Starting phenix.real_space_refine on Wed Feb 12 14:36:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7spa_25370/02_2025/7spa_25370.cif Found real_map, /net/cci-nas-00/data/ceres_data/7spa_25370/02_2025/7spa_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_25370/02_2025/7spa_25370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7spa_25370/02_2025/7spa_25370.map" model { file = "/net/cci-nas-00/data/ceres_data/7spa_25370/02_2025/7spa_25370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7spa_25370/02_2025/7spa_25370.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.85, per 1000 atoms: 0.64 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: 1.54 Conformation dependent library (CDL) restraints added in 821.0 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: 0.61 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: 1.58 Time building geometry restraints manager: 1.75 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.780 Find NCS groups from input model: 0.050 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:10.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 28.300 ------------------------------------------------------------------------------- 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 6166 Z= 0.275 Angle : 0.574 13.143 8357 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.005 0.000 TRP C 116 HIS 0.000 0.000 HIS A 174 PHE 0.004 0.001 PHE A 252 TYR 0.008 0.001 TYR A 299 ARG 0.002 0.000 ARG A 247 *********************** 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 : 0.690 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 1.1893 time to fit residues: 160.7418 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 : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.102613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085642 restraints weight = 12775.332| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.15 r_work: 0.3178 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6166 Z= 0.348 Angle : 0.671 6.180 8357 Z= 0.363 Chirality : 0.046 0.174 908 Planarity : 0.005 0.044 1028 Dihedral : 7.781 72.973 966 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.79 % Favored : 98.07 % Rotamer: Outliers : 2.87 % Allowed : 10.67 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.31), residues: 725 helix: 1.84 (0.29), residues: 321 sheet: 1.37 (0.44), residues: 143 loop : -0.69 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 262 HIS 0.004 0.002 HIS A 360 PHE 0.026 0.003 PHE A 321 TYR 0.024 0.002 TYR A 377 ARG 0.007 0.001 ARG B 98 *********************** 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 115 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.679 Fit side-chains REVERT: B 82 MET cc_start: 0.7313 (mtm) cc_final: 0.6814 (mtm) REVERT: B 83 ASP cc_start: 0.7079 (m-30) cc_final: 0.6339 (m-30) REVERT: C 80 LEU cc_start: 0.8944 (tt) cc_final: 0.8710 (tp) REVERT: C 115 TYR cc_start: 0.8443 (m-80) cc_final: 0.8204 (m-10) REVERT: A 151 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8340 (mt-10) REVERT: A 230 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: A 253 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7554 (m110) REVERT: A 254 VAL cc_start: 0.8841 (m) cc_final: 0.8573 (t) REVERT: A 255 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: A 303 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7548 (mmt-90) REVERT: A 311 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8160 (mtp) REVERT: A 379 PHE cc_start: 0.7600 (t80) cc_final: 0.7180 (t80) REVERT: A 382 MET cc_start: 0.8673 (mmm) cc_final: 0.8354 (mmm) REVERT: A 519 VAL cc_start: 0.9275 (t) cc_final: 0.9073 (t) outliers start: 18 outliers final: 5 residues processed: 109 average time/residue: 1.1885 time to fit residues: 135.8565 Evaluate side-chains 89 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 303 ARG Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 518 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.102334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.085513 restraints weight = 12948.013| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.15 r_work: 0.3173 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6166 Z= 0.190 Angle : 0.520 6.425 8357 Z= 0.283 Chirality : 0.042 0.187 908 Planarity : 0.003 0.042 1028 Dihedral : 6.983 70.594 966 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.52 % Rotamer: Outliers : 2.87 % Allowed : 15.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.31), residues: 725 helix: 1.91 (0.29), residues: 322 sheet: 1.47 (0.44), residues: 142 loop : -0.68 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 262 HIS 0.003 0.001 HIS A 174 PHE 0.016 0.001 PHE A 520 TYR 0.014 0.001 TYR A 377 ARG 0.004 0.001 ARG A 395 *********************** 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 105 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.693 Fit side-chains REVERT: A 253 ASN cc_start: 0.8449 (m110) cc_final: 0.8201 (m110) REVERT: A 254 VAL cc_start: 0.8795 (m) cc_final: 0.8518 (t) REVERT: A 311 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8067 (mtp) outliers start: 18 outliers final: 10 residues processed: 98 average time/residue: 1.1730 time to fit residues: 121.0556 Evaluate side-chains 90 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain C residue 1 GLN 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.097931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.081475 restraints weight = 13031.490| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.09 r_work: 0.3098 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6166 Z= 0.287 Angle : 0.597 6.657 8357 Z= 0.323 Chirality : 0.044 0.184 908 Planarity : 0.004 0.038 1028 Dihedral : 7.091 70.532 966 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.52 % Rotamer: Outliers : 3.98 % Allowed : 15.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.31), residues: 725 helix: 1.88 (0.29), residues: 317 sheet: 1.29 (0.43), residues: 151 loop : -0.62 (0.35), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 262 HIS 0.003 0.002 HIS A 195 PHE 0.020 0.002 PHE A 379 TYR 0.017 0.002 TYR C 115 ARG 0.007 0.001 ARG A 303 *********************** 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 114 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.658 Fit side-chains REVERT: A 254 VAL cc_start: 0.8962 (m) cc_final: 0.8654 (t) REVERT: A 311 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8042 (mtp) REVERT: A 346 TRP cc_start: 0.7352 (t60) cc_final: 0.7149 (t60) REVERT: A 349 GLU cc_start: 0.5379 (OUTLIER) cc_final: 0.5056 (mm-30) REVERT: A 446 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6744 (ppp) outliers start: 25 outliers final: 11 residues processed: 103 average time/residue: 1.0905 time to fit residues: 118.4661 Evaluate side-chains 93 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 380 LEU Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 487 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.099391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.082958 restraints weight = 12916.886| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.11 r_work: 0.3136 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6166 Z= 0.177 Angle : 0.537 6.861 8357 Z= 0.288 Chirality : 0.042 0.186 908 Planarity : 0.003 0.048 1028 Dihedral : 6.737 68.051 966 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.21 % Favored : 97.66 % Rotamer: Outliers : 2.39 % Allowed : 16.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.31), residues: 725 helix: 2.02 (0.29), residues: 314 sheet: 1.51 (0.44), residues: 141 loop : -0.73 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 262 HIS 0.002 0.001 HIS A 174 PHE 0.022 0.001 PHE A 447 TYR 0.012 0.001 TYR A 414 ARG 0.006 0.000 ARG A 303 *********************** 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 104 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.637 Fit side-chains REVERT: C 46 GLU cc_start: 0.8109 (pm20) cc_final: 0.7840 (mp0) REVERT: C 72 ASP cc_start: 0.5866 (p0) cc_final: 0.5603 (p0) REVERT: C 75 ARG cc_start: 0.8589 (mpp80) cc_final: 0.8226 (mpp80) REVERT: A 254 VAL cc_start: 0.8910 (m) cc_final: 0.8572 (t) REVERT: A 311 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7971 (mtp) REVERT: A 382 MET cc_start: 0.8880 (mmm) cc_final: 0.8623 (mmm) REVERT: A 446 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6747 (ppp) outliers start: 15 outliers final: 7 residues processed: 95 average time/residue: 1.1494 time to fit residues: 115.0316 Evaluate side-chains 94 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain C residue 68 THR 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 387 TYR Chi-restraints excluded: chain A residue 446 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.0020 chunk 12 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.099797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.083682 restraints weight = 12847.467| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.07 r_work: 0.3141 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6166 Z= 0.166 Angle : 0.528 7.128 8357 Z= 0.283 Chirality : 0.042 0.233 908 Planarity : 0.003 0.031 1028 Dihedral : 6.563 67.494 966 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 2.71 % Allowed : 17.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.31), residues: 725 helix: 1.99 (0.30), residues: 315 sheet: 1.51 (0.44), residues: 139 loop : -0.78 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 262 HIS 0.002 0.001 HIS A 360 PHE 0.025 0.001 PHE A 447 TYR 0.012 0.001 TYR A 414 ARG 0.005 0.000 ARG A 303 *********************** 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 103 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: C 46 GLU cc_start: 0.8123 (pm20) cc_final: 0.7882 (mp0) REVERT: A 46 TYR cc_start: 0.6138 (OUTLIER) cc_final: 0.4601 (t80) REVERT: A 254 VAL cc_start: 0.8907 (m) cc_final: 0.8569 (t) REVERT: A 266 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7429 (tp-100) REVERT: A 303 ARG cc_start: 0.7803 (tpp-160) cc_final: 0.7602 (tpp-160) REVERT: A 311 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7967 (mtp) REVERT: A 382 MET cc_start: 0.8895 (mmm) cc_final: 0.8666 (mmm) REVERT: A 390 ILE cc_start: 0.8343 (pp) cc_final: 0.8140 (mp) REVERT: A 446 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6705 (ppp) outliers start: 17 outliers final: 8 residues processed: 95 average time/residue: 1.1018 time to fit residues: 110.4435 Evaluate side-chains 93 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 255 GLU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 338 GLN 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 34 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 22 optimal weight: 0.0870 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.099787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.082735 restraints weight = 12952.946| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.21 r_work: 0.3110 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6166 Z= 0.151 Angle : 0.515 7.399 8357 Z= 0.276 Chirality : 0.041 0.220 908 Planarity : 0.003 0.030 1028 Dihedral : 6.386 66.154 966 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 2.39 % Allowed : 17.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.31), residues: 725 helix: 1.93 (0.30), residues: 318 sheet: 1.62 (0.44), residues: 139 loop : -0.78 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 262 HIS 0.002 0.001 HIS A 360 PHE 0.026 0.001 PHE A 447 TYR 0.011 0.001 TYR A 414 ARG 0.004 0.000 ARG A 303 *********************** 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 101 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.703 Fit side-chains REVERT: B 13 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7653 (mm-40) REVERT: C 46 GLU cc_start: 0.8084 (pm20) cc_final: 0.7829 (mp0) REVERT: C 82 MET cc_start: 0.8056 (mpp) cc_final: 0.7748 (mtm) REVERT: A 46 TYR cc_start: 0.6248 (OUTLIER) cc_final: 0.4714 (t80) REVERT: A 254 VAL cc_start: 0.8887 (m) cc_final: 0.8551 (t) REVERT: A 311 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8003 (mtp) REVERT: A 446 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6649 (ppp) outliers start: 15 outliers final: 7 residues processed: 94 average time/residue: 1.1271 time to fit residues: 111.7941 Evaluate side-chains 91 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 255 GLU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 446 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.097549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.081185 restraints weight = 13004.887| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.10 r_work: 0.3104 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6166 Z= 0.234 Angle : 0.562 7.635 8357 Z= 0.301 Chirality : 0.042 0.222 908 Planarity : 0.004 0.036 1028 Dihedral : 6.597 66.158 966 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 2.07 % Allowed : 17.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.31), residues: 725 helix: 1.90 (0.29), residues: 315 sheet: 1.36 (0.43), residues: 148 loop : -0.71 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 262 HIS 0.003 0.001 HIS A 360 PHE 0.026 0.001 PHE A 447 TYR 0.014 0.001 TYR C 115 ARG 0.006 0.001 ARG A 303 *********************** 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 93 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.7223 (mp10) cc_final: 0.6952 (mm110) REVERT: B 13 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7670 (mm-40) REVERT: B 86 LYS cc_start: 0.8269 (mtpm) cc_final: 0.7978 (mtmm) REVERT: C 46 GLU cc_start: 0.8119 (pm20) cc_final: 0.7856 (mp0) REVERT: A 46 TYR cc_start: 0.6016 (OUTLIER) cc_final: 0.4559 (t80) REVERT: A 254 VAL cc_start: 0.8986 (m) cc_final: 0.8660 (t) REVERT: A 311 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8010 (mtp) REVERT: A 446 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6742 (ppp) outliers start: 13 outliers final: 9 residues processed: 89 average time/residue: 1.1690 time to fit residues: 109.4921 Evaluate side-chains 89 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 446 MET Chi-restraints excluded: chain A residue 487 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 55 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.098426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.081532 restraints weight = 12942.900| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.17 r_work: 0.3082 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6166 Z= 0.176 Angle : 0.540 7.604 8357 Z= 0.288 Chirality : 0.041 0.215 908 Planarity : 0.004 0.055 1028 Dihedral : 6.483 65.089 966 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 2.23 % Allowed : 18.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.31), residues: 725 helix: 1.97 (0.30), residues: 314 sheet: 1.55 (0.45), residues: 139 loop : -0.80 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 262 HIS 0.002 0.001 HIS A 360 PHE 0.027 0.001 PHE A 447 TYR 0.012 0.001 TYR A 414 ARG 0.011 0.001 ARG A 303 *********************** 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 97 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7577 (tt) REVERT: B 66 ARG cc_start: 0.6956 (ttm110) cc_final: 0.6718 (mtp-110) REVERT: B 86 LYS cc_start: 0.8274 (mtpm) cc_final: 0.7983 (mttm) REVERT: C 46 GLU cc_start: 0.8131 (pm20) cc_final: 0.7846 (mp0) REVERT: A 46 TYR cc_start: 0.6034 (OUTLIER) cc_final: 0.4611 (t80) REVERT: A 254 VAL cc_start: 0.8967 (m) cc_final: 0.8616 (t) REVERT: A 311 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7984 (mtp) REVERT: A 446 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6734 (ppp) outliers start: 14 outliers final: 8 residues processed: 92 average time/residue: 1.2593 time to fit residues: 121.6591 Evaluate side-chains 91 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 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 446 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 0.0070 chunk 32 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.099018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.082057 restraints weight = 12978.493| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.17 r_work: 0.3091 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6166 Z= 0.165 Angle : 0.557 7.685 8357 Z= 0.297 Chirality : 0.041 0.212 908 Planarity : 0.004 0.043 1028 Dihedral : 6.411 64.630 966 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.76 % Favored : 97.10 % Rotamer: Outliers : 2.07 % Allowed : 19.27 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.31), residues: 725 helix: 1.98 (0.30), residues: 314 sheet: 1.59 (0.45), residues: 139 loop : -0.80 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 262 HIS 0.002 0.001 HIS A 360 PHE 0.028 0.001 PHE A 447 TYR 0.017 0.001 TYR C 115 ARG 0.012 0.000 ARG A 303 ********************** 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 96 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6818 (mm110) REVERT: B 18 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7585 (tt) REVERT: B 66 ARG cc_start: 0.7043 (ttm110) cc_final: 0.6733 (mtp-110) REVERT: B 86 LYS cc_start: 0.8248 (mtpm) cc_final: 0.7949 (mttm) REVERT: C 46 GLU cc_start: 0.8082 (pm20) cc_final: 0.7792 (mp0) REVERT: A 46 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.4611 (t80) REVERT: A 254 VAL cc_start: 0.8931 (m) cc_final: 0.8586 (t) REVERT: A 311 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8010 (mtp) REVERT: A 446 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6689 (ppp) outliers start: 13 outliers final: 7 residues processed: 91 average time/residue: 1.1544 time to fit residues: 110.7920 Evaluate side-chains 93 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 120 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 255 GLU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 446 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 33 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.099030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082057 restraints weight = 13080.085| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.19 r_work: 0.3089 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 6166 Z= 0.243 Angle : 1.009 59.200 8357 Z= 0.595 Chirality : 0.043 0.367 908 Planarity : 0.004 0.045 1028 Dihedral : 6.406 64.627 966 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.76 % Favored : 97.10 % Rotamer: Outliers : 2.55 % Allowed : 18.95 % Favored : 78.50 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.31), residues: 725 helix: 1.98 (0.30), residues: 314 sheet: 1.57 (0.45), residues: 139 loop : -0.80 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 262 HIS 0.002 0.001 HIS A 360 PHE 0.027 0.001 PHE A 447 TYR 0.016 0.001 TYR C 115 ARG 0.015 0.000 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4249.14 seconds wall clock time: 76 minutes 6.86 seconds (4566.86 seconds total)