Starting phenix.real_space_refine on Mon Jan 13 16:22:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r68_18948/01_2025/8r68_18948.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r68_18948/01_2025/8r68_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_18948/01_2025/8r68_18948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r68_18948/01_2025/8r68_18948.map" model { file = "/net/cci-nas-00/data/ceres_data/8r68_18948/01_2025/8r68_18948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r68_18948/01_2025/8r68_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-5571/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: 2.77, per 1000 atoms: 0.85 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: 0.70 Conformation dependent library (CDL) restraints added in 358.1 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: 0.34 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: 0.75 Time building geometry restraints manager: 0.82 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: 0.960 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.430 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.540 ------------------------------------------------------------------------------- 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 : 0.361 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: 0.1790 time to fit residues: 15.9603 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 : 0.353 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.278926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.240503 restraints weight = 4470.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.248232 restraints weight = 2635.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.253143 restraints weight = 1788.908| |-----------------------------------------------------------------------------| r_work (final): 0.4875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5386 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 : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.7428 (m-10) cc_final: 0.6646 (m-80) REVERT: A 384 ASN cc_start: 0.8164 (m-40) cc_final: 0.7954 (m-40) outliers start: 2 outliers final: 2 residues processed: 70 average time/residue: 0.1679 time to fit residues: 14.1470 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 : 0.319 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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 = 0.5058 r_free = 0.5058 target = 0.276489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.239218 restraints weight = 4328.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.246453 restraints weight = 2446.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.251009 restraints weight = 1640.267| |-----------------------------------------------------------------------------| r_work (final): 0.4860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5400 moved from start: 0.2664 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= 0.215 Angle : 0.638 6.554 4495 Z= 0.325 Chirality : 0.045 0.139 462 Planarity : 0.005 0.060 573 Dihedral : 5.421 29.038 434 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.19 % Allowed : 8.93 % Favored : 89.88 % 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: -2.07 (0.41), residues: 377 helix: -1.70 (0.40), residues: 147 sheet: -0.22 (0.89), residues: 32 loop : -1.24 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 358 HIS 0.003 0.001 HIS A 274 PHE 0.027 0.002 PHE A 368 TYR 0.014 0.002 TYR A 90 ARG 0.003 0.000 ARG A 369 *********************** 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 71 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.7484 (m-10) cc_final: 0.6663 (m-80) REVERT: A 384 ASN cc_start: 0.8172 (m-40) cc_final: 0.7946 (m-40) outliers start: 4 outliers final: 3 residues processed: 71 average time/residue: 0.1693 time to fit residues: 14.4142 Evaluate side-chains 67 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 0.0030 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 0.0020 chunk 11 optimal weight: 0.7980 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.5099 r_free = 0.5099 target = 0.281500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.244894 restraints weight = 4605.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.252648 restraints weight = 2599.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.257321 restraints weight = 1728.519| |-----------------------------------------------------------------------------| r_work (final): 0.4903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5295 moved from start: 0.2973 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= 0.181 Angle : 0.602 6.423 4495 Z= 0.306 Chirality : 0.044 0.138 462 Planarity : 0.005 0.057 573 Dihedral : 5.158 28.225 434 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.60 % Allowed : 13.69 % Favored : 85.71 % 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: -1.73 (0.40), residues: 153 sheet: -0.50 (0.90), residues: 32 loop : -0.96 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 312 HIS 0.003 0.001 HIS A 274 PHE 0.023 0.001 PHE A 368 TYR 0.013 0.001 TYR A 90 ARG 0.004 0.000 ARG A 270 *********************** 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 78 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.6368 (pm20) cc_final: 0.6059 (tt0) REVERT: A 272 GLN cc_start: 0.6536 (mt0) cc_final: 0.6215 (mt0) REVERT: A 277 LEU cc_start: 0.7494 (mt) cc_final: 0.6802 (mt) REVERT: A 384 ASN cc_start: 0.8168 (m-40) cc_final: 0.7951 (m-40) outliers start: 2 outliers final: 2 residues processed: 78 average time/residue: 0.1557 time to fit residues: 14.7962 Evaluate side-chains 69 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 223 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.275590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.235374 restraints weight = 4426.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.243050 restraints weight = 2515.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.247909 restraints weight = 1707.394| |-----------------------------------------------------------------------------| r_work (final): 0.4831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5520 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3327 Z= 0.255 Angle : 0.660 7.065 4495 Z= 0.336 Chirality : 0.045 0.145 462 Planarity : 0.005 0.056 573 Dihedral : 5.526 28.429 434 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.38 % Allowed : 14.88 % 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: -2.18 (0.42), residues: 377 helix: -1.90 (0.38), residues: 162 sheet: -0.47 (0.95), residues: 30 loop : -1.05 (0.46), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 312 HIS 0.002 0.001 HIS A 274 PHE 0.018 0.002 PHE A 368 TYR 0.013 0.002 TYR A 81 ARG 0.004 0.000 ARG A 369 *********************** 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 76 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.5199 (m100) cc_final: 0.4519 (m100) REVERT: A 384 ASN cc_start: 0.8240 (m-40) cc_final: 0.7983 (m-40) REVERT: A 459 MET cc_start: 0.4164 (ptt) cc_final: 0.3940 (ptt) outliers start: 8 outliers final: 6 residues processed: 73 average time/residue: 0.1700 time to fit residues: 14.9359 Evaluate side-chains 70 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 216 TRP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.280471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.243411 restraints weight = 4172.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.250553 restraints weight = 2359.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.255196 restraints weight = 1581.301| |-----------------------------------------------------------------------------| r_work (final): 0.4874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5401 moved from start: 0.3857 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= 0.210 Angle : 0.664 9.148 4495 Z= 0.332 Chirality : 0.044 0.143 462 Planarity : 0.005 0.057 573 Dihedral : 5.286 29.554 434 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.38 % Allowed : 15.48 % 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: -2.14 (0.42), residues: 377 helix: -1.76 (0.39), residues: 159 sheet: -0.77 (0.92), residues: 30 loop : -1.09 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 241 HIS 0.002 0.001 HIS A 443 PHE 0.014 0.002 PHE A 368 TYR 0.011 0.001 TYR A 90 ARG 0.002 0.000 ARG A 113 *********************** 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 74 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 209 ILE cc_start: 0.6220 (mm) cc_final: 0.6015 (mm) REVERT: A 312 TRP cc_start: 0.5686 (OUTLIER) cc_final: 0.4320 (m100) REVERT: A 367 LYS cc_start: 0.7654 (pptt) cc_final: 0.7368 (pptt) REVERT: A 384 ASN cc_start: 0.8169 (m-40) cc_final: 0.7951 (m-40) REVERT: A 459 MET cc_start: 0.3979 (ptt) cc_final: 0.3750 (ptt) outliers start: 8 outliers final: 7 residues processed: 69 average time/residue: 0.1656 time to fit residues: 13.9404 Evaluate side-chains 73 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 216 TRP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.275902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.236512 restraints weight = 4329.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.243551 restraints weight = 2438.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.248128 restraints weight = 1661.847| |-----------------------------------------------------------------------------| r_work (final): 0.4828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5457 moved from start: 0.4035 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= 0.209 Angle : 0.668 8.268 4495 Z= 0.335 Chirality : 0.044 0.154 462 Planarity : 0.005 0.055 573 Dihedral : 5.211 28.765 434 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.98 % Allowed : 15.77 % 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: -2.06 (0.43), residues: 377 helix: -1.80 (0.38), residues: 163 sheet: -0.80 (0.87), residues: 35 loop : -0.88 (0.49), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 285 HIS 0.004 0.001 HIS A 274 PHE 0.017 0.001 PHE A 368 TYR 0.011 0.001 TYR A 90 ARG 0.011 0.001 ARG A 454 *********************** 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 73 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 HIS cc_start: 0.5339 (OUTLIER) cc_final: 0.5131 (t-90) REVERT: A 346 MET cc_start: 0.3879 (mtt) cc_final: 0.3220 (mtt) REVERT: A 459 MET cc_start: 0.3828 (ptt) cc_final: 0.3535 (ptt) outliers start: 10 outliers final: 8 residues processed: 67 average time/residue: 0.1505 time to fit residues: 12.3424 Evaluate side-chains 71 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 216 TRP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 366 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 5 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.0570 chunk 24 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.0770 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5083 r_free = 0.5083 target = 0.278926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.239884 restraints weight = 4547.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.247775 restraints weight = 2559.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.252565 restraints weight = 1705.505| |-----------------------------------------------------------------------------| r_work (final): 0.4856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5403 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3327 Z= 0.185 Angle : 0.660 8.014 4495 Z= 0.329 Chirality : 0.043 0.153 462 Planarity : 0.005 0.056 573 Dihedral : 5.093 29.168 434 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.68 % Allowed : 15.77 % Favored : 81.55 % 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: -2.01 (0.43), residues: 377 helix: -1.74 (0.39), residues: 159 sheet: -0.83 (0.81), residues: 36 loop : -0.88 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 285 HIS 0.003 0.001 HIS A 337 PHE 0.017 0.001 PHE A 368 TYR 0.012 0.001 TYR A 90 ARG 0.007 0.000 ARG A 454 *********************** 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 72 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 HIS cc_start: 0.5410 (OUTLIER) cc_final: 0.5206 (t-90) REVERT: A 459 MET cc_start: 0.3881 (ptt) cc_final: 0.3595 (ptt) outliers start: 9 outliers final: 8 residues processed: 66 average time/residue: 0.1580 time to fit residues: 12.7586 Evaluate side-chains 67 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 216 TRP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5078 r_free = 0.5078 target = 0.279045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.239964 restraints weight = 4502.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.247696 restraints weight = 2558.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.252459 restraints weight = 1717.738| |-----------------------------------------------------------------------------| r_work (final): 0.4850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5409 moved from start: 0.4338 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= 0.202 Angle : 0.698 11.365 4495 Z= 0.343 Chirality : 0.044 0.161 462 Planarity : 0.005 0.054 573 Dihedral : 5.084 28.363 434 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.68 % Allowed : 16.07 % 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: -2.01 (0.43), residues: 377 helix: -1.68 (0.39), residues: 157 sheet: -0.93 (0.80), residues: 36 loop : -0.95 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 285 HIS 0.004 0.001 HIS A 337 PHE 0.017 0.001 PHE A 368 TYR 0.013 0.001 TYR A 338 ARG 0.008 0.000 ARG A 454 *********************** 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 72 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.3893 (ptt) cc_final: 0.3539 (ptt) outliers start: 9 outliers final: 8 residues processed: 67 average time/residue: 0.1642 time to fit residues: 13.3817 Evaluate side-chains 68 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 216 TRP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.0020 chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5153 r_free = 0.5153 target = 0.286440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.253682 restraints weight = 4406.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.259599 restraints weight = 2699.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.263332 restraints weight = 1925.773| |-----------------------------------------------------------------------------| r_work (final): 0.4984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5313 moved from start: 0.4623 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= 0.190 Angle : 0.700 9.439 4495 Z= 0.346 Chirality : 0.043 0.162 462 Planarity : 0.005 0.055 573 Dihedral : 5.071 28.284 434 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.68 % Allowed : 16.37 % Favored : 80.95 % 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: -2.01 (0.43), residues: 377 helix: -1.65 (0.39), residues: 157 sheet: -1.53 (0.98), residues: 27 loop : -0.88 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 358 HIS 0.004 0.001 HIS A 274 PHE 0.015 0.001 PHE A 368 TYR 0.014 0.001 TYR A 90 ARG 0.004 0.000 ARG A 454 ********************** 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 67 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 GLU cc_start: 0.6418 (tm-30) cc_final: 0.6142 (tm-30) outliers start: 9 outliers final: 9 residues processed: 62 average time/residue: 0.1532 time to fit residues: 11.7604 Evaluate side-chains 65 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 216 TRP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 419 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 27 optimal weight: 0.0770 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 0.0670 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5164 r_free = 0.5164 target = 0.286564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.253241 restraints weight = 4406.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.259422 restraints weight = 2678.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.263177 restraints weight = 1914.505| |-----------------------------------------------------------------------------| r_work (final): 0.4968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5298 moved from start: 0.4701 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= 0.184 Angle : 0.688 9.071 4495 Z= 0.339 Chirality : 0.043 0.165 462 Planarity : 0.004 0.054 573 Dihedral : 4.958 27.316 434 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.08 % Allowed : 17.56 % Favored : 80.36 % 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: -1.93 (0.43), residues: 377 helix: -1.59 (0.39), residues: 157 sheet: -1.74 (0.94), residues: 27 loop : -0.80 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 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 0.004 0.000 ARG A 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1517.08 seconds wall clock time: 28 minutes 1.89 seconds (1681.89 seconds total)