Starting phenix.real_space_refine on Fri Dec 27 06:40:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r68_18948/12_2024/8r68_18948.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r68_18948/12_2024/8r68_18948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r68_18948/12_2024/8r68_18948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r68_18948/12_2024/8r68_18948.map" model { file = "/net/cci-nas-00/data/ceres_data/8r68_18948/12_2024/8r68_18948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r68_18948/12_2024/8r68_18948.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2082 2.51 5 N 579 2.21 5 O 566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3241 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3241 Classifications: {'peptide': 391} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 374} Chain breaks: 6 Time building chain proxies: 2.87, per 1000 atoms: 0.89 Number of scatterers: 3241 At special positions: 0 Unit cell: (53.248, 59.904, 112.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 566 8.00 N 579 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.85 Conformation dependent library (CDL) restraints added in 515.9 milliseconds 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 49.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 60 through 65 removed outlier: 4.277A pdb=" N ARG A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.570A pdb=" N ASN A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 3.513A pdb=" N SER A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 159 removed outlier: 3.890A pdb=" N TYR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 194 removed outlier: 3.819A pdb=" N ARG A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 206 removed outlier: 3.658A pdb=" N GLU A 204 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS A 205 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 224 removed outlier: 3.691A pdb=" N PHE A 220 " --> pdb=" O TRP A 216 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 249 removed outlier: 3.542A pdb=" N SER A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 removed outlier: 4.197A pdb=" N ASP A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 261 " --> pdb=" O MET A 257 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY A 268 " --> pdb=" O TYR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.685A pdb=" N ALA A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N MET A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TRP A 312 " --> pdb=" O MET A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 324 removed outlier: 3.528A pdb=" N PHE A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 removed outlier: 4.150A pdb=" N TYR A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE A 342 " --> pdb=" O TYR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.758A pdb=" N TRP A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 359' Processing helix chain 'A' and resid 362 through 372 removed outlier: 3.545A pdb=" N VAL A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN A 372 " --> pdb=" O PHE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 468 Processing sheet with id=AA1, first strand: chain 'A' and resid 424 through 426 removed outlier: 8.932A pdb=" N SER A 377 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 351 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU A 379 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET A 408 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 441 " --> pdb=" O MET A 408 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 439 " --> pdb=" O ALA A 410 " (cutoff:3.500A) 101 hydrogen bonds defined for protein. 285 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: 1.02 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1044 1.34 - 1.45: 508 1.45 - 1.57: 1750 1.57 - 1.69: 0 1.69 - 1.80: 25 Bond restraints: 3327 Sorted by residual: bond pdb=" CA TRP A 312 " pdb=" CB TRP A 312 " ideal model delta sigma weight residual 1.537 1.524 0.013 1.38e-02 5.25e+03 8.67e-01 bond pdb=" CB ARG A 105 " pdb=" CG ARG A 105 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.39e-01 bond pdb=" CA ASP A 232 " pdb=" C ASP A 232 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.62e-01 bond pdb=" CB ASP A 386 " pdb=" CG ASP A 386 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.35e-01 bond pdb=" C ASP A 232 " pdb=" N PRO A 233 " ideal model delta sigma weight residual 1.334 1.352 -0.019 2.34e-02 1.83e+03 6.27e-01 ... (remaining 3322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 4275 1.25 - 2.49: 161 2.49 - 3.74: 40 3.74 - 4.98: 14 4.98 - 6.23: 5 Bond angle restraints: 4495 Sorted by residual: angle pdb=" N GLY A 311 " pdb=" CA GLY A 311 " pdb=" C GLY A 311 " ideal model delta sigma weight residual 115.31 111.52 3.79 1.24e+00 6.50e-01 9.36e+00 angle pdb=" CA ARG A 105 " pdb=" CB ARG A 105 " pdb=" CG ARG A 105 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.63e+00 angle pdb=" CA GLN A 234 " pdb=" CB GLN A 234 " pdb=" CG GLN A 234 " ideal model delta sigma weight residual 114.10 118.98 -4.88 2.00e+00 2.50e-01 5.96e+00 angle pdb=" N ASP A 271 " pdb=" CA ASP A 271 " pdb=" C ASP A 271 " ideal model delta sigma weight residual 110.44 113.34 -2.90 1.20e+00 6.94e-01 5.85e+00 angle pdb=" CA GLU A 448 " pdb=" CB GLU A 448 " pdb=" CG GLU A 448 " ideal model delta sigma weight residual 114.10 118.45 -4.35 2.00e+00 2.50e-01 4.73e+00 ... (remaining 4490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 1749 14.15 - 28.30: 139 28.30 - 42.45: 47 42.45 - 56.60: 11 56.60 - 70.75: 7 Dihedral angle restraints: 1953 sinusoidal: 816 harmonic: 1137 Sorted by residual: dihedral pdb=" CA ASP A 232 " pdb=" C ASP A 232 " pdb=" N PRO A 233 " pdb=" CA PRO A 233 " ideal model delta harmonic sigma weight residual 180.00 151.24 28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA TRP A 312 " pdb=" C TRP A 312 " pdb=" N LEU A 313 " pdb=" CA LEU A 313 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASN A 86 " pdb=" CB ASN A 86 " pdb=" CG ASN A 86 " pdb=" OD1 ASN A 86 " ideal model delta sinusoidal sigma weight residual 120.00 -173.52 -66.48 2 2.00e+01 2.50e-03 1.01e+01 ... (remaining 1950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 281 0.034 - 0.067: 136 0.067 - 0.100: 35 0.100 - 0.134: 8 0.134 - 0.167: 2 Chirality restraints: 462 Sorted by residual: chirality pdb=" CB ILE A 393 " pdb=" CA ILE A 393 " pdb=" CG1 ILE A 393 " pdb=" CG2 ILE A 393 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA VAL A 390 " pdb=" N VAL A 390 " pdb=" C VAL A 390 " pdb=" CB VAL A 390 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE A 209 " pdb=" N ILE A 209 " pdb=" C ILE A 209 " pdb=" CB ILE A 209 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 459 not shown) Planarity restraints: 573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 232 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO A 233 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 233 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 233 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 444 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO A 445 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 358 " -0.014 2.00e-02 2.50e+03 1.11e-02 3.10e+00 pdb=" CG TRP A 358 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 358 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 358 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 358 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 358 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 358 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 358 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 358 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 358 " -0.004 2.00e-02 2.50e+03 ... (remaining 570 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 551 2.76 - 3.30: 3237 3.30 - 3.83: 5264 3.83 - 4.37: 6481 4.37 - 4.90: 10254 Nonbonded interactions: 25787 Sorted by model distance: nonbonded pdb=" NH1 ARG A 113 " pdb=" OD2 ASP A 123 " model vdw 2.228 3.120 nonbonded pdb=" OD2 ASP A 317 " pdb=" OG1 THR A 349 " model vdw 2.248 3.040 nonbonded pdb=" O LEU A 313 " pdb=" OG1 THR A 349 " model vdw 2.253 3.040 nonbonded pdb=" O ALA A 247 " pdb=" NH2 ARG A 253 " model vdw 2.260 3.120 nonbonded pdb=" O ASP A 254 " pdb=" OG1 THR A 258 " model vdw 2.280 3.040 ... (remaining 25782 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.390 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5279 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 : 0.003 0.027 3327 Z= 0.185 Angle : 0.648 6.230 4495 Z= 0.345 Chirality : 0.041 0.167 462 Planarity : 0.006 0.071 573 Dihedral : 13.088 70.751 1217 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.30 % Allowed : 0.89 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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: -1.70 (0.43), residues: 377 helix: -1.79 (0.42), residues: 128 sheet: 0.61 (0.79), residues: 38 loop : -0.97 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 358 HIS 0.003 0.001 HIS A 443 PHE 0.010 0.001 PHE A 342 TYR 0.009 0.001 TYR A 156 ARG 0.008 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.7504 (m-10) cc_final: 0.6708 (m-80) REVERT: A 384 ASN cc_start: 0.8229 (m-40) cc_final: 0.7990 (m-40) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.1740 time to fit residues: 15.5248 Evaluate side-chains 61 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5379 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3327 Z= 0.233 Angle : 0.706 8.878 4495 Z= 0.356 Chirality : 0.045 0.147 462 Planarity : 0.006 0.065 573 Dihedral : 5.501 28.639 434 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.60 % Allowed : 7.44 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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: -1.92 (0.41), residues: 377 helix: -1.64 (0.40), residues: 140 sheet: 0.12 (0.78), residues: 38 loop : -1.20 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP A 312 HIS 0.002 0.001 HIS A 443 PHE 0.022 0.002 PHE A 368 TYR 0.016 0.002 TYR A 90 ARG 0.004 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.7536 (m-10) cc_final: 0.6712 (m-80) REVERT: A 384 ASN cc_start: 0.8237 (m-40) cc_final: 0.8000 (m-40) outliers start: 2 outliers final: 2 residues processed: 70 average time/residue: 0.1632 time to fit residues: 13.8872 Evaluate side-chains 64 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 223 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.0370 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.0010 chunk 38 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.4264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5277 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3327 Z= 0.179 Angle : 0.608 6.469 4495 Z= 0.310 Chirality : 0.044 0.134 462 Planarity : 0.005 0.060 573 Dihedral : 5.213 28.684 434 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.60 % Allowed : 9.82 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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: -1.90 (0.41), residues: 377 helix: -1.56 (0.41), residues: 145 sheet: -0.16 (0.89), residues: 32 loop : -1.13 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 285 HIS 0.004 0.001 HIS A 274 PHE 0.026 0.002 PHE A 368 TYR 0.015 0.001 TYR A 90 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.7538 (m-10) cc_final: 0.6694 (m-80) REVERT: A 384 ASN cc_start: 0.8216 (m-40) cc_final: 0.7985 (m-40) outliers start: 2 outliers final: 2 residues processed: 74 average time/residue: 0.1541 time to fit residues: 13.9114 Evaluate side-chains 68 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 223 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 0.0370 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5344 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3327 Z= 0.208 Angle : 0.637 8.398 4495 Z= 0.319 Chirality : 0.046 0.265 462 Planarity : 0.005 0.056 573 Dihedral : 5.405 27.428 434 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.19 % Allowed : 12.20 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.42), residues: 377 helix: -1.67 (0.40), residues: 149 sheet: -0.39 (0.91), residues: 32 loop : -1.19 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 312 HIS 0.003 0.001 HIS A 274 PHE 0.019 0.001 PHE A 368 TYR 0.014 0.002 TYR A 378 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.7564 (m-10) cc_final: 0.6714 (m-80) REVERT: A 248 GLN cc_start: 0.6250 (pm20) cc_final: 0.6032 (tt0) REVERT: A 277 LEU cc_start: 0.7668 (mt) cc_final: 0.6891 (mt) REVERT: A 384 ASN cc_start: 0.8199 (m-40) cc_final: 0.7957 (m-40) outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 0.1544 time to fit residues: 13.6281 Evaluate side-chains 69 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.0770 chunk 7 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5328 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3327 Z= 0.178 Angle : 0.619 9.179 4495 Z= 0.308 Chirality : 0.044 0.197 462 Planarity : 0.004 0.056 573 Dihedral : 5.213 27.967 434 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.19 % Allowed : 14.29 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.42), residues: 377 helix: -1.84 (0.38), residues: 161 sheet: -0.50 (0.90), residues: 32 loop : -0.87 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 285 HIS 0.003 0.001 HIS A 274 PHE 0.021 0.001 PHE A 368 TYR 0.012 0.001 TYR A 90 ARG 0.002 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.7552 (m-10) cc_final: 0.6703 (m-80) REVERT: A 384 ASN cc_start: 0.8200 (m-40) cc_final: 0.7962 (m-40) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.1669 time to fit residues: 14.6267 Evaluate side-chains 65 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.0370 chunk 12 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.0030 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.2266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5183 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3327 Z= 0.160 Angle : 0.629 8.420 4495 Z= 0.309 Chirality : 0.044 0.191 462 Planarity : 0.005 0.053 573 Dihedral : 4.980 26.678 434 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.89 % Allowed : 16.37 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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: -1.97 (0.42), residues: 377 helix: -1.79 (0.38), residues: 165 sheet: -0.50 (0.87), residues: 32 loop : -0.80 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 312 HIS 0.003 0.001 HIS A 274 PHE 0.016 0.001 PHE A 368 TYR 0.013 0.001 TYR A 90 ARG 0.005 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.7602 (m-10) cc_final: 0.6805 (m-80) REVERT: A 346 MET cc_start: 0.3878 (mtt) cc_final: 0.3178 (mtt) REVERT: A 367 LYS cc_start: 0.7757 (pptt) cc_final: 0.7336 (pptt) REVERT: A 384 ASN cc_start: 0.8188 (m-40) cc_final: 0.7960 (m-40) outliers start: 3 outliers final: 3 residues processed: 69 average time/residue: 0.1772 time to fit residues: 14.9048 Evaluate side-chains 66 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 25 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5282 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3327 Z= 0.175 Angle : 0.643 8.869 4495 Z= 0.316 Chirality : 0.044 0.204 462 Planarity : 0.005 0.052 573 Dihedral : 4.986 26.255 434 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.49 % Allowed : 16.07 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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: -1.71 (0.43), residues: 377 helix: -1.64 (0.39), residues: 162 sheet: -0.08 (0.92), residues: 30 loop : -0.68 (0.47), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 358 HIS 0.004 0.001 HIS A 274 PHE 0.015 0.001 PHE A 368 TYR 0.012 0.001 TYR A 90 ARG 0.005 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.7593 (m-10) cc_final: 0.7026 (m-80) REVERT: A 346 MET cc_start: 0.3632 (mtt) cc_final: 0.2750 (mtt) REVERT: A 384 ASN cc_start: 0.8204 (m-40) cc_final: 0.7948 (m-40) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.1531 time to fit residues: 13.1695 Evaluate side-chains 65 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 368 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.0000 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 0.0270 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.0270 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5170 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3327 Z= 0.155 Angle : 0.652 9.768 4495 Z= 0.313 Chirality : 0.043 0.190 462 Planarity : 0.005 0.051 573 Dihedral : 4.760 25.680 434 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.19 % Allowed : 16.67 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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: -1.64 (0.43), residues: 377 helix: -1.52 (0.41), residues: 156 sheet: -0.20 (0.91), residues: 30 loop : -0.71 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 358 HIS 0.007 0.001 HIS A 274 PHE 0.015 0.001 PHE A 368 TYR 0.013 0.001 TYR A 90 ARG 0.004 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.7559 (m-10) cc_final: 0.7048 (m-80) REVERT: A 384 ASN cc_start: 0.8160 (m-40) cc_final: 0.7894 (m-40) outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.1683 time to fit residues: 14.1608 Evaluate side-chains 63 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.0000 chunk 35 optimal weight: 0.0070 chunk 30 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 overall best weight: 0.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5180 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3327 Z= 0.158 Angle : 0.674 14.134 4495 Z= 0.316 Chirality : 0.043 0.203 462 Planarity : 0.005 0.050 573 Dihedral : 4.712 24.421 434 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.89 % Allowed : 17.26 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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: -1.66 (0.43), residues: 377 helix: -1.53 (0.40), residues: 163 sheet: -0.11 (0.92), residues: 30 loop : -0.71 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 358 HIS 0.006 0.001 HIS A 274 PHE 0.013 0.001 PHE A 368 TYR 0.013 0.001 TYR A 90 ARG 0.004 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 384 ASN cc_start: 0.8211 (m-40) cc_final: 0.7930 (m-40) REVERT: A 408 MET cc_start: -0.0718 (ptt) cc_final: -0.1517 (tpp) outliers start: 3 outliers final: 3 residues processed: 65 average time/residue: 0.1425 time to fit residues: 11.5693 Evaluate side-chains 61 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5267 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3327 Z= 0.177 Angle : 0.666 10.153 4495 Z= 0.323 Chirality : 0.044 0.221 462 Planarity : 0.005 0.050 573 Dihedral : 4.795 24.923 434 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.89 % Allowed : 17.86 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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: -1.59 (0.44), residues: 377 helix: -1.48 (0.40), residues: 163 sheet: -0.18 (0.88), residues: 32 loop : -0.63 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 358 HIS 0.009 0.001 HIS A 274 PHE 0.009 0.001 PHE A 368 TYR 0.013 0.001 TYR A 90 ARG 0.005 0.000 ARG A 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 384 ASN cc_start: 0.8301 (m-40) cc_final: 0.7967 (m-40) REVERT: A 408 MET cc_start: -0.0711 (ptt) cc_final: -0.1467 (tpp) outliers start: 3 outliers final: 3 residues processed: 59 average time/residue: 0.1447 time to fit residues: 10.7051 Evaluate side-chains 59 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5096 r_free = 0.5096 target = 0.281801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.244019 restraints weight = 4163.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.251806 restraints weight = 2230.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.256673 restraints weight = 1446.924| |-----------------------------------------------------------------------------| r_work (final): 0.4886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5359 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3327 Z= 0.196 Angle : 0.695 9.950 4495 Z= 0.335 Chirality : 0.045 0.215 462 Planarity : 0.005 0.052 573 Dihedral : 5.000 26.202 434 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.89 % Allowed : 17.86 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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: -1.54 (0.44), residues: 377 helix: -1.43 (0.40), residues: 162 sheet: -0.27 (0.88), residues: 32 loop : -0.61 (0.50), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 358 HIS 0.009 0.001 HIS A 274 PHE 0.010 0.001 PHE A 368 TYR 0.012 0.001 TYR A 90 ARG 0.005 0.000 ARG A 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1252.46 seconds wall clock time: 23 minutes 40.29 seconds (1420.29 seconds total)