Starting phenix.real_space_refine on Wed Mar 5 19:14:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zng_60270/03_2025/8zng_60270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zng_60270/03_2025/8zng_60270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zng_60270/03_2025/8zng_60270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zng_60270/03_2025/8zng_60270.map" model { file = "/net/cci-nas-00/data/ceres_data/8zng_60270/03_2025/8zng_60270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zng_60270/03_2025/8zng_60270.cif" } resolution = 2.5 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 2115 2.51 5 N 567 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 27 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: 3347 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: 3322 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 74 Unusual residues: {'AKG': 1, 'NDP': 1} Classifications: {'undetermined': 2, 'water': 16} Link IDs: {None: 17} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 187 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 187 " occ=0.50 Time building chain proxies: 4.36, per 1000 atoms: 1.30 Number of scatterers: 3347 At special positions: 0 Unit cell: (65.424, 63.168, 70.688, 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 567 7.00 C 2115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 820.8 milliseconds 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: 19 helices and 3 sheets defined 55.5% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.588A 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: 3.708A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 206 Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.800A pdb=" N TYR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.801A pdb=" N LEU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.975A pdb=" N ASP A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 365 through 391 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: 6.683A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.404A 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: 6.683A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279 removed outlier: 7.626A pdb=" N VAL A 217 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL A 242 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 195 hydrogen bonds defined for protein. 555 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: 0.89 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1086 1.34 - 1.46: 617 1.46 - 1.58: 1672 1.58 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3407 Sorted by residual: bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.614 0.219 3.80e-02 6.93e+02 3.33e+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 1.95e+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 1.03e+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 6.23e+00 bond pdb=" O2N NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.513 1.492 0.021 1.00e-02 1.00e+04 4.47e+00 ... (remaining 3402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.67: 4598 4.67 - 9.34: 25 9.34 - 14.02: 1 14.02 - 18.69: 1 18.69 - 23.36: 1 Bond angle restraints: 4626 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 107.74 131.10 -23.36 1.95e+00 2.62e-01 1.43e+02 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 117.90 -14.06 1.91e+00 2.73e-01 5.39e+01 angle pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 104.93 117.39 -12.46 2.66e+00 1.41e-01 2.20e+01 angle pdb=" O2N NDP A 500 " pdb=" PN NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 100.52 109.31 -8.79 1.91e+00 2.74e-01 2.11e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 112.22 5.24 1.17e+00 7.36e-01 2.02e+01 ... (remaining 4621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 1929 36.00 - 71.99: 84 71.99 - 107.99: 8 107.99 - 143.98: 0 143.98 - 179.98: 1 Dihedral angle restraints: 2022 sinusoidal: 829 harmonic: 1193 Sorted by residual: dihedral pdb=" CD BARG A 187 " pdb=" NE BARG A 187 " pdb=" CZ BARG A 187 " pdb=" NH1BARG A 187 " ideal model delta sinusoidal sigma weight residual 0.00 179.98 -179.98 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " ideal model delta sinusoidal sigma weight residual 175.04 67.30 107.74 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" CA ASP A 307 " pdb=" CB ASP A 307 " pdb=" CG ASP A 307 " pdb=" OD1 ASP A 307 " ideal model delta sinusoidal sigma weight residual -30.00 -86.71 56.71 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 2019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 390 0.050 - 0.100: 81 0.100 - 0.150: 27 0.150 - 0.200: 2 0.200 - 0.249: 2 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 -2.46 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE A 4 " pdb=" CA ILE A 4 " pdb=" CG1 ILE A 4 " pdb=" CG2 ILE A 4 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+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 2.40 0.19 2.00e-01 2.50e+01 9.10e-01 ... (remaining 499 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 500 " 0.085 2.00e-02 2.50e+03 5.31e-02 3.52e+01 pdb=" C3N NDP A 500 " 0.015 2.00e-02 2.50e+03 pdb=" C4N NDP A 500 " 0.013 2.00e-02 2.50e+03 pdb=" C7N NDP A 500 " -0.046 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 273 " -0.050 5.00e-02 4.00e+02 7.43e-02 8.84e+00 pdb=" N PRO A 274 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 150 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.026 5.00e-02 4.00e+02 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 1356 2.93 - 3.42: 3427 3.42 - 3.92: 6115 3.92 - 4.41: 6992 4.41 - 4.90: 11116 Nonbonded interactions: 29006 Sorted by model distance: nonbonded pdb=" OD1 ASP A 48 " pdb=" OG SER A 50 " model vdw 2.439 3.040 nonbonded pdb=" O LEU A 99 " pdb=" O HOH A 601 " model vdw 2.439 3.040 nonbonded pdb=" OE1 GLU A 354 " pdb=" O HOH A 602 " model vdw 2.481 3.040 nonbonded pdb=" NZ LYS A 177 " pdb=" OD1 ASN A 358 " model vdw 2.535 3.120 nonbonded pdb=" NE ARG A 65 " pdb=" O HOH A 601 " model vdw 2.549 3.120 ... (remaining 29001 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: 1.230 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.660 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 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 0.219 3407 Z= 0.438 Angle : 0.920 23.360 4626 Z= 0.499 Chirality : 0.048 0.249 502 Planarity : 0.006 0.074 592 Dihedral : 19.319 179.977 1262 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.24 % Allowed : 17.94 % Favored : 78.82 % 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: 1.28 (0.43), residues: 417 helix: 2.31 (0.38), residues: 200 sheet: -0.02 (0.69), residues: 64 loop : -0.75 (0.48), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.002 0.001 HIS A 388 PHE 0.013 0.002 PHE A 381 TYR 0.012 0.001 TYR A 408 ARG 0.002 0.000 ARG A 165 *********************** 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 79 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.385 Fit side-chains REVERT: A 388 HIS cc_start: 0.9048 (OUTLIER) cc_final: 0.8420 (p-80) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 1.5697 time to fit residues: 120.3561 Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 419 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.078630 restraints weight = 10966.512| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.66 r_work: 0.2648 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3407 Z= 0.290 Angle : 0.556 7.772 4626 Z= 0.294 Chirality : 0.047 0.194 502 Planarity : 0.005 0.048 592 Dihedral : 11.775 179.668 485 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.06 % Allowed : 21.18 % Favored : 76.76 % 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: 1.06 (0.41), residues: 417 helix: 2.13 (0.36), residues: 203 sheet: 0.61 (0.79), residues: 54 loop : -1.20 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 382 HIS 0.005 0.002 HIS A 388 PHE 0.014 0.002 PHE A 341 TYR 0.016 0.002 TYR A 363 ARG 0.003 0.000 ARG A 118 *********************** 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 62 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.387 Fit side-chains REVERT: A 265 ARG cc_start: 0.7776 (ttp-170) cc_final: 0.7292 (ttm170) outliers start: 6 outliers final: 3 residues processed: 60 average time/residue: 1.5989 time to fit residues: 98.2037 Evaluate side-chains 51 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.112335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.085507 restraints weight = 7092.965| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.11 r_work: 0.2716 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3407 Z= 0.150 Angle : 0.468 6.284 4626 Z= 0.246 Chirality : 0.043 0.205 502 Planarity : 0.004 0.046 592 Dihedral : 10.934 179.885 474 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.76 % Allowed : 20.88 % Favored : 77.35 % 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: 1.11 (0.41), residues: 417 helix: 2.19 (0.36), residues: 204 sheet: 0.54 (0.78), residues: 56 loop : -1.22 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.011 0.001 PHE A 381 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** 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 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.396 Fit side-chains REVERT: A 265 ARG cc_start: 0.7768 (ttp-170) cc_final: 0.7301 (ttm170) REVERT: A 286 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7494 (mm-30) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 1.5997 time to fit residues: 86.8959 Evaluate side-chains 48 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 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 0 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.0060 chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.106467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.078316 restraints weight = 9448.985| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.44 r_work: 0.2598 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2437 r_free = 0.2437 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2437 r_free = 0.2437 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3407 Z= 0.263 Angle : 0.525 7.149 4626 Z= 0.276 Chirality : 0.046 0.207 502 Planarity : 0.005 0.046 592 Dihedral : 10.608 179.679 471 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.65 % Allowed : 19.71 % Favored : 77.65 % 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: 0.94 (0.41), residues: 417 helix: 2.04 (0.36), residues: 204 sheet: 0.26 (0.76), residues: 61 loop : -1.23 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 382 HIS 0.005 0.001 HIS A 388 PHE 0.014 0.002 PHE A 341 TYR 0.015 0.002 TYR A 363 ARG 0.002 0.000 ARG A 165 *********************** 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 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.374 Fit side-chains REVERT: A 286 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7543 (mm-30) REVERT: A 290 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8118 (t70) outliers start: 8 outliers final: 3 residues processed: 55 average time/residue: 1.6008 time to fit residues: 90.1161 Evaluate side-chains 53 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.108462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.080195 restraints weight = 10753.358| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 2.59 r_work: 0.2582 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2461 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3407 Z= 0.255 Angle : 0.519 6.930 4626 Z= 0.273 Chirality : 0.046 0.204 502 Planarity : 0.005 0.047 592 Dihedral : 10.524 179.669 471 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.35 % Allowed : 20.00 % Favored : 77.65 % 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: 0.97 (0.41), residues: 417 helix: 2.00 (0.36), residues: 204 sheet: 0.65 (0.79), residues: 56 loop : -1.24 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.014 0.002 PHE A 381 TYR 0.015 0.002 TYR A 363 ARG 0.002 0.000 ARG A 165 *********************** 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 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.383 Fit side-chains REVERT: A 265 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7396 (mtt-85) REVERT: A 286 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7598 (mm-30) REVERT: A 290 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8177 (t70) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 1.5987 time to fit residues: 85.1121 Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.0040 chunk 14 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.085229 restraints weight = 15634.578| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.01 r_work: 0.2663 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3407 Z= 0.144 Angle : 0.460 6.047 4626 Z= 0.240 Chirality : 0.043 0.212 502 Planarity : 0.004 0.047 592 Dihedral : 10.253 179.997 471 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.35 % Allowed : 19.71 % Favored : 77.94 % 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: 1.19 (0.42), residues: 417 helix: 2.23 (0.36), residues: 204 sheet: 0.64 (0.78), residues: 56 loop : -1.15 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.002 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 165 *********************** 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 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.370 Fit side-chains REVERT: A 16 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8376 (ttt90) REVERT: A 256 ASP cc_start: 0.8473 (t70) cc_final: 0.7903 (t70) REVERT: A 265 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7316 (mtt-85) REVERT: A 290 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7912 (t70) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 1.5705 time to fit residues: 83.6773 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 0.0170 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.078116 restraints weight = 13465.880| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 2.84 r_work: 0.2533 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2412 r_free = 0.2412 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2412 r_free = 0.2412 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3407 Z= 0.265 Angle : 0.527 6.778 4626 Z= 0.277 Chirality : 0.046 0.213 502 Planarity : 0.005 0.046 592 Dihedral : 10.296 179.691 471 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.65 % Allowed : 19.41 % Favored : 77.94 % 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: 0.99 (0.42), residues: 417 helix: 2.05 (0.36), residues: 204 sheet: 0.28 (0.75), residues: 61 loop : -1.15 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 382 HIS 0.005 0.001 HIS A 388 PHE 0.014 0.002 PHE A 341 TYR 0.014 0.002 TYR A 363 ARG 0.002 0.000 ARG A 165 *********************** 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 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.371 Fit side-chains REVERT: A 256 ASP cc_start: 0.8566 (t70) cc_final: 0.7979 (t70) REVERT: A 265 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7466 (mtt-85) REVERT: A 290 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8136 (t70) outliers start: 8 outliers final: 4 residues processed: 52 average time/residue: 1.5372 time to fit residues: 81.8780 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.0570 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.3251 r_free = 0.3251 target = 0.113229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.084963 restraints weight = 11861.553| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.75 r_work: 0.2676 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3407 Z= 0.137 Angle : 0.464 5.862 4626 Z= 0.241 Chirality : 0.043 0.217 502 Planarity : 0.004 0.047 592 Dihedral : 10.007 179.944 471 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.94 % Allowed : 18.82 % Favored : 78.24 % 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: 1.23 (0.42), residues: 417 helix: 2.23 (0.36), residues: 204 sheet: 0.65 (0.78), residues: 56 loop : -1.09 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.002 0.000 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 165 *********************** 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 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.383 Fit side-chains REVERT: A 256 ASP cc_start: 0.8540 (t70) cc_final: 0.7945 (t70) REVERT: A 265 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7440 (mtt-85) REVERT: A 290 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8113 (t70) outliers start: 9 outliers final: 4 residues processed: 52 average time/residue: 1.5714 time to fit residues: 83.7967 Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 0.0370 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.111343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.082928 restraints weight = 11894.523| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.73 r_work: 0.2662 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3407 Z= 0.169 Angle : 0.490 6.559 4626 Z= 0.253 Chirality : 0.043 0.220 502 Planarity : 0.004 0.047 592 Dihedral : 9.967 179.897 471 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.35 % Allowed : 19.41 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.42), residues: 417 helix: 2.21 (0.36), residues: 204 sheet: 0.62 (0.77), residues: 56 loop : -1.09 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 165 *********************** 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 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.379 Fit side-chains REVERT: A 256 ASP cc_start: 0.8556 (t70) cc_final: 0.7970 (t70) REVERT: A 265 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7453 (mtt-85) REVERT: A 290 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8147 (t70) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 1.5865 time to fit residues: 84.5148 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.109777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.081395 restraints weight = 11832.214| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.70 r_work: 0.2603 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3407 Z= 0.211 Angle : 0.517 6.971 4626 Z= 0.268 Chirality : 0.044 0.219 502 Planarity : 0.004 0.047 592 Dihedral : 9.989 179.786 471 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.06 % Allowed : 19.71 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.42), residues: 417 helix: 2.12 (0.36), residues: 204 sheet: 0.65 (0.78), residues: 56 loop : -1.11 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.012 0.002 PHE A 381 TYR 0.012 0.001 TYR A 363 ARG 0.002 0.000 ARG A 165 ********************** 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 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.349 Fit side-chains REVERT: A 256 ASP cc_start: 0.8553 (t70) cc_final: 0.7973 (t70) REVERT: A 265 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7445 (mtt-85) REVERT: A 267 HIS cc_start: 0.8769 (m90) cc_final: 0.8556 (m-70) REVERT: A 290 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8166 (t70) outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 1.4841 time to fit residues: 80.6686 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 35 optimal weight: 0.0040 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.112128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.084237 restraints weight = 10151.946| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.54 r_work: 0.2690 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3407 Z= 0.156 Angle : 0.490 6.781 4626 Z= 0.252 Chirality : 0.043 0.224 502 Planarity : 0.004 0.047 592 Dihedral : 9.886 179.971 471 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.06 % Allowed : 20.00 % Favored : 77.94 % 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: 1.21 (0.42), residues: 417 helix: 2.20 (0.36), residues: 204 sheet: 0.64 (0.78), residues: 56 loop : -1.07 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3350.06 seconds wall clock time: 58 minutes 16.63 seconds (3496.63 seconds total)