Starting phenix.real_space_refine on Wed Mar 5 21:51:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqr_60389/03_2025/8zqr_60389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqr_60389/03_2025/8zqr_60389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zqr_60389/03_2025/8zqr_60389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqr_60389/03_2025/8zqr_60389.map" model { file = "/net/cci-nas-00/data/ceres_data/8zqr_60389/03_2025/8zqr_60389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqr_60389/03_2025/8zqr_60389.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.079 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 20 5.16 5 C 2524 2.51 5 N 564 2.21 5 O 670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3778 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3739 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 22, 'TRANS': 463} Chain breaks: 2 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.12, per 1000 atoms: 0.83 Number of scatterers: 3778 At special positions: 0 Unit cell: (83.3, 75.65, 94.35, 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 20 16.00 O 670 8.00 N 564 7.00 C 2524 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 301 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 490.3 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: 884 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 73.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 4 through 21 removed outlier: 3.874A pdb=" N LEU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 17 " --> pdb=" O VAL A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 removed outlier: 3.624A pdb=" N ALA A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TRP A 62 " --> pdb=" O MET A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 77 removed outlier: 4.332A pdb=" N ALA A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.576A pdb=" N TRP A 84 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 102 removed outlier: 4.002A pdb=" N ILE A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.502A pdb=" N ARG A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.296A pdb=" N PHE A 118 " --> pdb=" O MET A 114 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 removed outlier: 4.205A pdb=" N MET A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 Processing helix chain 'A' and resid 160 through 179 removed outlier: 4.297A pdb=" N ILE A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 208 removed outlier: 3.840A pdb=" N VAL A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Proline residue: A 204 - end of helix removed outlier: 3.668A pdb=" N SER A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.712A pdb=" N PHE A 258 " --> pdb=" O TRP A 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 297 removed outlier: 3.838A pdb=" N ILE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'A' and resid 329 through 346 removed outlier: 3.770A pdb=" N GLY A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 362 removed outlier: 4.493A pdb=" N SER A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 399 removed outlier: 3.520A pdb=" N VAL A 385 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 409 removed outlier: 3.532A pdb=" N LEU A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.854A pdb=" N CYS A 423 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 450 removed outlier: 3.607A pdb=" N ALA A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 437 " --> pdb=" O TYR A 433 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 502 removed outlier: 3.550A pdb=" N ILE A 492 " --> pdb=" O PHE A 488 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467 220 hydrogen bonds defined for protein. 654 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: 0.90 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 564 1.30 - 1.43: 1102 1.43 - 1.56: 2184 1.56 - 1.68: 0 1.68 - 1.81: 35 Bond restraints: 3885 Sorted by residual: bond pdb=" N ILE A 68 " pdb=" CA ILE A 68 " ideal model delta sigma weight residual 1.459 1.388 0.071 1.25e-02 6.40e+03 3.25e+01 bond pdb=" CA VAL A 63 " pdb=" C VAL A 63 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.27e-02 6.20e+03 2.22e+01 bond pdb=" CA GLY A 65 " pdb=" C GLY A 65 " ideal model delta sigma weight residual 1.514 1.451 0.064 1.41e-02 5.03e+03 2.04e+01 bond pdb=" CA VAL A 63 " pdb=" CB VAL A 63 " ideal model delta sigma weight residual 1.540 1.480 0.060 1.36e-02 5.41e+03 1.94e+01 bond pdb=" C VAL A 63 " pdb=" O VAL A 63 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.19e-02 7.06e+03 1.93e+01 ... (remaining 3880 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 5192 2.72 - 5.44: 89 5.44 - 8.16: 22 8.16 - 10.89: 2 10.89 - 13.61: 1 Bond angle restraints: 5306 Sorted by residual: angle pdb=" C ASN A 69 " pdb=" CA ASN A 69 " pdb=" CB ASN A 69 " ideal model delta sigma weight residual 109.34 120.14 -10.80 1.55e+00 4.16e-01 4.86e+01 angle pdb=" N ILE A 68 " pdb=" CA ILE A 68 " pdb=" C ILE A 68 " ideal model delta sigma weight residual 109.34 122.95 -13.61 2.08e+00 2.31e-01 4.28e+01 angle pdb=" N GLY A 70 " pdb=" CA GLY A 70 " pdb=" C GLY A 70 " ideal model delta sigma weight residual 112.77 120.83 -8.06 1.28e+00 6.10e-01 3.97e+01 angle pdb=" N ASP A 317 " pdb=" CA ASP A 317 " pdb=" C ASP A 317 " ideal model delta sigma weight residual 113.38 107.46 5.92 1.23e+00 6.61e-01 2.32e+01 angle pdb=" O GLY A 66 " pdb=" C GLY A 66 " pdb=" N TYR A 67 " ideal model delta sigma weight residual 122.70 128.75 -6.05 1.30e+00 5.92e-01 2.17e+01 ... (remaining 5301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 1992 21.90 - 43.79: 205 43.79 - 65.68: 30 65.68 - 87.58: 11 87.58 - 109.47: 4 Dihedral angle restraints: 2242 sinusoidal: 845 harmonic: 1397 Sorted by residual: dihedral pdb=" C ILE A 68 " pdb=" N ILE A 68 " pdb=" CA ILE A 68 " pdb=" CB ILE A 68 " ideal model delta harmonic sigma weight residual -122.00 -136.16 14.16 0 2.50e+00 1.60e-01 3.21e+01 dihedral pdb=" CA GLU A 376 " pdb=" C GLU A 376 " pdb=" N ILE A 377 " pdb=" CA ILE A 377 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA LYS A 375 " pdb=" C LYS A 375 " pdb=" N GLU A 376 " pdb=" CA GLU A 376 " ideal model delta harmonic sigma weight residual 180.00 -156.95 -23.05 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 2239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 613 0.136 - 0.273: 7 0.273 - 0.409: 1 0.409 - 0.545: 3 0.545 - 0.682: 1 Chirality restraints: 625 Sorted by residual: chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 1.75 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CB VAL A 63 " pdb=" CA VAL A 63 " pdb=" CG1 VAL A 63 " pdb=" CG2 VAL A 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CA VAL A 63 " pdb=" N VAL A 63 " pdb=" C VAL A 63 " pdb=" CB VAL A 63 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.30e+00 ... (remaining 622 not shown) Planarity restraints: 641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 66 " -0.013 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C GLY A 66 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY A 66 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR A 67 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 203 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO A 204 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 406 " 0.018 2.00e-02 2.50e+03 1.31e-02 4.28e+00 pdb=" CG TRP A 406 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 406 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 406 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 406 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 406 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 406 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 406 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 406 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 406 " 0.009 2.00e-02 2.50e+03 ... (remaining 638 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 736 2.76 - 3.30: 3602 3.30 - 3.83: 5919 3.83 - 4.37: 6563 4.37 - 4.90: 11532 Nonbonded interactions: 28352 Sorted by model distance: nonbonded pdb=" O ILE A 294 " pdb=" OG1 THR A 298 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR A 113 " pdb=" OE1 GLN A 255 " model vdw 2.298 3.040 nonbonded pdb=" N ASP A 512 " pdb=" OD1 ASP A 512 " model vdw 2.374 3.120 nonbonded pdb=" OH TYR A 433 " pdb=" O PHE A 514 " model vdw 2.400 3.040 nonbonded pdb=" OG1 THR A 303 " pdb=" N ALA A 304 " model vdw 2.427 3.120 ... (remaining 28347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.320 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.390 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.005 0.071 3885 Z= 0.307 Angle : 0.922 13.607 5306 Z= 0.524 Chirality : 0.064 0.682 625 Planarity : 0.006 0.056 640 Dihedral : 18.433 109.470 1358 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.76 % Allowed : 26.72 % Favored : 72.52 % Cbeta Deviations : 0.45 % 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: -0.86 (0.39), residues: 480 helix: 0.31 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -2.28 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 406 HIS 0.003 0.001 HIS A 221 PHE 0.014 0.001 PHE A 140 TYR 0.016 0.001 TYR A 67 ARG 0.002 0.000 ARG A 107 *********************** 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 81 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.428 Fit side-chains REVERT: A 73 GLU cc_start: 0.8223 (tt0) cc_final: 0.7654 (tt0) REVERT: A 371 ASN cc_start: 0.7652 (p0) cc_final: 0.7186 (m110) outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.1390 time to fit residues: 14.0661 Evaluate side-chains 75 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 432 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.153273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.134350 restraints weight = 5927.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137275 restraints weight = 3322.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139248 restraints weight = 2262.897| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3885 Z= 0.231 Angle : 0.729 9.551 5306 Z= 0.361 Chirality : 0.044 0.321 625 Planarity : 0.006 0.050 640 Dihedral : 9.838 65.232 583 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.09 % Allowed : 25.45 % Favored : 69.47 % 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: -0.18 (0.41), residues: 480 helix: 0.87 (0.31), residues: 327 sheet: None (None), residues: 0 loop : -2.33 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 406 HIS 0.003 0.001 HIS A 162 PHE 0.011 0.001 PHE A 479 TYR 0.014 0.001 TYR A 439 ARG 0.002 0.000 ARG A 125 *********************** 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 99 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.380 Fit side-chains REVERT: A 62 TRP cc_start: 0.8451 (m100) cc_final: 0.8145 (m100) REVERT: A 73 GLU cc_start: 0.8541 (tt0) cc_final: 0.8143 (tt0) REVERT: A 284 MET cc_start: 0.7557 (tpp) cc_final: 0.7300 (tpt) REVERT: A 448 THR cc_start: 0.8758 (m) cc_final: 0.8555 (m) outliers start: 20 outliers final: 14 residues processed: 90 average time/residue: 0.1302 time to fit residues: 15.1506 Evaluate side-chains 83 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 350 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.155996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137305 restraints weight = 5849.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140323 restraints weight = 3290.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142294 restraints weight = 2237.116| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3885 Z= 0.187 Angle : 0.654 9.463 5306 Z= 0.321 Chirality : 0.043 0.306 625 Planarity : 0.005 0.042 640 Dihedral : 6.743 54.718 582 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.34 % Allowed : 26.46 % Favored : 68.19 % 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: 0.09 (0.41), residues: 480 helix: 0.91 (0.30), residues: 335 sheet: None (None), residues: 0 loop : -1.94 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 406 HIS 0.002 0.001 HIS A 209 PHE 0.011 0.001 PHE A 140 TYR 0.017 0.001 TYR A 496 ARG 0.002 0.000 ARG A 125 *********************** 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 105 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.410 Fit side-chains REVERT: A 73 GLU cc_start: 0.8431 (tt0) cc_final: 0.8211 (tt0) REVERT: A 97 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8172 (mp) REVERT: A 120 GLN cc_start: 0.6919 (mt0) cc_final: 0.6542 (mp10) REVERT: A 284 MET cc_start: 0.7493 (tpp) cc_final: 0.7267 (tpt) REVERT: A 496 TYR cc_start: 0.7216 (t80) cc_final: 0.6165 (m-10) outliers start: 21 outliers final: 12 residues processed: 99 average time/residue: 0.1398 time to fit residues: 17.5837 Evaluate side-chains 84 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 412 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.156317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137655 restraints weight = 5919.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140682 restraints weight = 3302.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.142622 restraints weight = 2231.863| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3885 Z= 0.194 Angle : 0.670 9.582 5306 Z= 0.323 Chirality : 0.043 0.298 625 Planarity : 0.005 0.042 640 Dihedral : 6.174 54.542 582 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.07 % Allowed : 28.50 % Favored : 67.43 % 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: 0.20 (0.41), residues: 480 helix: 1.00 (0.30), residues: 334 sheet: None (None), residues: 0 loop : -1.90 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 406 HIS 0.001 0.001 HIS A 209 PHE 0.011 0.001 PHE A 140 TYR 0.015 0.001 TYR A 364 ARG 0.002 0.000 ARG A 125 *********************** 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 91 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.375 Fit side-chains REVERT: A 97 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8138 (mp) REVERT: A 284 MET cc_start: 0.7551 (tpp) cc_final: 0.7117 (tpt) REVERT: A 496 TYR cc_start: 0.7256 (t80) cc_final: 0.6216 (m-10) outliers start: 16 outliers final: 11 residues processed: 84 average time/residue: 0.1260 time to fit residues: 13.9613 Evaluate side-chains 85 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 350 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.153344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.134593 restraints weight = 6036.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.137697 restraints weight = 3322.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139759 restraints weight = 2216.667| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3885 Z= 0.214 Angle : 0.654 9.567 5306 Z= 0.317 Chirality : 0.043 0.298 625 Planarity : 0.005 0.041 640 Dihedral : 6.081 54.540 582 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.34 % Allowed : 26.72 % Favored : 67.94 % 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: 0.19 (0.41), residues: 480 helix: 0.99 (0.30), residues: 334 sheet: None (None), residues: 0 loop : -1.89 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 406 HIS 0.002 0.001 HIS A 209 PHE 0.010 0.001 PHE A 479 TYR 0.014 0.001 TYR A 67 ARG 0.003 0.000 ARG A 125 *********************** 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 102 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.409 Fit side-chains REVERT: A 67 TYR cc_start: 0.8634 (t80) cc_final: 0.8408 (t80) REVERT: A 97 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8085 (mp) REVERT: A 284 MET cc_start: 0.7539 (tpp) cc_final: 0.7189 (tpt) REVERT: A 411 ASP cc_start: 0.8190 (t0) cc_final: 0.7944 (t0) REVERT: A 496 TYR cc_start: 0.7315 (t80) cc_final: 0.6276 (m-10) outliers start: 21 outliers final: 17 residues processed: 94 average time/residue: 0.1245 time to fit residues: 15.2328 Evaluate side-chains 89 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 412 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 10 optimal weight: 0.0470 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 0.0970 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.156900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.138354 restraints weight = 5970.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.141277 restraints weight = 3441.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.143317 restraints weight = 2365.134| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3885 Z= 0.153 Angle : 0.617 9.613 5306 Z= 0.301 Chirality : 0.042 0.294 625 Planarity : 0.004 0.041 640 Dihedral : 5.863 54.568 582 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.33 % Allowed : 27.74 % Favored : 67.94 % 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: 0.47 (0.41), residues: 480 helix: 1.19 (0.30), residues: 334 sheet: None (None), residues: 0 loop : -1.76 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 406 HIS 0.001 0.000 HIS A 162 PHE 0.011 0.001 PHE A 140 TYR 0.014 0.001 TYR A 364 ARG 0.002 0.000 ARG A 125 *********************** 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 90 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.378 Fit side-chains REVERT: A 97 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8096 (mp) REVERT: A 177 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7338 (tp) REVERT: A 284 MET cc_start: 0.7524 (tpp) cc_final: 0.7118 (tpt) REVERT: A 411 ASP cc_start: 0.8060 (t0) cc_final: 0.7849 (t0) REVERT: A 496 TYR cc_start: 0.7237 (t80) cc_final: 0.6249 (m-10) outliers start: 17 outliers final: 11 residues processed: 82 average time/residue: 0.1208 time to fit residues: 13.1668 Evaluate side-chains 82 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 412 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.0040 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.4970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.157964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139133 restraints weight = 6008.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.142144 restraints weight = 3418.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.144237 restraints weight = 2334.111| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3885 Z= 0.159 Angle : 0.617 9.588 5306 Z= 0.298 Chirality : 0.041 0.290 625 Planarity : 0.004 0.040 640 Dihedral : 5.804 54.686 582 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.58 % Allowed : 28.75 % Favored : 66.67 % 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: 0.63 (0.41), residues: 480 helix: 1.30 (0.30), residues: 334 sheet: None (None), residues: 0 loop : -1.67 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 406 HIS 0.001 0.001 HIS A 162 PHE 0.011 0.001 PHE A 140 TYR 0.020 0.001 TYR A 364 ARG 0.002 0.000 ARG A 125 *********************** 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 94 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.383 Fit side-chains REVERT: A 73 GLU cc_start: 0.8268 (tt0) cc_final: 0.7847 (tp30) REVERT: A 97 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8044 (mp) REVERT: A 177 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7212 (tp) REVERT: A 284 MET cc_start: 0.7562 (tpp) cc_final: 0.7160 (tpt) REVERT: A 496 TYR cc_start: 0.7259 (t80) cc_final: 0.6278 (m-10) outliers start: 18 outliers final: 14 residues processed: 87 average time/residue: 0.1392 time to fit residues: 15.4322 Evaluate side-chains 85 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 432 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 0.0060 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.158645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.140009 restraints weight = 5940.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143081 restraints weight = 3382.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.145005 restraints weight = 2297.657| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3885 Z= 0.158 Angle : 0.610 9.600 5306 Z= 0.295 Chirality : 0.041 0.291 625 Planarity : 0.004 0.040 640 Dihedral : 5.697 54.652 582 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.33 % Allowed : 30.03 % Favored : 65.65 % 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: 0.70 (0.41), residues: 480 helix: 1.33 (0.30), residues: 335 sheet: None (None), residues: 0 loop : -1.58 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 406 HIS 0.001 0.000 HIS A 209 PHE 0.009 0.001 PHE A 140 TYR 0.018 0.001 TYR A 364 ARG 0.002 0.000 ARG A 125 *********************** 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 89 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.402 Fit side-chains REVERT: A 73 GLU cc_start: 0.8217 (tt0) cc_final: 0.7882 (tp30) REVERT: A 97 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 177 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7173 (tp) REVERT: A 284 MET cc_start: 0.7533 (tpp) cc_final: 0.7136 (tpt) REVERT: A 496 TYR cc_start: 0.7251 (t80) cc_final: 0.6272 (m-10) outliers start: 17 outliers final: 11 residues processed: 82 average time/residue: 0.1355 time to fit residues: 14.2349 Evaluate side-chains 82 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 432 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.0070 chunk 43 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.156922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.138253 restraints weight = 5951.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.141238 restraints weight = 3400.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.143240 restraints weight = 2324.377| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3885 Z= 0.176 Angle : 0.646 9.503 5306 Z= 0.308 Chirality : 0.041 0.278 625 Planarity : 0.004 0.039 640 Dihedral : 5.691 54.694 582 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.33 % Allowed : 29.52 % Favored : 66.16 % 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: 0.71 (0.41), residues: 480 helix: 1.31 (0.30), residues: 335 sheet: None (None), residues: 0 loop : -1.53 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 406 HIS 0.002 0.001 HIS A 162 PHE 0.010 0.001 PHE A 140 TYR 0.016 0.001 TYR A 364 ARG 0.002 0.000 ARG A 125 *********************** 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 87 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.411 Fit side-chains REVERT: A 73 GLU cc_start: 0.8238 (tt0) cc_final: 0.7859 (tt0) REVERT: A 97 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7999 (mp) REVERT: A 177 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7015 (tp) REVERT: A 284 MET cc_start: 0.7538 (tpp) cc_final: 0.7129 (tpt) REVERT: A 496 TYR cc_start: 0.7260 (t80) cc_final: 0.6272 (m-10) outliers start: 17 outliers final: 13 residues processed: 82 average time/residue: 0.1427 time to fit residues: 14.8636 Evaluate side-chains 83 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 432 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.0270 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.157514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139069 restraints weight = 5987.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.142013 restraints weight = 3439.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.144059 restraints weight = 2348.515| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3885 Z= 0.167 Angle : 0.638 9.555 5306 Z= 0.308 Chirality : 0.041 0.276 625 Planarity : 0.004 0.039 640 Dihedral : 5.659 54.659 582 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.07 % Allowed : 31.30 % Favored : 64.63 % 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: 0.78 (0.41), residues: 480 helix: 1.40 (0.30), residues: 330 sheet: None (None), residues: 0 loop : -1.51 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 406 HIS 0.001 0.000 HIS A 162 PHE 0.010 0.001 PHE A 140 TYR 0.019 0.001 TYR A 364 ARG 0.002 0.000 ARG A 125 ********************** 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 85 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.415 Fit side-chains REVERT: A 73 GLU cc_start: 0.8214 (tt0) cc_final: 0.7814 (tt0) REVERT: A 97 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7965 (mp) REVERT: A 177 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7000 (tp) REVERT: A 284 MET cc_start: 0.7518 (tpp) cc_final: 0.7123 (tpt) REVERT: A 496 TYR cc_start: 0.7246 (t80) cc_final: 0.6278 (m-10) outliers start: 16 outliers final: 11 residues processed: 80 average time/residue: 0.1324 time to fit residues: 13.6947 Evaluate side-chains 79 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 432 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 0.9980 chunk 36 optimal weight: 0.0870 chunk 3 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 37 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.0170 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.157569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.139451 restraints weight = 5838.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.142369 restraints weight = 3344.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.144383 restraints weight = 2281.002| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3885 Z= 0.161 Angle : 0.624 9.576 5306 Z= 0.301 Chirality : 0.041 0.275 625 Planarity : 0.004 0.039 640 Dihedral : 5.632 54.793 582 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.82 % Allowed : 30.79 % Favored : 65.39 % 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: 0.92 (0.42), residues: 480 helix: 1.48 (0.30), residues: 329 sheet: None (None), residues: 0 loop : -1.33 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 406 HIS 0.001 0.000 HIS A 162 PHE 0.013 0.001 PHE A 258 TYR 0.020 0.001 TYR A 364 ARG 0.002 0.000 ARG A 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1533.51 seconds wall clock time: 27 minutes 25.24 seconds (1645.24 seconds total)