Starting phenix.real_space_refine on Mon Jan 13 17:10:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8znb_60266/01_2025/8znb_60266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8znb_60266/01_2025/8znb_60266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8znb_60266/01_2025/8znb_60266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8znb_60266/01_2025/8znb_60266.map" model { file = "/net/cci-nas-00/data/ceres_data/8znb_60266/01_2025/8znb_60266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8znb_60266/01_2025/8znb_60266.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2113 2.51 5 N 564 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3342 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Conformer: "B" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} bond proxies already assigned to first conformer: 3321 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 69 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1, 'water': 21} Link IDs: {None: 21} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 89 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 89 " occ=0.50 Time building chain proxies: 4.28, per 1000 atoms: 1.28 Number of scatterers: 3342 At special positions: 0 Unit cell: (66.176, 61.664, 73.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 648 8.00 N 564 7.00 C 2113 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: 1.23 Conformation dependent library (CDL) restraints added in 1.2 seconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 56.0% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.745A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.795A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.722A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.565A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 235 removed outlier: 3.701A pdb=" N TYR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 removed outlier: 4.008A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.676A pdb=" N ALA A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.548A pdb=" N GLU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.985A pdb=" N ASN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.664A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.664A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 250 removed outlier: 7.291A pdb=" N ILE A 215 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL A 242 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL A 217 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 547 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 938 1.33 - 1.45: 548 1.45 - 1.57: 1881 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3399 Sorted by residual: bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.612 0.221 3.80e-02 6.93e+02 3.38e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.603 0.154 3.50e-02 8.16e+02 1.93e+01 bond pdb=" C PRO A 252 " pdb=" N ASP A 253 " ideal model delta sigma weight residual 1.335 1.384 -0.050 1.36e-02 5.41e+03 1.33e+01 bond pdb=" C2B NDP A 500 " pdb=" O2B NDP A 500 " ideal model delta sigma weight residual 1.330 1.423 -0.093 2.90e-02 1.19e+03 1.02e+01 bond pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 1.368 1.448 -0.080 3.20e-02 9.77e+02 6.22e+00 ... (remaining 3394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 4599 4.88 - 9.76: 14 9.76 - 14.64: 2 14.64 - 19.52: 1 19.52 - 24.40: 1 Bond angle restraints: 4617 Sorted by residual: angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 132.14 -24.40 1.95e+00 2.62e-01 1.56e+02 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 118.94 -15.10 1.91e+00 2.73e-01 6.22e+01 angle pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 104.93 119.33 -14.40 2.66e+00 1.41e-01 2.93e+01 angle pdb=" O2N NDP A 500 " pdb=" PN NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 100.52 109.57 -9.05 1.91e+00 2.74e-01 2.24e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 112.31 5.15 1.17e+00 7.36e-01 1.95e+01 ... (remaining 4612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1819 17.98 - 35.97: 143 35.97 - 53.95: 36 53.95 - 71.94: 10 71.94 - 89.92: 7 Dihedral angle restraints: 2015 sinusoidal: 822 harmonic: 1193 Sorted by residual: dihedral pdb=" CA THR A 148 " pdb=" C THR A 148 " pdb=" N ASN A 149 " pdb=" CA ASN A 149 " ideal model delta harmonic sigma weight residual 180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 163.45 16.55 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU A 303 " pdb=" CG GLU A 303 " pdb=" CD GLU A 303 " pdb=" OE1 GLU A 303 " ideal model delta sinusoidal sigma weight residual 0.00 88.04 -88.04 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 2012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 400 0.052 - 0.104: 84 0.104 - 0.156: 16 0.156 - 0.208: 1 0.208 - 0.260: 1 Chirality restraints: 502 Sorted by residual: chirality pdb=" C4D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" C5D NDP A 500 " pdb=" O4D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.45 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C1B NDP A 500 " pdb=" C2B NDP A 500 " pdb=" N9A NDP A 500 " pdb=" O4B NDP A 500 " both_signs ideal model delta sigma weight residual False 2.59 2.41 0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" C2D NDP A 500 " pdb=" C1D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" O2D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.56 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 499 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO A 150 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 393 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C ILE A 393 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE A 393 " 0.009 2.00e-02 2.50e+03 pdb=" N HIS A 394 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 394 " -0.013 2.00e-02 2.50e+03 1.09e-02 1.79e+00 pdb=" CG HIS A 394 " 0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS A 394 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS A 394 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 394 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 394 " -0.011 2.00e-02 2.50e+03 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1290 2.92 - 3.41: 3444 3.41 - 3.91: 5994 3.91 - 4.40: 6792 4.40 - 4.90: 10962 Nonbonded interactions: 28482 Sorted by model distance: nonbonded pdb=" NE ARG A 65 " pdb=" O HOH A 601 " model vdw 2.421 3.120 nonbonded pdb=" OH TYR A 408 " pdb=" O LYS A 419 " model vdw 2.443 3.040 nonbonded pdb=" OE1 GLU A 354 " pdb=" O HOH A 602 " model vdw 2.449 3.040 nonbonded pdb=" NZ LYS A 177 " pdb=" OD1 ASN A 358 " model vdw 2.449 3.120 nonbonded pdb=" NZ LYS A 177 " pdb=" OE2 GLU A 354 " model vdw 2.464 3.120 ... (remaining 28477 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.490 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 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 : 0.007 0.221 3399 Z= 0.492 Angle : 0.945 24.400 4617 Z= 0.541 Chirality : 0.047 0.260 502 Planarity : 0.005 0.045 589 Dihedral : 15.547 89.920 1255 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.06 % Allowed : 0.59 % Favored : 97.35 % 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: 0.61 (0.41), residues: 417 helix: 1.83 (0.37), residues: 202 sheet: -0.52 (0.69), residues: 64 loop : -1.15 (0.45), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 92 HIS 0.008 0.002 HIS A 394 PHE 0.010 0.002 PHE A 341 TYR 0.013 0.002 TYR A 226 ARG 0.003 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.354 Fit side-chains REVERT: A 187 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7563 (ttm110) REVERT: A 333 LYS cc_start: 0.8444 (mtpp) cc_final: 0.8192 (mtpt) REVERT: A 386 ASN cc_start: 0.8503 (m-40) cc_final: 0.8166 (m110) REVERT: A 388 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.7957 (t70) outliers start: 7 outliers final: 0 residues processed: 86 average time/residue: 1.3012 time to fit residues: 115.0023 Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 267 HIS ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.138366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.092197 restraints weight = 10747.670| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.75 r_work: 0.2787 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3399 Z= 0.207 Angle : 0.533 8.196 4617 Z= 0.283 Chirality : 0.045 0.140 502 Planarity : 0.004 0.046 589 Dihedral : 6.315 52.138 470 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.65 % Allowed : 12.06 % Favored : 85.29 % 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: 0.97 (0.41), residues: 417 helix: 2.06 (0.36), residues: 201 sheet: -0.10 (0.72), residues: 62 loop : -0.95 (0.45), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.003 0.001 HIS A 267 PHE 0.009 0.002 PHE A 57 TYR 0.010 0.001 TYR A 363 ARG 0.002 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.363 Fit side-chains REVERT: A 187 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7750 (ttm110) REVERT: A 333 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8231 (mtpt) REVERT: A 383 GLU cc_start: 0.8308 (tt0) cc_final: 0.7956 (mt-10) REVERT: A 388 HIS cc_start: 0.8851 (OUTLIER) cc_final: 0.8039 (t70) outliers start: 9 outliers final: 2 residues processed: 65 average time/residue: 1.3518 time to fit residues: 90.3445 Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 0.2980 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.135641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.092105 restraints weight = 15150.953| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.96 r_work: 0.2741 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3399 Z= 0.206 Angle : 0.533 6.154 4617 Z= 0.278 Chirality : 0.045 0.146 502 Planarity : 0.005 0.047 589 Dihedral : 6.345 54.328 470 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.53 % Allowed : 13.53 % Favored : 82.94 % 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: 0.82 (0.42), residues: 417 helix: 1.96 (0.36), residues: 206 sheet: -0.61 (0.68), residues: 69 loop : -0.95 (0.47), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.002 0.001 HIS A 267 PHE 0.009 0.002 PHE A 341 TYR 0.012 0.001 TYR A 363 ARG 0.002 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.385 Fit side-chains REVERT: A 8 GLU cc_start: 0.7935 (pt0) cc_final: 0.7395 (tt0) REVERT: A 187 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.7562 (ttm110) REVERT: A 214 LYS cc_start: 0.8789 (mmtp) cc_final: 0.8245 (mppt) REVERT: A 252 PRO cc_start: 0.8033 (Cg_endo) cc_final: 0.7764 (Cg_exo) REVERT: A 297 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8410 (pp) REVERT: A 333 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8223 (mtpt) REVERT: A 383 GLU cc_start: 0.8292 (tt0) cc_final: 0.7861 (mt-10) REVERT: A 388 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.7802 (t70) REVERT: A 419 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7991 (mttp) outliers start: 12 outliers final: 2 residues processed: 64 average time/residue: 1.4381 time to fit residues: 94.5289 Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.090363 restraints weight = 14643.643| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.96 r_work: 0.2700 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3399 Z= 0.232 Angle : 0.557 9.255 4617 Z= 0.291 Chirality : 0.046 0.154 502 Planarity : 0.005 0.047 589 Dihedral : 6.524 57.982 470 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.65 % Allowed : 15.00 % Favored : 82.35 % 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: 0.73 (0.41), residues: 417 helix: 1.84 (0.36), residues: 208 sheet: -0.59 (0.67), residues: 69 loop : -1.00 (0.47), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.002 0.001 HIS A 267 PHE 0.011 0.002 PHE A 341 TYR 0.013 0.001 TYR A 363 ARG 0.001 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.371 Fit side-chains REVERT: A 187 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7553 (ttm110) REVERT: A 214 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8301 (mttp) REVERT: A 297 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8348 (pp) REVERT: A 333 LYS cc_start: 0.8599 (mtpp) cc_final: 0.8306 (mtpt) REVERT: A 383 GLU cc_start: 0.8292 (tt0) cc_final: 0.7815 (mt-10) REVERT: A 388 HIS cc_start: 0.8915 (OUTLIER) cc_final: 0.7872 (t70) REVERT: A 419 LYS cc_start: 0.8341 (mtpt) cc_final: 0.8007 (mttp) outliers start: 9 outliers final: 2 residues processed: 59 average time/residue: 1.5121 time to fit residues: 91.4977 Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 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 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.135649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.092684 restraints weight = 11793.663| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.68 r_work: 0.2783 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3399 Z= 0.172 Angle : 0.499 6.151 4617 Z= 0.263 Chirality : 0.044 0.149 502 Planarity : 0.004 0.047 589 Dihedral : 6.388 59.861 470 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.35 % Allowed : 17.06 % Favored : 80.59 % 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: 0.79 (0.42), residues: 417 helix: 1.90 (0.37), residues: 209 sheet: -0.56 (0.68), residues: 69 loop : -1.01 (0.47), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 92 HIS 0.002 0.001 HIS A 267 PHE 0.009 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.001 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.509 Fit side-chains REVERT: A 214 LYS cc_start: 0.8883 (mmtp) cc_final: 0.8380 (mttp) REVERT: A 297 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8387 (pp) REVERT: A 333 LYS cc_start: 0.8620 (mtpp) cc_final: 0.8397 (mtpt) REVERT: A 388 HIS cc_start: 0.8878 (OUTLIER) cc_final: 0.7772 (t70) REVERT: A 419 LYS cc_start: 0.8319 (mtpt) cc_final: 0.8017 (mttp) outliers start: 8 outliers final: 1 residues processed: 60 average time/residue: 1.5556 time to fit residues: 95.8527 Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 29 optimal weight: 0.0970 chunk 13 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 overall best weight: 0.8778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.136606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.093566 restraints weight = 13786.171| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.92 r_work: 0.2781 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3399 Z= 0.157 Angle : 0.508 10.227 4617 Z= 0.258 Chirality : 0.043 0.150 502 Planarity : 0.004 0.047 589 Dihedral : 5.486 58.074 466 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.47 % Allowed : 17.65 % Favored : 80.88 % 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: 0.93 (0.42), residues: 417 helix: 2.01 (0.37), residues: 209 sheet: -0.50 (0.68), residues: 69 loop : -0.92 (0.48), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 92 HIS 0.002 0.001 HIS A 267 PHE 0.008 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.384 Fit side-chains REVERT: A 214 LYS cc_start: 0.8894 (mmtp) cc_final: 0.8416 (mttp) REVERT: A 297 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8359 (pp) REVERT: A 333 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8383 (mtpt) REVERT: A 388 HIS cc_start: 0.8834 (OUTLIER) cc_final: 0.7694 (t70) REVERT: A 419 LYS cc_start: 0.8310 (mtpt) cc_final: 0.7995 (mttp) outliers start: 5 outliers final: 1 residues processed: 58 average time/residue: 1.4191 time to fit residues: 84.7899 Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.089534 restraints weight = 11056.935| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.61 r_work: 0.2708 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3399 Z= 0.271 Angle : 0.565 9.759 4617 Z= 0.291 Chirality : 0.046 0.167 502 Planarity : 0.005 0.047 589 Dihedral : 5.854 58.780 466 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.18 % Allowed : 17.65 % Favored : 81.18 % 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: 0.88 (0.42), residues: 417 helix: 1.98 (0.37), residues: 208 sheet: -0.39 (0.69), residues: 67 loop : -1.03 (0.47), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 HIS 0.002 0.001 HIS A 75 PHE 0.013 0.002 PHE A 341 TYR 0.015 0.002 TYR A 363 ARG 0.002 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.415 Fit side-chains REVERT: A 214 LYS cc_start: 0.8875 (mmtp) cc_final: 0.8409 (mttp) REVERT: A 297 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8387 (pp) REVERT: A 333 LYS cc_start: 0.8595 (mtpp) cc_final: 0.8387 (mtpt) REVERT: A 383 GLU cc_start: 0.8304 (tt0) cc_final: 0.7845 (mt-10) REVERT: A 388 HIS cc_start: 0.8949 (OUTLIER) cc_final: 0.7762 (t70) outliers start: 4 outliers final: 1 residues processed: 58 average time/residue: 1.3375 time to fit residues: 79.8036 Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.0970 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.135641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.091361 restraints weight = 10199.395| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.69 r_work: 0.2788 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3399 Z= 0.157 Angle : 0.518 9.125 4617 Z= 0.264 Chirality : 0.043 0.151 502 Planarity : 0.004 0.046 589 Dihedral : 5.548 57.864 466 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.76 % Allowed : 17.35 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.42), residues: 417 helix: 2.10 (0.37), residues: 208 sheet: -0.12 (0.73), residues: 63 loop : -0.91 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.002 0.000 HIS A 267 PHE 0.008 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.002 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.367 Fit side-chains REVERT: A 5 ASP cc_start: 0.8340 (t0) cc_final: 0.8131 (t0) REVERT: A 214 LYS cc_start: 0.8885 (mmtp) cc_final: 0.8453 (mttt) REVERT: A 232 LYS cc_start: 0.8613 (tptm) cc_final: 0.8301 (tmtm) REVERT: A 297 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8383 (pp) REVERT: A 333 LYS cc_start: 0.8615 (mtpp) cc_final: 0.8386 (mtpt) REVERT: A 383 GLU cc_start: 0.8332 (tt0) cc_final: 0.7840 (mt-10) REVERT: A 388 HIS cc_start: 0.8840 (OUTLIER) cc_final: 0.7735 (t70) outliers start: 6 outliers final: 2 residues processed: 58 average time/residue: 1.3802 time to fit residues: 82.2690 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.0570 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.093207 restraints weight = 11159.554| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.81 r_work: 0.2810 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3399 Z= 0.150 Angle : 0.541 11.560 4617 Z= 0.265 Chirality : 0.043 0.156 502 Planarity : 0.004 0.045 589 Dihedral : 5.406 56.502 466 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.88 % Allowed : 18.24 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.43), residues: 417 helix: 2.11 (0.37), residues: 209 sheet: -0.50 (0.67), residues: 69 loop : -0.87 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.002 0.000 HIS A 267 PHE 0.010 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.317 Fit side-chains REVERT: A 5 ASP cc_start: 0.8295 (t0) cc_final: 0.8030 (t0) REVERT: A 214 LYS cc_start: 0.8868 (mmtp) cc_final: 0.8480 (mttp) REVERT: A 232 LYS cc_start: 0.8601 (tptm) cc_final: 0.8286 (tmtm) REVERT: A 297 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8332 (pp) REVERT: A 388 HIS cc_start: 0.8758 (OUTLIER) cc_final: 0.7696 (t70) REVERT: A 392 ASN cc_start: 0.8781 (t0) cc_final: 0.8544 (t0) outliers start: 3 outliers final: 1 residues processed: 58 average time/residue: 1.3757 time to fit residues: 81.9763 Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.133432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.089418 restraints weight = 8994.840| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.55 r_work: 0.2747 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3399 Z= 0.220 Angle : 0.576 11.797 4617 Z= 0.288 Chirality : 0.044 0.164 502 Planarity : 0.004 0.043 589 Dihedral : 5.621 57.025 466 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.18 % Allowed : 17.94 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.42), residues: 417 helix: 2.08 (0.36), residues: 208 sheet: -0.01 (0.72), residues: 62 loop : -1.07 (0.46), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 382 HIS 0.002 0.001 HIS A 267 PHE 0.011 0.002 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.002 0.000 ARG A 187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.390 Fit side-chains REVERT: A 214 LYS cc_start: 0.8874 (mmtp) cc_final: 0.8454 (mttp) REVERT: A 232 LYS cc_start: 0.8625 (tptm) cc_final: 0.8293 (tmtm) REVERT: A 297 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8347 (pp) REVERT: A 383 GLU cc_start: 0.8335 (tt0) cc_final: 0.7857 (mt-10) REVERT: A 388 HIS cc_start: 0.8902 (OUTLIER) cc_final: 0.7918 (t70) outliers start: 4 outliers final: 1 residues processed: 57 average time/residue: 1.3663 time to fit residues: 80.1619 Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 0.0060 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.0770 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.5154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.093422 restraints weight = 11644.049| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.87 r_work: 0.2806 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3399 Z= 0.153 Angle : 0.536 10.943 4617 Z= 0.267 Chirality : 0.043 0.158 502 Planarity : 0.004 0.045 589 Dihedral : 5.390 56.271 466 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.18 % Allowed : 17.94 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.42), residues: 417 helix: 2.12 (0.37), residues: 209 sheet: -0.18 (0.70), residues: 64 loop : -1.07 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.002 0.000 HIS A 267 PHE 0.010 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3574.43 seconds wall clock time: 65 minutes 23.89 seconds (3923.89 seconds total)