASN cc_start: 0.8365 (m110) cc_final: 0.8032 (m110) REVERT: A 303 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7528 (tpp-160) REVERT: A 311 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8049 (mtp) outliers start: 27 outliers final: 7 residues processed: 101 average time/residue: 0.6061 time to fit residues: 64.0401 Evaluate side-chains 85 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 68 THR 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 303 ARG 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: 3.9990 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN A 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.099731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.082886 restraints weight = 13155.971| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.17 r_work: 0.3135 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6167 Z= 0.139 Angle : 0.534 6.586 8359 Z= 0.290 Chirality : 0.042 0.208 908 Planarity : 0.003 0.036 1028 Dihedral : 6.619 69.016 966 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.93 % Favored : 97.93 % Rotamer: Outliers : 3.82 % Allowed : 15.61 % Favored : 80.57 % 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: 1.50 (0.31), residues: 725 helix: 2.07 (0.29), residues: 315 sheet: 1.68 (0.45), residues: 140 loop : -0.71 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 303 TYR 0.012 0.001 TYR A 414 PHE 0.023 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 covalent geometry : bond 0.00304 ( 6166) covalent geometry : angle 0.53449 ( 8357) SS BOND : bond 0.00284 ( 1) SS BOND : angle 0.31166 ( 2) hydrogen bonds : bond 0.04907 ( 315) hydrogen bonds : angle 4.08913 ( 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 109 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: B 58 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.8087 (m-80) REVERT: B 72 ASP cc_start: 0.7615 (t70) cc_final: 0.7341 (t70) REVERT: C 46 GLU cc_start: 0.8004 (pm20) cc_final: 0.7783 (mp0) REVERT: A 253 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8201 (m110) REVERT: A 254 VAL cc_start: 0.8896 (m) cc_final: 0.8532 (t) REVERT: A 311 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7974 (mtp) outliers start: 24 outliers final: 8 residues processed: 97 average time/residue: 0.5519 time to fit residues: 56.2439 Evaluate side-chains 92 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR 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 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: 6.9990 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.097271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.081173 restraints weight = 12842.907| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.99 r_work: 0.3107 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6167 Z= 0.169 Angle : 0.565 7.475 8359 Z= 0.307 Chirality : 0.043 0.225 908 Planarity : 0.004 0.043 1028 Dihedral : 6.797 67.604 966 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.21 % Favored : 97.66 % Rotamer: Outliers : 3.66 % Allowed : 15.76 % Favored : 80.57 % 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: 1.31 (0.31), residues: 725 helix: 1.85 (0.29), residues: 317 sheet: 1.24 (0.44), residues: 152 loop : -0.61 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 303 TYR 0.013 0.002 TYR A 528 PHE 0.023 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 covalent geometry : bond 0.00379 ( 6166) covalent geometry : angle 0.56541 ( 8357) SS BOND : bond 0.00290 ( 1) SS BOND : angle 0.28811 ( 2) hydrogen bonds : bond 0.05284 ( 315) hydrogen bonds : angle 4.19242 ( 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 112 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7759 (mm-40) REVERT: B 58 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.8202 (m-80) REVERT: C 46 GLU cc_start: 0.8027 (pm20) cc_final: 0.7780 (mp0) REVERT: C 77 THR cc_start: 0.8654 (m) cc_final: 0.8239 (t) REVERT: A 46 TYR cc_start: 0.6138 (OUTLIER) cc_final: 0.4669 (t80) REVERT: A 254 VAL cc_start: 0.8943 (m) cc_final: 0.8605 (t) REVERT: A 266 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7573 (tp-100) REVERT: A 311 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8036 (mtp) outliers start: 23 outliers final: 13 residues processed: 102 average time/residue: 0.5807 time to fit residues: 62.2322 Evaluate side-chains 98 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 2 VAL 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 349 GLU Chi-restraints excluded: chain A residue 387 TYR 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: 0.0470 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN A 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.098948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.082803 restraints weight = 13055.212| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.02 r_work: 0.3136 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.5345 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= 0.118 Angle : 0.533 7.270 8359 Z= 0.288 Chirality : 0.042 0.215 908 Planarity : 0.004 0.045 1028 Dihedral : 6.556 66.352 966 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 2.87 % Allowed : 16.56 % Favored : 80.57 % 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: 1.33 (0.31), residues: 725 helix: 1.90 (0.30), residues: 318 sheet: 1.38 (0.43), residues: 149 loop : -0.73 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 75 TYR 0.012 0.001 TYR A 387 PHE 0.025 0.001 PHE A 447 TRP 0.009 0.001 TRP A 262 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6166) covalent geometry : angle 0.53325 ( 8357) SS BOND : bond 0.00382 ( 1) SS BOND : angle 0.41342 ( 2) hydrogen bonds : bond 0.04581 ( 315) hydrogen bonds : angle 4.04203 ( 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 100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: B 58 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.8161 (m-80) REVERT: C 46 GLU cc_start: 0.7936 (pm20) cc_final: 0.7729 (mp0) REVERT: A 46 TYR cc_start: 0.6027 (OUTLIER) cc_final: 0.4581 (t80) REVERT: A 254 VAL cc_start: 0.8902 (m) cc_final: 0.8576 (t) REVERT: A 266 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7476 (tp-100) REVERT: A 311 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7976 (mtp) outliers start: 18 outliers final: 8 residues processed: 95 average time/residue: 0.5593 time to fit residues: 55.7762 Evaluate side-chains 87 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 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 255 GLU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 349 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.079812 restraints weight = 13068.453| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.95 r_work: 0.3072 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6167 Z= 0.224 Angle : 0.633 7.622 8359 Z= 0.341 Chirality : 0.045 0.238 908 Planarity : 0.005 0.073 1028 Dihedral : 6.996 67.159 966 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 2.87 % Allowed : 16.88 % Favored : 80.25 % 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: 1.11 (0.31), residues: 725 helix: 1.73 (0.29), residues: 317 sheet: 0.95 (0.42), residues: 160 loop : -0.68 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 75 TYR 0.016 0.002 TYR A 430 PHE 0.026 0.002 PHE A 447 TRP 0.013 0.001 TRP A 262 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 6166) covalent geometry : angle 0.63315 ( 8357) SS BOND : bond 0.00179 ( 1) SS BOND : angle 0.33246 ( 2) hydrogen bonds : bond 0.05714 ( 315) hydrogen bonds : angle 4.27528 ( 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 94 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: B 58 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: C 46 GLU cc_start: 0.8122 (pm20) cc_final: 0.7803 (mp0) REVERT: C 77 THR cc_start: 0.8552 (m) cc_final: 0.8242 (t) REVERT: A 46 TYR cc_start: 0.6081 (OUTLIER) cc_final: 0.4620 (t80) REVERT: A 254 VAL cc_start: 0.9020 (m) cc_final: 0.8715 (t) REVERT: A 266 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7633 (tp-100) REVERT: A 303 ARG cc_start: 0.7782 (tpp-160) cc_final: 0.7348 (ttm170) REVERT: A 311 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8028 (mtp) REVERT: A 349 GLU cc_start: 0.5773 (OUTLIER) cc_final: 0.4920 (mp0) outliers start: 18 outliers final: 9 residues processed: 88 average time/residue: 0.5273 time to fit residues: 48.7917 Evaluate side-chains 88 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 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 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 349 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.081493 restraints weight = 13119.729| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.04 r_work: 0.3114 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6167 Z= 0.132 Angle : 0.555 8.260 8359 Z= 0.299 Chirality : 0.042 0.221 908 Planarity : 0.004 0.061 1028 Dihedral : 6.699 65.512 966 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 3.03 % Allowed : 16.56 % 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: 1.17 (0.31), residues: 725 helix: 1.82 (0.29), residues: 318 sheet: 1.15 (0.43), residues: 149 loop : -0.78 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 75 TYR 0.012 0.001 TYR A 414 PHE 0.027 0.001 PHE A 447 TRP 0.009 0.001 TRP A 262 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6166) covalent geometry : angle 0.55510 ( 8357) SS BOND : bond 0.00346 ( 1) SS BOND : angle 0.43253 ( 2) hydrogen bonds : bond 0.04783 ( 315) hydrogen bonds : angle 4.11288 ( 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 95 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 46 GLU cc_start: 0.7389 (pm20) cc_final: 0.6908 (pp20) REVERT: B 58 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.8234 (m-80) REVERT: C 46 GLU cc_start: 0.8101 (pm20) cc_final: 0.7767 (mp0) REVERT: A 46 TYR cc_start: 0.6009 (OUTLIER) cc_final: 0.4540 (t80) REVERT: A 254 VAL cc_start: 0.8992 (m) cc_final: 0.8668 (t) REVERT: A 266 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7487 (tp-100) REVERT: A 311 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7954 (mtp) REVERT: A 349 GLU cc_start: 0.5341 (OUTLIER) cc_final: 0.4990 (mm-30) outliers start: 19 outliers final: 9 residues processed: 88 average time/residue: 0.5518 time to fit residues: 50.9892 Evaluate side-chains 88 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 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 255 GLU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 487 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.097942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.081966 restraints weight = 12971.999| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.00 r_work: 0.3113 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.5568 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= 0.132 Angle : 0.556 8.415 8359 Z= 0.299 Chirality : 0.042 0.220 908 Planarity : 0.004 0.058 1028 Dihedral : 6.637 65.182 966 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 2.23 % Allowed : 17.52 % Favored : 80.25 % 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: 1.93 (0.29), residues: 314 sheet: 1.15 (0.43), residues: 149 loop : -0.79 (0.35), residues: 262 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 covalent geometry : bond 0.00289 ( 6166) covalent geometry : angle 0.55564 ( 8357) SS BOND : bond 0.00323 ( 1) SS BOND : angle 0.43446 ( 2) hydrogen bonds : bond 0.04759 ( 315) hydrogen bonds : angle 4.08652 ( 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 89 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: B 46 GLU cc_start: 0.7381 (pm20) cc_final: 0.6940 (pp20) REVERT: B 58 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8246 (m-80) REVERT: C 46 GLU cc_start: 0.8065 (pm20) cc_final: 0.7773 (mp0) REVERT: A 46 TYR cc_start: 0.6011 (OUTLIER) cc_final: 0.4547 (t80) REVERT: A 254 VAL cc_start: 0.8974 (m) cc_final: 0.8655 (t) REVERT: A 266 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7568 (tp-100) REVERT: A 311 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7950 (mtp) outliers start: 14 outliers final: 9 residues processed: 84 average time/residue: 0.5342 time to fit residues: 47.2627 Evaluate side-chains 87 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 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 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 255 GLU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 487 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.096929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.080829 restraints weight = 12996.012| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.99 r_work: 0.3097 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.5653 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= 0.151 Angle : 0.571 8.395 8359 Z= 0.307 Chirality : 0.043 0.223 908 Planarity : 0.004 0.059 1028 Dihedral : 6.681 64.726 966 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 2.39 % Allowed : 17.36 % Favored : 80.25 % 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: 1.16 (0.31), residues: 725 helix: 1.86 (0.29), residues: 315 sheet: 1.07 (0.43), residues: 149 loop : -0.77 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 75 TYR 0.013 0.001 TYR A 414 PHE 0.028 0.001 PHE A 447 TRP 0.012 0.001 TRP A 262 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6166) covalent geometry : angle 0.57067 ( 8357) SS BOND : bond 0.00280 ( 1) SS BOND : angle 0.43408 ( 2) hydrogen bonds : bond 0.04981 ( 315) hydrogen bonds : angle 4.10814 ( 885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2210.26 seconds wall clock time: 38 minutes 21.26 seconds (2301.26 seconds total)