Starting phenix.real_space_refine on Thu Oct 22 18:37:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/33aw_59318/10_2026/33aw_59318.cif Found real_map, /net/cci-nas-00/data/ceres_data/33aw_59318/10_2026/33aw_59318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/33aw_59318/10_2026/33aw_59318.cif" } default_model = "/net/cci-nas-00/data/ceres_data/33aw_59318/10_2026/33aw_59318.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/33aw_59318/10_2026/33aw_59318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/33aw_59318/10_2026/33aw_59318.map" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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 2259 2.51 5 N 625 2.21 5 O 691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3589 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3589 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 440} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 1.10, per 1000 atoms: 0.31 Number of scatterers: 3589 At special positions: 0 Unit cell: (88.35, 98.8125, 84.8625, 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 691 8.00 N 625 7.00 C 2259 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: 0.32 Conformation dependent library (CDL) restraints added in 121.8 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 876 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 6 sheets defined 49.7% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 43 through 55 Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 118 through 134 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 181 through 193 removed outlier: 4.263A pdb=" N HIS A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 229 removed outlier: 3.898A pdb=" N ALA A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 253 removed outlier: 3.711A pdb=" N GLN A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.578A pdb=" N ALA A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 281 removed outlier: 3.516A pdb=" N GLN A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 328 through 349 Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 386 through 397 removed outlier: 3.536A pdb=" N THR A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 415 Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 442 through 475 removed outlier: 3.889A pdb=" N ILE A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 6.857A pdb=" N LEU A 96 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER A 63 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU A 94 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 95 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 111 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL A 30 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY A 112 " --> pdb=" O ALA A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 82 removed outlier: 4.193A pdb=" N HIS A 88 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS A 82 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N PHE A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 145 removed outlier: 6.221A pdb=" N VAL A 144 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 286 removed outlier: 6.035A pdb=" N VAL A 285 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.074A pdb=" N LEU A 379 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL A 422 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU A 381 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TYR A 424 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS A 383 " --> pdb=" O TYR A 424 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 522 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: 0.46 Time building geometry restraints manager: 0.43 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: 1226 1.34 - 1.46: 744 1.46 - 1.58: 1662 1.58 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3657 Sorted by residual: bond pdb=" N ARG A 436 " pdb=" CA ARG A 436 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.56e+00 bond pdb=" N THR A 437 " pdb=" CA THR A 437 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.26e-02 6.30e+03 4.63e+00 bond pdb=" CA ARG A 436 " pdb=" C ARG A 436 " ideal model delta sigma weight residual 1.520 1.540 -0.019 1.22e-02 6.72e+03 2.48e+00 bond pdb=" CB TRP A 119 " pdb=" CG TRP A 119 " ideal model delta sigma weight residual 1.498 1.452 0.046 3.10e-02 1.04e+03 2.17e+00 bond pdb=" CG LEU A 117 " pdb=" CD1 LEU A 117 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.15e+00 ... (remaining 3652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 4885 2.14 - 4.28: 74 4.28 - 6.42: 7 6.42 - 8.55: 1 8.55 - 10.69: 1 Bond angle restraints: 4968 Sorted by residual: angle pdb=" CB MET A 330 " pdb=" CG MET A 330 " pdb=" SD MET A 330 " ideal model delta sigma weight residual 112.70 123.39 -10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CA THR A 437 " pdb=" CB THR A 437 " pdb=" OG1 THR A 437 " ideal model delta sigma weight residual 109.60 104.45 5.15 1.50e+00 4.44e-01 1.18e+01 angle pdb=" OG1 THR A 170 " pdb=" CB THR A 170 " pdb=" CG2 THR A 170 " ideal model delta sigma weight residual 109.30 103.36 5.94 2.00e+00 2.50e-01 8.82e+00 angle pdb=" CA THR A 437 " pdb=" C THR A 437 " pdb=" O THR A 437 " ideal model delta sigma weight residual 121.06 118.22 2.84 1.16e+00 7.43e-01 5.98e+00 angle pdb=" C THR A 437 " pdb=" N ARG A 438 " pdb=" CA ARG A 438 " ideal model delta sigma weight residual 122.72 119.56 3.16 1.38e+00 5.25e-01 5.24e+00 ... (remaining 4963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 1907 17.81 - 35.62: 233 35.62 - 53.43: 61 53.43 - 71.24: 14 71.24 - 89.05: 12 Dihedral angle restraints: 2227 sinusoidal: 875 harmonic: 1352 Sorted by residual: dihedral pdb=" CD ARG A 436 " pdb=" NE ARG A 436 " pdb=" CZ ARG A 436 " pdb=" NH1 ARG A 436 " ideal model delta sinusoidal sigma weight residual 0.00 89.05 -89.05 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" CA ASP A 71 " pdb=" C ASP A 71 " pdb=" N TYR A 72 " pdb=" CA TYR A 72 " ideal model delta harmonic sigma weight residual 180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN A 386 " pdb=" C ASN A 386 " pdb=" N THR A 387 " pdb=" CA THR A 387 " ideal model delta harmonic sigma weight residual -180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 2224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 357 0.033 - 0.066: 148 0.066 - 0.098: 46 0.098 - 0.131: 16 0.131 - 0.164: 5 Chirality restraints: 572 Sorted by residual: chirality pdb=" CB THR A 170 " pdb=" CA THR A 170 " pdb=" OG1 THR A 170 " pdb=" CG2 THR A 170 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CB VAL A 135 " pdb=" CA VAL A 135 " pdb=" CG1 VAL A 135 " pdb=" CG2 VAL A 135 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA VAL A 135 " pdb=" N VAL A 135 " pdb=" C VAL A 135 " pdb=" CB VAL A 135 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 569 not shown) Planarity restraints: 651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 436 " 1.108 9.50e-02 1.11e+02 4.96e-01 1.49e+02 pdb=" NE ARG A 436 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG A 436 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 436 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 436 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 114 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 115 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 16 " -0.008 2.00e-02 2.50e+03 1.05e-02 1.92e+00 pdb=" CG PHE A 16 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 16 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 16 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 16 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 16 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 16 " -0.001 2.00e-02 2.50e+03 ... (remaining 648 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 2307 3.05 - 3.51: 3826 3.51 - 3.97: 5279 3.97 - 4.44: 6048 4.44 - 4.90: 9555 Nonbonded interactions: 27015 Sorted by model distance: nonbonded pdb=" O GLU A 392 " pdb=" OE1 GLU A 392 " model vdw 2.584 3.040 nonbonded pdb=" CB ARG A 436 " pdb=" NE ARG A 436 " model vdw 2.597 2.816 nonbonded pdb=" C SER A 160 " pdb=" OG SER A 160 " model vdw 2.612 2.616 nonbonded pdb=" O GLY A 228 " pdb=" OG SER A 229 " model vdw 2.617 3.040 nonbonded pdb=" N THR A 209 " pdb=" OG1 THR A 209 " model vdw 2.633 2.496 ... (remaining 27010 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: 1.160 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: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.480 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 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 : 0.006 0.048 3657 Z= 0.247 Angle : 0.683 10.693 4968 Z= 0.367 Chirality : 0.042 0.164 572 Planarity : 0.020 0.496 651 Dihedral : 18.177 89.054 1351 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.01 % Favored : 94.77 % Rotamer: Outliers : 2.13 % Allowed : 26.67 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.39), residues: 459 helix: 1.21 (0.36), residues: 201 sheet: -1.58 (0.48), residues: 84 loop : -0.49 (0.51), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 441 TYR 0.018 0.002 TYR A 466 PHE 0.024 0.002 PHE A 16 TRP 0.004 0.001 TRP A 418 HIS 0.006 0.002 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 ( 3657) covalent geometry : angle 0.68252 / 0.37 ( 4968) hydrogen bonds : bond 0.17104 / 10.37 ( 184) hydrogen bonds : angle 7.83787 / 5.90 ( 522) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.116 Fit side-chains REVERT: A 265 LEU cc_start: 0.7648 (mp) cc_final: 0.7337 (mp) REVERT: A 435 PHE cc_start: 0.7496 (t80) cc_final: 0.7295 (t80) outliers start: 8 outliers final: 4 residues processed: 60 average time/residue: 0.0766 time to fit residues: 5.6841 Evaluate side-chains 48 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.0370 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.185218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.174079 restraints weight = 4334.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.173012 restraints weight = 8165.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.170192 restraints weight = 8744.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.168892 restraints weight = 9103.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.168713 restraints weight = 7408.078| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3657 Z= 0.144 Angle : 0.559 6.984 4968 Z= 0.287 Chirality : 0.039 0.128 572 Planarity : 0.005 0.061 651 Dihedral : 4.808 22.567 509 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.00 % Allowed : 26.13 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.40), residues: 459 helix: 1.56 (0.36), residues: 203 sheet: -1.26 (0.50), residues: 84 loop : -0.35 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 438 TYR 0.009 0.001 TYR A 424 PHE 0.015 0.002 PHE A 107 TRP 0.009 0.002 TRP A 418 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 3657) covalent geometry : angle 0.55935 / 0.29 ( 4968) hydrogen bonds : bond 0.03182 / 1.99 ( 184) hydrogen bonds : angle 5.47222 / 4.12 ( 522) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7719 (mtp85) cc_final: 0.7311 (mtt90) REVERT: A 119 TRP cc_start: 0.8664 (OUTLIER) cc_final: 0.5167 (m-10) REVERT: A 190 MET cc_start: 0.7687 (mmm) cc_final: 0.7319 (mmt) REVERT: A 265 LEU cc_start: 0.7712 (mp) cc_final: 0.7371 (mp) outliers start: 15 outliers final: 9 residues processed: 73 average time/residue: 0.0791 time to fit residues: 7.0687 Evaluate side-chains 63 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 457 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: [33, 43, 13, 0, 9, 15, 29, 30, 5, 38, 17] chunk 33 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.189741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.179235 restraints weight = 4390.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.175997 restraints weight = 9859.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.174225 restraints weight = 10541.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.169712 restraints weight = 7531.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.168666 restraints weight = 8447.838| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 3657 Z= 0.233 Angle : 0.633 6.654 4968 Z= 0.324 Chirality : 0.042 0.147 572 Planarity : 0.005 0.061 651 Dihedral : 5.061 29.932 506 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.36 % Favored : 95.42 % Rotamer: Outliers : 6.13 % Allowed : 26.13 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.40), residues: 459 helix: 1.33 (0.36), residues: 204 sheet: -1.10 (0.54), residues: 83 loop : -0.42 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 76 TYR 0.010 0.002 TYR A 424 PHE 0.024 0.003 PHE A 122 TRP 0.005 0.001 TRP A 418 HIS 0.005 0.001 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 ( 3657) covalent geometry : angle 0.63320 / 0.32 ( 4968) hydrogen bonds : bond 0.03331 / 2.12 ( 184) hydrogen bonds : angle 5.26444 / 3.97 ( 522) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.144 Fit side-chains REVERT: A 11 MET cc_start: 0.8743 (tpp) cc_final: 0.8409 (tpp) REVERT: A 119 TRP cc_start: 0.8767 (OUTLIER) cc_final: 0.5348 (m-10) REVERT: A 265 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7499 (mp) REVERT: A 307 ASN cc_start: 0.7349 (t0) cc_final: 0.7112 (t0) REVERT: A 441 ARG cc_start: 0.5784 (mmm160) cc_final: 0.4972 (mtp-110) outliers start: 23 outliers final: 16 residues processed: 71 average time/residue: 0.0685 time to fit residues: 6.1439 Evaluate side-chains 65 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 457 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: [0, 34, 2, 36, 13, 10, 38, 11, 29, 28, 12] chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.192753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.179575 restraints weight = 4315.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.175620 restraints weight = 10482.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.174754 restraints weight = 11423.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.173150 restraints weight = 10245.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.173083 restraints weight = 9461.674| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3657 Z= 0.131 Angle : 0.546 6.525 4968 Z= 0.281 Chirality : 0.039 0.137 572 Planarity : 0.004 0.031 651 Dihedral : 4.600 20.901 506 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.36 % Favored : 95.42 % Rotamer: Outliers : 5.33 % Allowed : 27.47 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.41), residues: 459 helix: 1.67 (0.36), residues: 204 sheet: -0.71 (0.55), residues: 87 loop : -0.25 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 436 TYR 0.007 0.001 TYR A 424 PHE 0.019 0.002 PHE A 16 TRP 0.017 0.002 TRP A 418 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 3657) covalent geometry : angle 0.54603 / 0.28 ( 4968) hydrogen bonds : bond 0.02721 / 1.76 ( 184) hydrogen bonds : angle 4.81492 / 3.68 ( 522) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.146 Fit side-chains REVERT: A 11 MET cc_start: 0.8643 (tpp) cc_final: 0.8384 (tpp) REVERT: A 119 TRP cc_start: 0.8691 (OUTLIER) cc_final: 0.5367 (m-10) REVERT: A 190 MET cc_start: 0.7998 (mmm) cc_final: 0.7635 (mmt) REVERT: A 265 LEU cc_start: 0.7825 (mp) cc_final: 0.7436 (mp) outliers start: 20 outliers final: 14 residues processed: 67 average time/residue: 0.0437 time to fit residues: 3.9513 Evaluate side-chains 66 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 457 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: [15, 4, 17, 24, 30, 25, 42, 11, 18, 45, 38] chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.182120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.171390 restraints weight = 4462.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.159203 restraints weight = 9309.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.155529 restraints weight = 7898.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.154559 restraints weight = 7988.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.155255 restraints weight = 5812.835| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3657 Z= 0.204 Angle : 0.586 6.144 4968 Z= 0.301 Chirality : 0.040 0.148 572 Planarity : 0.004 0.031 651 Dihedral : 4.834 28.274 505 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.07 % Allowed : 26.93 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.40), residues: 459 helix: 1.59 (0.36), residues: 204 sheet: -0.81 (0.56), residues: 83 loop : -0.32 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 436 TYR 0.008 0.001 TYR A 97 PHE 0.022 0.002 PHE A 122 TRP 0.007 0.002 TRP A 418 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 ( 3657) covalent geometry : angle 0.58580 / 0.30 ( 4968) hydrogen bonds : bond 0.02821 / 1.82 ( 184) hydrogen bonds : angle 4.82860 / 3.69 ( 522) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.159 Fit side-chains REVERT: A 11 MET cc_start: 0.8646 (tpp) cc_final: 0.8428 (tpp) REVERT: A 119 TRP cc_start: 0.8799 (OUTLIER) cc_final: 0.5539 (m-10) REVERT: A 190 MET cc_start: 0.8210 (mmm) cc_final: 0.7764 (mmt) REVERT: A 265 LEU cc_start: 0.7820 (mp) cc_final: 0.7456 (mp) outliers start: 19 outliers final: 16 residues processed: 60 average time/residue: 0.0469 time to fit residues: 3.9034 Evaluate side-chains 65 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 457 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: [34, 36, 32, 24, 9, 30, 3, 39, 13, 40, 37] chunk 34 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.185299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.172894 restraints weight = 4428.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.168499 restraints weight = 9013.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.166889 restraints weight = 9353.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.162956 restraints weight = 9209.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.161925 restraints weight = 8417.352| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3657 Z= 0.133 Angle : 0.525 5.682 4968 Z= 0.268 Chirality : 0.039 0.139 572 Planarity : 0.004 0.031 651 Dihedral : 4.490 21.607 505 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.60 % Allowed : 27.20 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.41), residues: 459 helix: 1.84 (0.36), residues: 204 sheet: -0.64 (0.54), residues: 87 loop : -0.20 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 280 TYR 0.011 0.001 TYR A 344 PHE 0.021 0.002 PHE A 16 TRP 0.006 0.001 TRP A 388 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 3657) covalent geometry : angle 0.52515 / 0.27 ( 4968) hydrogen bonds : bond 0.02563 / 1.66 ( 184) hydrogen bonds : angle 4.64683 / 3.56 ( 522) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.157 Fit side-chains REVERT: A 11 MET cc_start: 0.8673 (tpp) cc_final: 0.8420 (tpp) REVERT: A 119 TRP cc_start: 0.8723 (OUTLIER) cc_final: 0.5451 (m-10) REVERT: A 190 MET cc_start: 0.8125 (mmm) cc_final: 0.7631 (mmt) REVERT: A 265 LEU cc_start: 0.7858 (mp) cc_final: 0.7449 (mp) outliers start: 21 outliers final: 15 residues processed: 66 average time/residue: 0.0515 time to fit residues: 4.5340 Evaluate side-chains 64 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 457 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: [15, 28, 33, 5, 1, 26, 10, 23, 32, 18, 29] chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.186398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.172410 restraints weight = 4449.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.171470 restraints weight = 10296.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.170041 restraints weight = 9671.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.169208 restraints weight = 8222.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.169045 restraints weight = 7609.192| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3657 Z= 0.118 Angle : 0.523 6.341 4968 Z= 0.266 Chirality : 0.038 0.136 572 Planarity : 0.003 0.028 651 Dihedral : 4.267 21.046 505 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.53 % Allowed : 26.67 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.41), residues: 459 helix: 2.02 (0.37), residues: 204 sheet: -0.62 (0.54), residues: 82 loop : -0.30 (0.52), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 469 TYR 0.016 0.001 TYR A 344 PHE 0.011 0.001 PHE A 122 TRP 0.006 0.001 TRP A 388 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 3657) covalent geometry : angle 0.52300 / 0.27 ( 4968) hydrogen bonds : bond 0.02357 / 1.54 ( 184) hydrogen bonds : angle 4.48926 / 3.44 ( 522) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.140 Fit side-chains REVERT: A 11 MET cc_start: 0.8703 (tpp) cc_final: 0.8404 (tpp) REVERT: A 47 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8282 (mm) REVERT: A 190 MET cc_start: 0.8141 (mmm) cc_final: 0.7647 (mmt) REVERT: A 265 LEU cc_start: 0.7827 (mp) cc_final: 0.7387 (mp) outliers start: 17 outliers final: 13 residues processed: 67 average time/residue: 0.0448 time to fit residues: 4.1431 Evaluate side-chains 64 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: [37, 25, 18, 43, 20, 40, 8, 29, 39, 15, 33] chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 33 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.186241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.173208 restraints weight = 4450.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.162964 restraints weight = 10092.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.161829 restraints weight = 10729.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.158834 restraints weight = 8097.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.158936 restraints weight = 7330.115| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3657 Z= 0.124 Angle : 0.537 7.398 4968 Z= 0.274 Chirality : 0.039 0.139 572 Planarity : 0.004 0.027 651 Dihedral : 4.268 21.086 505 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.07 % Allowed : 26.67 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.41), residues: 459 helix: 2.04 (0.36), residues: 204 sheet: -0.64 (0.54), residues: 82 loop : -0.31 (0.52), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 436 TYR 0.014 0.001 TYR A 344 PHE 0.018 0.002 PHE A 16 TRP 0.006 0.001 TRP A 388 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 ( 3657) covalent geometry : angle 0.53720 / 0.27 ( 4968) hydrogen bonds : bond 0.02422 / 1.58 ( 184) hydrogen bonds : angle 4.47078 / 3.41 ( 522) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.132 Fit side-chains REVERT: A 11 MET cc_start: 0.8799 (tpp) cc_final: 0.8481 (tpp) REVERT: A 47 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8144 (mm) REVERT: A 190 MET cc_start: 0.8159 (mmm) cc_final: 0.7634 (mmt) REVERT: A 265 LEU cc_start: 0.7881 (mp) cc_final: 0.7468 (mp) outliers start: 19 outliers final: 16 residues processed: 65 average time/residue: 0.0440 time to fit residues: 4.0284 Evaluate side-chains 67 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: [30, 26, 19, 11, 23, 39, 8, 32, 13, 33, 34] chunk 30 optimal weight: 6.9990 chunk 26 optimal weight: 0.0470 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.188231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.175726 restraints weight = 4384.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.168891 restraints weight = 9537.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.167868 restraints weight = 10017.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.165041 restraints weight = 9091.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.164607 restraints weight = 7688.894| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3657 Z= 0.103 Angle : 0.524 8.521 4968 Z= 0.264 Chirality : 0.039 0.130 572 Planarity : 0.003 0.026 651 Dihedral : 4.016 20.793 505 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.27 % Allowed : 27.73 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.41), residues: 459 helix: 2.25 (0.36), residues: 204 sheet: -0.58 (0.54), residues: 82 loop : -0.28 (0.52), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 436 TYR 0.018 0.001 TYR A 466 PHE 0.008 0.001 PHE A 107 TRP 0.007 0.001 TRP A 388 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.10 ( 3657) covalent geometry : angle 0.52399 / 0.26 ( 4968) hydrogen bonds : bond 0.02280 / 1.47 ( 184) hydrogen bonds : angle 4.39846 / 3.34 ( 522) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.165 Fit side-chains REVERT: A 11 MET cc_start: 0.8824 (tpp) cc_final: 0.8510 (tpp) REVERT: A 47 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8235 (mm) REVERT: A 190 MET cc_start: 0.8173 (mmm) cc_final: 0.7684 (mmt) REVERT: A 265 LEU cc_start: 0.7878 (mp) cc_final: 0.7515 (mp) outliers start: 16 outliers final: 14 residues processed: 67 average time/residue: 0.0443 time to fit residues: 4.0978 Evaluate side-chains 69 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: [36, 14, 6, 42, 22, 25, 1, 35, 4, 45, 21] chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.0030 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 HIS A 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.195734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.176914 restraints weight = 4431.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.173657 restraints weight = 9580.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.172778 restraints weight = 10127.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.171572 restraints weight = 7326.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.171220 restraints weight = 8078.893| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3657 Z= 0.151 Angle : 0.549 5.607 4968 Z= 0.281 Chirality : 0.040 0.144 572 Planarity : 0.004 0.026 651 Dihedral : 4.311 23.841 505 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.00 % Allowed : 29.07 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.41), residues: 459 helix: 2.11 (0.36), residues: 204 sheet: -0.68 (0.54), residues: 82 loop : -0.31 (0.52), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 436 TYR 0.018 0.001 TYR A 466 PHE 0.020 0.002 PHE A 16 TRP 0.003 0.001 TRP A 388 HIS 0.009 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 3657) covalent geometry : angle 0.54935 / 0.28 ( 4968) hydrogen bonds : bond 0.02489 / 1.61 ( 184) hydrogen bonds : angle 4.49296 / 3.40 ( 522) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 11 MET cc_start: 0.8670 (tpp) cc_final: 0.8371 (tpp) REVERT: A 47 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8322 (mm) REVERT: A 190 MET cc_start: 0.8212 (mmm) cc_final: 0.7668 (mmt) REVERT: A 265 LEU cc_start: 0.8100 (mp) cc_final: 0.7734 (mp) outliers start: 15 outliers final: 13 residues processed: 66 average time/residue: 0.0514 time to fit residues: 4.4832 Evaluate side-chains 70 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 119 TRP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: [23, 4, 42, 8, 12, 3, 10, 41, 9, 2, 39] chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.185709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.152738 restraints weight = 4409.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.150609 restraints weight = 8761.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.151746 restraints weight = 8240.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.151780 restraints weight = 4922.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.152508 restraints weight = 4634.474| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3657 Z= 0.150 Angle : 0.559 7.221 4968 Z= 0.284 Chirality : 0.040 0.143 572 Planarity : 0.004 0.027 651 Dihedral : 4.346 23.129 505 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.00 % Allowed : 29.60 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.41), residues: 459 helix: 2.05 (0.36), residues: 204 sheet: -0.67 (0.55), residues: 82 loop : -0.34 (0.52), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 436 TYR 0.019 0.001 TYR A 466 PHE 0.015 0.001 PHE A 122 TRP 0.003 0.001 TRP A 388 HIS 0.008 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 3657) covalent geometry : angle 0.55940 / 0.28 ( 4968) hydrogen bonds : bond 0.02542 / 1.66 ( 184) hydrogen bonds : angle 4.52884 / 3.43 ( 522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 773.82 seconds wall clock time: 14 minutes 1.89 seconds (841.89 seconds total)