Starting phenix.real_space_refine on Mon Jan 13 19:37:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6p_50237/01_2025/9f6p_50237.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6p_50237/01_2025/9f6p_50237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f6p_50237/01_2025/9f6p_50237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6p_50237/01_2025/9f6p_50237.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6p_50237/01_2025/9f6p_50237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6p_50237/01_2025/9f6p_50237.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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: 5 Type Number sf(0) Gaussians Mn 1 7.51 5 S 22 5.16 5 C 2460 2.51 5 N 606 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 3720 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3719 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.90, per 1000 atoms: 0.78 Number of scatterers: 3720 At special positions: 0 Unit cell: (83.328, 69.006, 79.422, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 1 24.99 S 22 16.00 O 631 8.00 N 606 7.00 C 2460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 354 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 433.1 milliseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 886 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 84.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.913A pdb=" N SER A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.918A pdb=" N ASP A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 118 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 130 through 164 removed outlier: 3.566A pdb=" N SER A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 188 removed outlier: 3.849A pdb=" N GLY A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 218 removed outlier: 3.627A pdb=" N ARG A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 Processing helix chain 'A' and resid 237 through 252 removed outlier: 4.224A pdb=" N ILE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 4.035A pdb=" N ILE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 311 removed outlier: 4.347A pdb=" N ILE A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 344 through 357 Processing helix chain 'A' and resid 357 through 391 removed outlier: 4.293A pdb=" N LEU A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 420 through 439 Processing helix chain 'A' and resid 439 through 451 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 462 through 488 Processing helix chain 'A' and resid 497 through 523 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.721A pdb=" N TYR A 537 " --> pdb=" O HIS A 533 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 906 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: 1.00 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1151 1.34 - 1.46: 954 1.46 - 1.58: 1675 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 3814 Sorted by residual: bond pdb=" N MET A 253 " pdb=" CA MET A 253 " ideal model delta sigma weight residual 1.454 1.477 -0.023 1.30e-02 5.92e+03 3.21e+00 bond pdb=" N LEU A 437 " pdb=" CA LEU A 437 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.28e-02 6.10e+03 2.45e+00 bond pdb=" CA ARG A 218 " pdb=" CB ARG A 218 " ideal model delta sigma weight residual 1.522 1.532 -0.010 7.00e-03 2.04e+04 1.86e+00 bond pdb=" CB GLU A 268 " pdb=" CG GLU A 268 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CB ARG A 193 " pdb=" CG ARG A 193 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 ... (remaining 3809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 5013 2.10 - 4.19: 143 4.19 - 6.29: 31 6.29 - 8.39: 9 8.39 - 10.48: 6 Bond angle restraints: 5202 Sorted by residual: angle pdb=" N LEU A 437 " pdb=" CA LEU A 437 " pdb=" CB LEU A 437 " ideal model delta sigma weight residual 110.28 104.86 5.42 1.55e+00 4.16e-01 1.22e+01 angle pdb=" CB MET A 68 " pdb=" CG MET A 68 " pdb=" SD MET A 68 " ideal model delta sigma weight residual 112.70 123.09 -10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CA GLN A 312 " pdb=" CB GLN A 312 " pdb=" CG GLN A 312 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CA LYS A 91 " pdb=" CB LYS A 91 " pdb=" CG LYS A 91 " ideal model delta sigma weight residual 114.10 120.30 -6.20 2.00e+00 2.50e-01 9.60e+00 angle pdb=" CA LEU A 391 " pdb=" CB LEU A 391 " pdb=" CG LEU A 391 " ideal model delta sigma weight residual 116.30 126.78 -10.48 3.50e+00 8.16e-02 8.97e+00 ... (remaining 5197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 1790 15.84 - 31.68: 291 31.68 - 47.52: 90 47.52 - 63.36: 29 63.36 - 79.20: 4 Dihedral angle restraints: 2204 sinusoidal: 819 harmonic: 1385 Sorted by residual: dihedral pdb=" CB CYS A 322 " pdb=" SG CYS A 322 " pdb=" SG CYS A 354 " pdb=" CB CYS A 354 " ideal model delta sinusoidal sigma weight residual -86.00 -156.87 70.87 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CA ALA A 342 " pdb=" C ALA A 342 " pdb=" N VAL A 343 " pdb=" CA VAL A 343 " ideal model delta harmonic sigma weight residual 180.00 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA TYR A 311 " pdb=" C TYR A 311 " pdb=" N GLN A 312 " pdb=" CA GLN A 312 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 2201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 509 0.062 - 0.124: 96 0.124 - 0.186: 8 0.186 - 0.247: 2 0.247 - 0.309: 1 Chirality restraints: 616 Sorted by residual: chirality pdb=" CG LEU A 102 " pdb=" CB LEU A 102 " pdb=" CD1 LEU A 102 " pdb=" CD2 LEU A 102 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CB VAL A 174 " pdb=" CA VAL A 174 " pdb=" CG1 VAL A 174 " pdb=" CG2 VAL A 174 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB THR A 177 " pdb=" CA THR A 177 " pdb=" OG1 THR A 177 " pdb=" CG2 THR A 177 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.09e-01 ... (remaining 613 not shown) Planarity restraints: 643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 311 " -0.016 2.00e-02 2.50e+03 1.31e-02 3.43e+00 pdb=" CG TYR A 311 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 311 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 311 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 311 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 311 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 311 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 311 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 270 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" CG ASP A 270 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP A 270 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 270 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 230 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 231 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.022 5.00e-02 4.00e+02 ... (remaining 640 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 46 2.65 - 3.21: 3781 3.21 - 3.78: 6236 3.78 - 4.34: 7513 4.34 - 4.90: 12437 Nonbonded interactions: 30013 Sorted by model distance: nonbonded pdb=" OD1 ASN A 77 " pdb="MN MN A 701 " model vdw 2.090 2.320 nonbonded pdb=" O SER A 374 " pdb=" OG1 THR A 378 " model vdw 2.263 3.040 nonbonded pdb=" O LYS A 131 " pdb=" OG1 THR A 135 " model vdw 2.332 3.040 nonbonded pdb=" O CYS A 518 " pdb=" ND1 HIS A 522 " model vdw 2.341 3.120 nonbonded pdb=" OG SER A 451 " pdb=" OD1 ASN A 461 " model vdw 2.351 3.040 ... (remaining 30008 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: 0.380 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3814 Z= 0.253 Angle : 0.929 10.484 5202 Z= 0.454 Chirality : 0.048 0.309 616 Planarity : 0.005 0.040 643 Dihedral : 18.008 79.197 1312 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.05 % Allowed : 44.10 % Favored : 53.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.38), residues: 480 helix: 1.66 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -1.89 (0.59), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 138 HIS 0.003 0.001 HIS A 522 PHE 0.024 0.002 PHE A 184 TYR 0.029 0.002 TYR A 311 ARG 0.008 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 58 LEU cc_start: 0.2433 (OUTLIER) cc_final: 0.2194 (tp) REVERT: A 68 MET cc_start: 0.6634 (tpp) cc_final: 0.5464 (tpt) REVERT: A 135 THR cc_start: 0.9084 (m) cc_final: 0.8877 (t) REVERT: A 178 ILE cc_start: 0.8263 (tp) cc_final: 0.7995 (pt) REVERT: A 214 TYR cc_start: 0.7164 (t80) cc_final: 0.6904 (t80) REVERT: A 228 LEU cc_start: 0.8310 (tp) cc_final: 0.7999 (tt) REVERT: A 278 ARG cc_start: 0.7002 (tmt170) cc_final: 0.6615 (mtm-85) REVERT: A 287 GLU cc_start: 0.8032 (tt0) cc_final: 0.7327 (tm-30) REVERT: A 393 LEU cc_start: 0.8120 (tt) cc_final: 0.7906 (mt) REVERT: A 475 LEU cc_start: 0.8984 (tp) cc_final: 0.8659 (pp) REVERT: A 537 TYR cc_start: 0.8050 (m-10) cc_final: 0.7696 (m-10) outliers start: 8 outliers final: 4 residues processed: 153 average time/residue: 0.1456 time to fit residues: 27.7291 Evaluate side-chains 116 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.0030 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN A 461 ASN A 529 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.154610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.134675 restraints weight = 7421.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138455 restraints weight = 3956.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.141049 restraints weight = 2474.325| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3814 Z= 0.212 Angle : 0.695 7.063 5202 Z= 0.345 Chirality : 0.040 0.139 616 Planarity : 0.005 0.040 643 Dihedral : 6.291 48.847 527 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.67 % Allowed : 35.13 % Favored : 58.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.38), residues: 480 helix: 1.73 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -2.05 (0.57), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 94 HIS 0.008 0.001 HIS A 126 PHE 0.036 0.002 PHE A 72 TYR 0.013 0.001 TYR A 311 ARG 0.005 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 66 PHE cc_start: 0.7766 (m-80) cc_final: 0.7505 (m-10) REVERT: A 67 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7085 (pp) REVERT: A 72 PHE cc_start: 0.7880 (m-80) cc_final: 0.7442 (m-80) REVERT: A 107 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8690 (mm-40) REVERT: A 178 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7862 (pt) REVERT: A 214 TYR cc_start: 0.7285 (t80) cc_final: 0.7058 (t80) REVERT: A 228 LEU cc_start: 0.8391 (tp) cc_final: 0.8052 (tt) REVERT: A 278 ARG cc_start: 0.7229 (tmt170) cc_final: 0.6879 (mtm-85) REVERT: A 287 GLU cc_start: 0.7978 (tt0) cc_final: 0.7698 (tm-30) REVERT: A 364 TRP cc_start: 0.8561 (OUTLIER) cc_final: 0.8125 (t60) REVERT: A 378 THR cc_start: 0.9203 (m) cc_final: 0.8948 (p) REVERT: A 484 VAL cc_start: 0.7618 (t) cc_final: 0.7273 (p) REVERT: A 535 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7424 (m-80) outliers start: 26 outliers final: 9 residues processed: 137 average time/residue: 0.1279 time to fit residues: 22.3750 Evaluate side-chains 127 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 364 TRP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 535 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.152454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131415 restraints weight = 7684.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135122 restraints weight = 4216.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.137659 restraints weight = 2720.713| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3814 Z= 0.228 Angle : 0.669 8.773 5202 Z= 0.332 Chirality : 0.040 0.207 616 Planarity : 0.005 0.040 643 Dihedral : 5.473 50.727 522 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 8.46 % Allowed : 32.05 % Favored : 59.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.38), residues: 480 helix: 1.60 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -2.04 (0.57), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 94 HIS 0.008 0.001 HIS A 126 PHE 0.027 0.002 PHE A 483 TYR 0.009 0.001 TYR A 283 ARG 0.003 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7128 (pp) REVERT: A 81 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7452 (t70) REVERT: A 91 LYS cc_start: 0.8757 (mmtt) cc_final: 0.7645 (mtmt) REVERT: A 178 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8192 (pt) REVERT: A 195 LEU cc_start: 0.7377 (tp) cc_final: 0.6930 (tt) REVERT: A 214 TYR cc_start: 0.7242 (t80) cc_final: 0.6629 (t80) REVERT: A 228 LEU cc_start: 0.8530 (tp) cc_final: 0.8144 (tt) REVERT: A 278 ARG cc_start: 0.7219 (tmt170) cc_final: 0.6884 (mtm-85) REVERT: A 364 TRP cc_start: 0.8624 (OUTLIER) cc_final: 0.7072 (t-100) REVERT: A 423 ASP cc_start: 0.8118 (m-30) cc_final: 0.7891 (m-30) REVERT: A 466 LYS cc_start: 0.7774 (mttm) cc_final: 0.7367 (mttm) REVERT: A 484 VAL cc_start: 0.7576 (t) cc_final: 0.7252 (p) outliers start: 33 outliers final: 17 residues processed: 132 average time/residue: 0.1349 time to fit residues: 22.7121 Evaluate side-chains 131 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 364 TRP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** 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 = 0.3923 r_free = 0.3923 target = 0.150468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130383 restraints weight = 7534.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133946 restraints weight = 3993.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136379 restraints weight = 2520.632| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3814 Z= 0.247 Angle : 0.650 7.688 5202 Z= 0.325 Chirality : 0.039 0.138 616 Planarity : 0.005 0.038 643 Dihedral : 5.197 53.317 522 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 9.23 % Allowed : 32.31 % Favored : 58.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.38), residues: 480 helix: 1.64 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -2.15 (0.56), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 94 HIS 0.006 0.001 HIS A 126 PHE 0.016 0.002 PHE A 301 TYR 0.009 0.001 TYR A 190 ARG 0.002 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7020 (pp) REVERT: A 68 MET cc_start: 0.6152 (tpt) cc_final: 0.5482 (tpt) REVERT: A 73 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8127 (tm) REVERT: A 81 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7382 (t70) REVERT: A 91 LYS cc_start: 0.8792 (mmtt) cc_final: 0.7635 (mtmt) REVERT: A 135 THR cc_start: 0.9048 (m) cc_final: 0.8804 (t) REVERT: A 154 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9254 (mp) REVERT: A 206 MET cc_start: 0.9011 (ppp) cc_final: 0.8795 (ppp) REVERT: A 228 LEU cc_start: 0.8541 (tp) cc_final: 0.8190 (tt) REVERT: A 276 ASP cc_start: 0.7361 (m-30) cc_final: 0.7076 (m-30) REVERT: A 278 ARG cc_start: 0.7212 (tmt170) cc_final: 0.6862 (mtm-85) REVERT: A 364 TRP cc_start: 0.8663 (OUTLIER) cc_final: 0.7117 (t-100) outliers start: 36 outliers final: 18 residues processed: 131 average time/residue: 0.1269 time to fit residues: 21.3602 Evaluate side-chains 121 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 TRP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 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 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS A 533 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.148683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128575 restraints weight = 7898.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132183 restraints weight = 4236.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134516 restraints weight = 2681.018| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3814 Z= 0.225 Angle : 0.680 8.732 5202 Z= 0.332 Chirality : 0.040 0.145 616 Planarity : 0.005 0.038 643 Dihedral : 4.474 35.775 520 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 8.46 % Allowed : 31.79 % Favored : 59.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.38), residues: 480 helix: 1.65 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -2.16 (0.55), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 94 HIS 0.005 0.001 HIS A 126 PHE 0.035 0.002 PHE A 72 TYR 0.015 0.001 TYR A 214 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7106 (pp) REVERT: A 68 MET cc_start: 0.6067 (tpt) cc_final: 0.5651 (tpt) REVERT: A 73 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8215 (tm) REVERT: A 91 LYS cc_start: 0.8790 (mmtt) cc_final: 0.7632 (mtmt) REVERT: A 135 THR cc_start: 0.8994 (m) cc_final: 0.8755 (t) REVERT: A 152 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 206 MET cc_start: 0.9000 (ppp) cc_final: 0.8794 (ppp) REVERT: A 228 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8173 (tt) REVERT: A 276 ASP cc_start: 0.7302 (m-30) cc_final: 0.6990 (m-30) REVERT: A 278 ARG cc_start: 0.7271 (tmt170) cc_final: 0.6937 (mtm-85) REVERT: A 529 HIS cc_start: 0.3176 (m90) cc_final: 0.2920 (t-90) outliers start: 33 outliers final: 22 residues processed: 129 average time/residue: 0.1243 time to fit residues: 20.7239 Evaluate side-chains 125 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 0.0370 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN A 532 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.152191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.132544 restraints weight = 7441.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.136265 restraints weight = 3913.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.138953 restraints weight = 2412.848| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3814 Z= 0.221 Angle : 0.689 12.019 5202 Z= 0.333 Chirality : 0.040 0.141 616 Planarity : 0.005 0.037 643 Dihedral : 4.464 35.231 520 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 7.44 % Allowed : 34.10 % Favored : 58.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.38), residues: 480 helix: 1.59 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -2.19 (0.56), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 94 HIS 0.005 0.001 HIS A 126 PHE 0.050 0.002 PHE A 72 TYR 0.015 0.001 TYR A 214 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7093 (pp) REVERT: A 73 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8136 (tm) REVERT: A 91 LYS cc_start: 0.8775 (mmtt) cc_final: 0.7614 (mtmt) REVERT: A 135 THR cc_start: 0.9012 (m) cc_final: 0.8774 (t) REVERT: A 152 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 183 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6970 (p90) REVERT: A 228 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8175 (tt) REVERT: A 276 ASP cc_start: 0.7328 (m-30) cc_final: 0.7074 (m-30) REVERT: A 278 ARG cc_start: 0.7263 (tmt170) cc_final: 0.6938 (mtm-85) REVERT: A 466 LYS cc_start: 0.7797 (mttm) cc_final: 0.7422 (mttm) REVERT: A 529 HIS cc_start: 0.3009 (m90) cc_final: 0.2748 (t-90) outliers start: 29 outliers final: 19 residues processed: 124 average time/residue: 0.1319 time to fit residues: 21.1554 Evaluate side-chains 121 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN A 532 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.151423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131572 restraints weight = 7534.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135245 restraints weight = 4006.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137706 restraints weight = 2519.221| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3814 Z= 0.224 Angle : 0.716 12.525 5202 Z= 0.340 Chirality : 0.039 0.135 616 Planarity : 0.005 0.038 643 Dihedral : 4.460 34.824 520 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 7.44 % Allowed : 34.36 % Favored : 58.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.38), residues: 480 helix: 1.57 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.29 (0.53), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 94 HIS 0.005 0.001 HIS A 126 PHE 0.044 0.002 PHE A 72 TYR 0.009 0.001 TYR A 214 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 72 PHE cc_start: 0.6930 (m-80) cc_final: 0.6729 (m-80) REVERT: A 73 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8071 (tm) REVERT: A 91 LYS cc_start: 0.8773 (mmtt) cc_final: 0.7622 (mtmt) REVERT: A 97 LEU cc_start: 0.8383 (tt) cc_final: 0.8031 (tp) REVERT: A 135 THR cc_start: 0.9013 (m) cc_final: 0.8790 (t) REVERT: A 152 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7691 (tm-30) REVERT: A 187 LEU cc_start: 0.8246 (tt) cc_final: 0.7870 (pp) REVERT: A 228 LEU cc_start: 0.8546 (tp) cc_final: 0.8175 (tt) REVERT: A 278 ARG cc_start: 0.7341 (tmt170) cc_final: 0.6941 (mtm-85) REVERT: A 364 TRP cc_start: 0.8773 (OUTLIER) cc_final: 0.7157 (t-100) REVERT: A 466 LYS cc_start: 0.7801 (mttm) cc_final: 0.7419 (mttm) outliers start: 29 outliers final: 22 residues processed: 122 average time/residue: 0.1236 time to fit residues: 19.3467 Evaluate side-chains 122 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 TRP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN A 532 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.149661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.129398 restraints weight = 7535.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133054 restraints weight = 3983.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135697 restraints weight = 2508.545| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3814 Z= 0.246 Angle : 0.734 13.405 5202 Z= 0.348 Chirality : 0.040 0.141 616 Planarity : 0.005 0.038 643 Dihedral : 4.502 35.297 520 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 7.69 % Allowed : 35.64 % Favored : 56.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.38), residues: 480 helix: 1.50 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -2.36 (0.53), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 171 HIS 0.005 0.001 HIS A 126 PHE 0.042 0.002 PHE A 72 TYR 0.017 0.001 TYR A 214 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 68 MET cc_start: 0.5413 (tpt) cc_final: 0.5056 (tpt) REVERT: A 73 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8068 (tm) REVERT: A 91 LYS cc_start: 0.8823 (mmtt) cc_final: 0.7698 (mtmt) REVERT: A 135 THR cc_start: 0.9048 (m) cc_final: 0.8843 (t) REVERT: A 152 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7780 (tm-30) REVERT: A 228 LEU cc_start: 0.8535 (tp) cc_final: 0.8148 (tt) REVERT: A 269 ILE cc_start: 0.8445 (mt) cc_final: 0.7956 (mm) REVERT: A 278 ARG cc_start: 0.7268 (tmt170) cc_final: 0.6853 (mtm-85) REVERT: A 341 VAL cc_start: 0.7024 (OUTLIER) cc_final: 0.6790 (p) REVERT: A 364 TRP cc_start: 0.8746 (OUTLIER) cc_final: 0.7089 (t-100) REVERT: A 466 LYS cc_start: 0.7867 (mttm) cc_final: 0.7467 (mttm) REVERT: A 484 VAL cc_start: 0.7457 (t) cc_final: 0.7201 (p) outliers start: 30 outliers final: 23 residues processed: 119 average time/residue: 0.1227 time to fit residues: 18.8676 Evaluate side-chains 125 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 TRP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN A 532 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.150863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.130540 restraints weight = 7398.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.134268 restraints weight = 3956.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.136721 restraints weight = 2501.908| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 3814 Z= 0.232 Angle : 0.735 13.603 5202 Z= 0.350 Chirality : 0.040 0.138 616 Planarity : 0.005 0.039 643 Dihedral : 4.478 34.731 520 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 7.18 % Allowed : 37.44 % Favored : 55.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.38), residues: 480 helix: 1.57 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.41 (0.52), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 171 HIS 0.005 0.001 HIS A 126 PHE 0.042 0.002 PHE A 72 TYR 0.015 0.001 TYR A 214 ARG 0.006 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7980 (tm) REVERT: A 91 LYS cc_start: 0.8798 (mmtt) cc_final: 0.7682 (mtmt) REVERT: A 152 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7710 (tm-30) REVERT: A 228 LEU cc_start: 0.8520 (tp) cc_final: 0.8173 (tt) REVERT: A 269 ILE cc_start: 0.8689 (mt) cc_final: 0.8317 (mm) REVERT: A 278 ARG cc_start: 0.7262 (tmt170) cc_final: 0.6840 (mtm-85) REVERT: A 341 VAL cc_start: 0.7166 (OUTLIER) cc_final: 0.6949 (p) REVERT: A 364 TRP cc_start: 0.8747 (OUTLIER) cc_final: 0.7051 (t-100) REVERT: A 466 LYS cc_start: 0.7943 (mttm) cc_final: 0.7548 (mttm) outliers start: 28 outliers final: 23 residues processed: 122 average time/residue: 0.1247 time to fit residues: 19.5369 Evaluate side-chains 127 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 TRP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN A 532 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.152220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.132312 restraints weight = 7658.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.136087 restraints weight = 4039.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138771 restraints weight = 2522.641| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 3814 Z= 0.248 Angle : 0.764 13.489 5202 Z= 0.370 Chirality : 0.042 0.254 616 Planarity : 0.005 0.047 643 Dihedral : 4.562 35.237 520 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 6.92 % Allowed : 38.21 % Favored : 54.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.38), residues: 480 helix: 1.53 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -2.37 (0.52), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 171 HIS 0.005 0.001 HIS A 126 PHE 0.041 0.002 PHE A 72 TYR 0.026 0.001 TYR A 214 ARG 0.006 0.000 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7862 (tm) REVERT: A 91 LYS cc_start: 0.8818 (mmtt) cc_final: 0.7738 (mtmt) REVERT: A 97 LEU cc_start: 0.8472 (tt) cc_final: 0.8162 (tp) REVERT: A 152 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 228 LEU cc_start: 0.8492 (tp) cc_final: 0.8174 (tt) REVERT: A 269 ILE cc_start: 0.8718 (mt) cc_final: 0.8339 (mm) REVERT: A 278 ARG cc_start: 0.7238 (tmt170) cc_final: 0.6869 (mtm-85) REVERT: A 466 LYS cc_start: 0.7910 (mttm) cc_final: 0.7516 (mttm) outliers start: 27 outliers final: 24 residues processed: 118 average time/residue: 0.1292 time to fit residues: 19.6778 Evaluate side-chains 122 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 16 optimal weight: 0.0670 chunk 8 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.151636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.131489 restraints weight = 7608.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135254 restraints weight = 4023.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137918 restraints weight = 2535.299| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3814 Z= 0.239 Angle : 0.773 13.451 5202 Z= 0.373 Chirality : 0.041 0.203 616 Planarity : 0.005 0.047 643 Dihedral : 4.591 36.663 520 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.64 % Allowed : 39.49 % Favored : 54.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.38), residues: 480 helix: 1.55 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.45 (0.53), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 171 HIS 0.005 0.001 HIS A 126 PHE 0.040 0.002 PHE A 72 TYR 0.018 0.001 TYR A 214 ARG 0.006 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1409.52 seconds wall clock time: 26 minutes 1.28 seconds (1561.28 seconds total)