Starting phenix.real_space_refine on Sat May 10 08:42:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jo4_36455/05_2025/8jo4_36455_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jo4_36455/05_2025/8jo4_36455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jo4_36455/05_2025/8jo4_36455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jo4_36455/05_2025/8jo4_36455.map" model { file = "/net/cci-nas-00/data/ceres_data/8jo4_36455/05_2025/8jo4_36455_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jo4_36455/05_2025/8jo4_36455_neut.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.078 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 6 5.49 5 Mg 1 5.21 5 S 27 5.16 5 C 3616 2.51 5 N 951 2.21 5 O 1117 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5719 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2846 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 11, 'TRANS': 338} Chain: "B" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2809 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.01, per 1000 atoms: 0.70 Number of scatterers: 5719 At special positions: 0 Unit cell: (64.17, 80.91, 113.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 27 16.00 P 6 15.00 Mg 1 11.99 O 1117 8.00 N 951 7.00 C 3616 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: 1.34 Conformation dependent library (CDL) restraints added in 814.1 milliseconds 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1348 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 59.8% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 41 through 55 removed outlier: 3.659A pdb=" N PHE A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 72 Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.693A pdb=" N SER A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 118 Processing helix chain 'A' and resid 121 through 134 removed outlier: 4.226A pdb=" N PHE A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 160 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 244 through 259 removed outlier: 3.795A pdb=" N SER A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 Processing helix chain 'A' and resid 288 through 297 removed outlier: 3.552A pdb=" N VAL A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 removed outlier: 3.660A pdb=" N ALA A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 352 Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 80 through 93 Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 114 through 128 Processing helix chain 'B' and resid 139 through 147 removed outlier: 3.782A pdb=" N SER B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 198 Processing helix chain 'B' and resid 204 through 218 Processing helix chain 'B' and resid 224 through 235 Processing helix chain 'B' and resid 254 through 262 removed outlier: 3.548A pdb=" N CYS B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 263 through 264 No H-bonds generated for 'chain 'B' and resid 263 through 264' Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 339 through 350 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.908A pdb=" N GLN B 356 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.728A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 193 Processing sheet with id=AA2, first strand: chain 'B' and resid 31 through 34 removed outlier: 6.180A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N CYS B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 74 Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA6, first strand: chain 'B' and resid 171 through 172 removed outlier: 6.274A pdb=" N ASN B 299 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 243 317 hydrogen bonds defined for protein. 873 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: 1.59 Time building geometry restraints manager: 1.60 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: 1854 1.34 - 1.46: 1040 1.46 - 1.57: 2881 1.57 - 1.69: 10 1.69 - 1.81: 47 Bond restraints: 5832 Sorted by residual: bond pdb=" N ILE A 316 " pdb=" CA ILE A 316 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.17e-02 7.31e+03 1.03e+01 bond pdb=" N ILE B 359 " pdb=" CA ILE B 359 " ideal model delta sigma weight residual 1.461 1.490 -0.030 1.08e-02 8.57e+03 7.65e+00 bond pdb=" N ASN A 164 " pdb=" CA ASN A 164 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.27e-02 6.20e+03 7.00e+00 bond pdb=" N SER A 22 " pdb=" CA SER A 22 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 4.92e+00 bond pdb=" N ARG A 185 " pdb=" CA ARG A 185 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.33e-02 5.65e+03 4.87e+00 ... (remaining 5827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 7744 1.67 - 3.33: 128 3.33 - 5.00: 28 5.00 - 6.67: 2 6.67 - 8.34: 3 Bond angle restraints: 7905 Sorted by residual: angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 131.70 8.17 1.00e+00 1.00e+00 6.67e+01 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 132.54 4.29 1.00e+00 1.00e+00 1.84e+01 angle pdb=" C SER B 273 " pdb=" CA SER B 273 " pdb=" CB SER B 273 " ideal model delta sigma weight residual 111.78 103.44 8.34 2.20e+00 2.07e-01 1.44e+01 angle pdb=" N THR B 360 " pdb=" CA THR B 360 " pdb=" C THR B 360 " ideal model delta sigma weight residual 110.55 105.47 5.08 1.35e+00 5.49e-01 1.41e+01 angle pdb=" N ILE B 359 " pdb=" CA ILE B 359 " pdb=" C ILE B 359 " ideal model delta sigma weight residual 108.12 103.61 4.51 1.34e+00 5.57e-01 1.13e+01 ... (remaining 7900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 3312 17.66 - 35.32: 198 35.32 - 52.98: 61 52.98 - 70.64: 16 70.64 - 88.30: 4 Dihedral angle restraints: 3591 sinusoidal: 1502 harmonic: 2089 Sorted by residual: dihedral pdb=" C SER B 273 " pdb=" N SER B 273 " pdb=" CA SER B 273 " pdb=" CB SER B 273 " ideal model delta harmonic sigma weight residual -122.60 -113.53 -9.07 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" CA PHE A 238 " pdb=" C PHE A 238 " pdb=" N VAL A 239 " pdb=" CA VAL A 239 " ideal model delta harmonic sigma weight residual 180.00 163.26 16.74 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA HIS B 163 " pdb=" C HIS B 163 " pdb=" N ASN B 164 " pdb=" CA ASN B 164 " ideal model delta harmonic sigma weight residual 180.00 163.36 16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 3588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 739 0.056 - 0.112: 126 0.112 - 0.168: 15 0.168 - 0.224: 3 0.224 - 0.280: 2 Chirality restraints: 885 Sorted by residual: chirality pdb=" CA ILE B 359 " pdb=" N ILE B 359 " pdb=" C ILE B 359 " pdb=" CB ILE B 359 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA MET A 162 " pdb=" N MET A 162 " pdb=" C MET A 162 " pdb=" CB MET A 162 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA SER B 273 " pdb=" N SER B 273 " pdb=" C SER B 273 " pdb=" CB SER B 273 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 882 not shown) Planarity restraints: 1004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 211 " -0.044 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO A 212 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 165 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B 166 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 161 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C VAL A 161 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL A 161 " 0.008 2.00e-02 2.50e+03 pdb=" N MET A 162 " 0.007 2.00e-02 2.50e+03 ... (remaining 1001 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 589 2.74 - 3.28: 5909 3.28 - 3.82: 10157 3.82 - 4.36: 12580 4.36 - 4.90: 21365 Nonbonded interactions: 50600 Sorted by model distance: nonbonded pdb=" NE2 HIS B 90 " pdb=" OE2 GLU B 95 " model vdw 2.202 3.120 nonbonded pdb=" OE2 GLU A 343 " pdb=" OG SER B 352 " model vdw 2.216 3.040 nonbonded pdb=" OG SER A 175 " pdb=" OD2 ASP A 298 " model vdw 2.228 3.040 nonbonded pdb=" O GLY B 158 " pdb=" OG1 THR B 305 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASP A 23 " pdb=" OG SER A 100 " model vdw 2.243 3.040 ... (remaining 50595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.910 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.660 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5832 Z= 0.213 Angle : 0.588 8.337 7905 Z= 0.350 Chirality : 0.046 0.280 885 Planarity : 0.004 0.067 1004 Dihedral : 13.286 88.300 2243 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.99 % Favored : 97.87 % Rotamer: Outliers : 3.21 % Allowed : 4.01 % Favored : 92.78 % 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 (0.32), residues: 703 helix: 1.15 (0.27), residues: 377 sheet: -0.26 (0.58), residues: 71 loop : 0.54 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 277 HIS 0.005 0.001 HIS A 300 PHE 0.012 0.001 PHE A 125 TYR 0.011 0.001 TYR A 42 ARG 0.002 0.000 ARG B 198 Details of bonding type rmsd hydrogen bonds : bond 0.12606 ( 315) hydrogen bonds : angle 5.43081 ( 873) covalent geometry : bond 0.00430 ( 5832) covalent geometry : angle 0.58827 ( 7905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7429 (tt) REVERT: A 129 ASN cc_start: 0.6919 (t0) cc_final: 0.6595 (t0) REVERT: A 162 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6515 (mtp) REVERT: B 35 SER cc_start: 0.8187 (p) cc_final: 0.7903 (t) REVERT: B 298 ASN cc_start: 0.7642 (m-40) cc_final: 0.7382 (m-40) REVERT: B 336 GLU cc_start: 0.6742 (pm20) cc_final: 0.6372 (pm20) outliers start: 20 outliers final: 7 residues processed: 142 average time/residue: 0.1813 time to fit residues: 32.9719 Evaluate side-chains 97 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 346 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 299 ASN B 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.154550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.131852 restraints weight = 6336.569| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.66 r_work: 0.3481 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5832 Z= 0.149 Angle : 0.507 4.809 7905 Z= 0.270 Chirality : 0.043 0.156 885 Planarity : 0.004 0.062 1004 Dihedral : 10.224 85.961 856 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.28 % Favored : 98.58 % Rotamer: Outliers : 3.05 % Allowed : 10.11 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.32), residues: 703 helix: 1.29 (0.26), residues: 382 sheet: 0.46 (0.58), residues: 71 loop : 0.59 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 277 HIS 0.006 0.001 HIS B 75 PHE 0.013 0.001 PHE A 125 TYR 0.035 0.001 TYR A 52 ARG 0.004 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 315) hydrogen bonds : angle 4.41785 ( 873) covalent geometry : bond 0.00341 ( 5832) covalent geometry : angle 0.50695 ( 7905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7304 (tt) REVERT: A 129 ASN cc_start: 0.7146 (t0) cc_final: 0.6733 (t0) REVERT: B 95 GLU cc_start: 0.6601 (tp30) cc_final: 0.5598 (tp30) REVERT: B 298 ASN cc_start: 0.7441 (m-40) cc_final: 0.7184 (m-40) REVERT: B 336 GLU cc_start: 0.6834 (pm20) cc_final: 0.6515 (pm20) outliers start: 19 outliers final: 9 residues processed: 110 average time/residue: 0.1776 time to fit residues: 25.5134 Evaluate side-chains 92 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 331 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 20 optimal weight: 0.0170 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 75 HIS B 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.153634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.131291 restraints weight = 6466.537| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.67 r_work: 0.3468 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5832 Z= 0.153 Angle : 0.508 5.187 7905 Z= 0.267 Chirality : 0.043 0.165 885 Planarity : 0.004 0.061 1004 Dihedral : 9.308 87.560 845 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.71 % Favored : 98.15 % Rotamer: Outliers : 2.41 % Allowed : 9.79 % Favored : 87.80 % 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: 1.49 (0.32), residues: 703 helix: 1.43 (0.26), residues: 382 sheet: 0.66 (0.60), residues: 71 loop : 0.60 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 277 HIS 0.004 0.001 HIS B 75 PHE 0.013 0.001 PHE B 257 TYR 0.047 0.002 TYR A 52 ARG 0.005 0.001 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 315) hydrogen bonds : angle 4.27768 ( 873) covalent geometry : bond 0.00359 ( 5832) covalent geometry : angle 0.50755 ( 7905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 129 ASN cc_start: 0.7199 (t0) cc_final: 0.6795 (t0) REVERT: A 186 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6460 (mt-10) REVERT: B 95 GLU cc_start: 0.6619 (tp30) cc_final: 0.5583 (tp30) REVERT: B 134 MET cc_start: 0.7763 (ttp) cc_final: 0.7328 (ttp) REVERT: B 298 ASN cc_start: 0.7415 (m-40) cc_final: 0.7099 (m-40) REVERT: B 315 MET cc_start: 0.7199 (tpp) cc_final: 0.6980 (tpp) REVERT: B 336 GLU cc_start: 0.7024 (pm20) cc_final: 0.6647 (pm20) outliers start: 15 outliers final: 8 residues processed: 98 average time/residue: 0.1727 time to fit residues: 22.3125 Evaluate side-chains 88 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 178 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 0.0050 chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.158817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.135240 restraints weight = 6512.323| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.82 r_work: 0.3495 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5832 Z= 0.112 Angle : 0.467 7.810 7905 Z= 0.247 Chirality : 0.041 0.129 885 Planarity : 0.004 0.059 1004 Dihedral : 8.610 81.704 843 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.56 % Favored : 98.29 % Rotamer: Outliers : 2.25 % Allowed : 11.72 % Favored : 86.04 % 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: 1.84 (0.32), residues: 703 helix: 1.69 (0.26), residues: 383 sheet: 0.86 (0.61), residues: 71 loop : 0.77 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.002 0.001 HIS A 300 PHE 0.015 0.001 PHE B 257 TYR 0.044 0.001 TYR A 52 ARG 0.005 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 315) hydrogen bonds : angle 4.07507 ( 873) covalent geometry : bond 0.00252 ( 5832) covalent geometry : angle 0.46696 ( 7905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.631 Fit side-chains REVERT: A 33 GLU cc_start: 0.7420 (tp30) cc_final: 0.7216 (tp30) REVERT: A 129 ASN cc_start: 0.7131 (t0) cc_final: 0.6726 (t0) REVERT: A 134 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7470 (mt-10) REVERT: A 186 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6520 (mt-10) REVERT: A 295 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.6907 (mp) REVERT: A 307 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7785 (mtp180) REVERT: B 95 GLU cc_start: 0.6540 (tp30) cc_final: 0.5581 (tp30) REVERT: B 108 THR cc_start: 0.7552 (p) cc_final: 0.7218 (p) REVERT: B 243 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6762 (mm-30) REVERT: B 336 GLU cc_start: 0.7026 (pm20) cc_final: 0.6688 (pm20) outliers start: 14 outliers final: 6 residues processed: 109 average time/residue: 0.1942 time to fit residues: 27.3522 Evaluate side-chains 92 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.157129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.133492 restraints weight = 6412.797| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.81 r_work: 0.3481 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5832 Z= 0.129 Angle : 0.477 6.992 7905 Z= 0.254 Chirality : 0.042 0.129 885 Planarity : 0.004 0.059 1004 Dihedral : 8.396 82.447 841 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.85 % Favored : 98.01 % Rotamer: Outliers : 1.93 % Allowed : 13.48 % Favored : 84.59 % 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: 1.86 (0.32), residues: 703 helix: 1.66 (0.26), residues: 382 sheet: 0.94 (0.60), residues: 71 loop : 0.84 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 277 HIS 0.003 0.001 HIS A 300 PHE 0.017 0.001 PHE A 24 TYR 0.038 0.001 TYR A 52 ARG 0.005 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 315) hydrogen bonds : angle 4.07116 ( 873) covalent geometry : bond 0.00298 ( 5832) covalent geometry : angle 0.47700 ( 7905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 129 ASN cc_start: 0.7132 (t0) cc_final: 0.6733 (t0) REVERT: A 134 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7471 (mt-10) REVERT: A 186 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6591 (mt-10) REVERT: A 295 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.6930 (mp) REVERT: A 340 MET cc_start: 0.8066 (tmm) cc_final: 0.7811 (ttp) REVERT: B 95 GLU cc_start: 0.6596 (tp30) cc_final: 0.5630 (tp30) REVERT: B 134 MET cc_start: 0.7161 (ttp) cc_final: 0.6939 (ttt) REVERT: B 243 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6683 (mm-30) REVERT: B 336 GLU cc_start: 0.7059 (pm20) cc_final: 0.6712 (pm20) outliers start: 12 outliers final: 6 residues processed: 97 average time/residue: 0.1789 time to fit residues: 22.9048 Evaluate side-chains 94 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 62 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.158877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135425 restraints weight = 6413.135| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.81 r_work: 0.3520 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5832 Z= 0.111 Angle : 0.457 5.836 7905 Z= 0.243 Chirality : 0.041 0.126 885 Planarity : 0.004 0.059 1004 Dihedral : 8.154 80.422 841 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.42 % Favored : 98.44 % Rotamer: Outliers : 2.25 % Allowed : 13.64 % Favored : 84.11 % 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: 2.01 (0.32), residues: 703 helix: 1.78 (0.26), residues: 382 sheet: 1.13 (0.61), residues: 71 loop : 0.88 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.003 0.001 HIS A 300 PHE 0.015 0.001 PHE B 257 TYR 0.022 0.001 TYR A 52 ARG 0.004 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 315) hydrogen bonds : angle 3.95892 ( 873) covalent geometry : bond 0.00249 ( 5832) covalent geometry : angle 0.45680 ( 7905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.675 Fit side-chains REVERT: A 33 GLU cc_start: 0.7357 (tp30) cc_final: 0.6784 (mt-10) REVERT: A 127 GLU cc_start: 0.7239 (mp0) cc_final: 0.6778 (mp0) REVERT: A 129 ASN cc_start: 0.7100 (t0) cc_final: 0.6699 (t0) REVERT: A 295 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.6960 (mp) REVERT: A 307 ARG cc_start: 0.8296 (ptp-110) cc_final: 0.8049 (mtm110) REVERT: A 340 MET cc_start: 0.8027 (tmm) cc_final: 0.7778 (ttp) REVERT: B 95 GLU cc_start: 0.6488 (tp30) cc_final: 0.5519 (tp30) REVERT: B 108 THR cc_start: 0.7453 (p) cc_final: 0.7168 (p) REVERT: B 243 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6703 (mm-30) REVERT: B 336 GLU cc_start: 0.6950 (pm20) cc_final: 0.6593 (pm20) outliers start: 14 outliers final: 9 residues processed: 104 average time/residue: 0.1865 time to fit residues: 25.4719 Evaluate side-chains 95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.153278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130701 restraints weight = 6523.433| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.71 r_work: 0.3458 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5832 Z= 0.183 Angle : 0.528 7.153 7905 Z= 0.278 Chirality : 0.044 0.131 885 Planarity : 0.004 0.060 1004 Dihedral : 8.381 83.357 841 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.28 % Favored : 97.58 % Rotamer: Outliers : 2.25 % Allowed : 13.80 % Favored : 83.95 % 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: 1.75 (0.32), residues: 703 helix: 1.57 (0.26), residues: 382 sheet: 1.07 (0.64), residues: 69 loop : 0.74 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 277 HIS 0.004 0.001 HIS A 300 PHE 0.022 0.002 PHE A 24 TYR 0.023 0.002 TYR A 52 ARG 0.007 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 315) hydrogen bonds : angle 4.11013 ( 873) covalent geometry : bond 0.00434 ( 5832) covalent geometry : angle 0.52787 ( 7905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.642 Fit side-chains REVERT: A 33 GLU cc_start: 0.7404 (tp30) cc_final: 0.6843 (mt-10) REVERT: A 52 TYR cc_start: 0.7479 (m-80) cc_final: 0.7236 (m-80) REVERT: A 127 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: A 129 ASN cc_start: 0.7002 (t0) cc_final: 0.6613 (t0) REVERT: A 186 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6610 (mt-10) REVERT: A 307 ARG cc_start: 0.8251 (ptp-110) cc_final: 0.7810 (mtp180) REVERT: A 340 MET cc_start: 0.8141 (tmm) cc_final: 0.7819 (ttp) REVERT: B 243 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6684 (mm-30) REVERT: B 315 MET cc_start: 0.7156 (tpp) cc_final: 0.6943 (tpp) REVERT: B 336 GLU cc_start: 0.7086 (pm20) cc_final: 0.6748 (pm20) outliers start: 14 outliers final: 10 residues processed: 94 average time/residue: 0.1863 time to fit residues: 23.1355 Evaluate side-chains 94 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.155306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133179 restraints weight = 6420.712| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.67 r_work: 0.3491 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5832 Z= 0.136 Angle : 0.497 7.325 7905 Z= 0.262 Chirality : 0.042 0.127 885 Planarity : 0.004 0.059 1004 Dihedral : 8.287 82.166 841 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.25 % Allowed : 13.80 % Favored : 83.95 % 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: 1.84 (0.32), residues: 703 helix: 1.62 (0.26), residues: 382 sheet: 1.11 (0.65), residues: 69 loop : 0.82 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 277 HIS 0.003 0.001 HIS A 300 PHE 0.023 0.002 PHE A 31 TYR 0.013 0.001 TYR A 42 ARG 0.005 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 315) hydrogen bonds : angle 4.05120 ( 873) covalent geometry : bond 0.00318 ( 5832) covalent geometry : angle 0.49721 ( 7905) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.620 Fit side-chains REVERT: A 33 GLU cc_start: 0.7393 (tp30) cc_final: 0.6850 (mt-10) REVERT: A 52 TYR cc_start: 0.7373 (m-80) cc_final: 0.7139 (m-80) REVERT: A 127 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: A 129 ASN cc_start: 0.6981 (t0) cc_final: 0.6600 (t0) REVERT: A 186 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6601 (mt-10) REVERT: A 307 ARG cc_start: 0.8197 (ptp-110) cc_final: 0.7795 (mtp180) REVERT: A 340 MET cc_start: 0.8115 (tmm) cc_final: 0.7864 (ttp) REVERT: B 95 GLU cc_start: 0.6600 (tp30) cc_final: 0.6013 (mm-30) REVERT: B 243 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6722 (mm-30) REVERT: B 315 MET cc_start: 0.7142 (tpp) cc_final: 0.6914 (tpp) REVERT: B 336 GLU cc_start: 0.7041 (pm20) cc_final: 0.6691 (pm20) outliers start: 14 outliers final: 11 residues processed: 95 average time/residue: 0.1830 time to fit residues: 22.8409 Evaluate side-chains 98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.155312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132158 restraints weight = 6511.426| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.79 r_work: 0.3472 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5832 Z= 0.145 Angle : 0.502 8.007 7905 Z= 0.265 Chirality : 0.042 0.129 885 Planarity : 0.004 0.059 1004 Dihedral : 8.251 82.339 841 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.25 % Allowed : 13.96 % Favored : 83.79 % 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: 1.81 (0.32), residues: 703 helix: 1.61 (0.26), residues: 382 sheet: 1.09 (0.65), residues: 69 loop : 0.79 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 277 HIS 0.003 0.001 HIS A 300 PHE 0.035 0.002 PHE A 31 TYR 0.014 0.001 TYR A 42 ARG 0.005 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 315) hydrogen bonds : angle 4.04633 ( 873) covalent geometry : bond 0.00344 ( 5832) covalent geometry : angle 0.50214 ( 7905) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.619 Fit side-chains REVERT: A 33 GLU cc_start: 0.7424 (tp30) cc_final: 0.6846 (mt-10) REVERT: A 127 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: A 129 ASN cc_start: 0.7120 (t0) cc_final: 0.6725 (t0) REVERT: A 186 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6659 (mt-10) REVERT: A 340 MET cc_start: 0.8152 (tmm) cc_final: 0.7881 (ttp) REVERT: B 243 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6690 (mm-30) REVERT: B 336 GLU cc_start: 0.7076 (pm20) cc_final: 0.6724 (pm20) outliers start: 14 outliers final: 10 residues processed: 95 average time/residue: 0.1667 time to fit residues: 21.3704 Evaluate side-chains 97 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 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 = 0.3849 r_free = 0.3849 target = 0.154865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132294 restraints weight = 6546.533| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.72 r_work: 0.3472 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5832 Z= 0.159 Angle : 0.514 6.083 7905 Z= 0.275 Chirality : 0.043 0.130 885 Planarity : 0.004 0.059 1004 Dihedral : 8.248 83.234 841 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.25 % Allowed : 14.13 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.32), residues: 703 helix: 1.54 (0.26), residues: 382 sheet: 1.00 (0.63), residues: 69 loop : 0.73 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 277 HIS 0.003 0.001 HIS B 90 PHE 0.038 0.002 PHE A 31 TYR 0.015 0.001 TYR A 52 ARG 0.005 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 315) hydrogen bonds : angle 4.12223 ( 873) covalent geometry : bond 0.00377 ( 5832) covalent geometry : angle 0.51402 ( 7905) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.687 Fit side-chains REVERT: A 33 GLU cc_start: 0.7415 (tp30) cc_final: 0.6840 (mt-10) REVERT: A 52 TYR cc_start: 0.7559 (m-80) cc_final: 0.7100 (m-80) REVERT: A 127 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: A 129 ASN cc_start: 0.6989 (t0) cc_final: 0.6617 (t0) REVERT: A 186 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6640 (mt-10) REVERT: A 340 MET cc_start: 0.8137 (tmm) cc_final: 0.7850 (ttp) REVERT: B 243 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6661 (mm-30) REVERT: B 336 GLU cc_start: 0.7080 (pm20) cc_final: 0.6740 (pm20) outliers start: 14 outliers final: 11 residues processed: 96 average time/residue: 0.1657 time to fit residues: 21.3371 Evaluate side-chains 99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 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 = 0.3864 r_free = 0.3864 target = 0.156431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133252 restraints weight = 6542.464| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.79 r_work: 0.3490 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5832 Z= 0.131 Angle : 0.496 5.368 7905 Z= 0.265 Chirality : 0.042 0.145 885 Planarity : 0.004 0.059 1004 Dihedral : 8.104 81.983 841 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.25 % Allowed : 14.61 % Favored : 83.15 % 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: 1.83 (0.32), residues: 703 helix: 1.61 (0.26), residues: 382 sheet: 1.12 (0.65), residues: 69 loop : 0.80 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 277 HIS 0.003 0.001 HIS B 90 PHE 0.034 0.002 PHE A 31 TYR 0.016 0.001 TYR A 52 ARG 0.005 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 315) hydrogen bonds : angle 4.06151 ( 873) covalent geometry : bond 0.00305 ( 5832) covalent geometry : angle 0.49555 ( 7905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3112.44 seconds wall clock time: 55 minutes 0.61 seconds (3300.61 seconds total)