Starting phenix.real_space_refine on Fri Jul 25 08:15:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wxj_37909/07_2025/8wxj_37909_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wxj_37909/07_2025/8wxj_37909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wxj_37909/07_2025/8wxj_37909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wxj_37909/07_2025/8wxj_37909.map" model { file = "/net/cci-nas-00/data/ceres_data/8wxj_37909/07_2025/8wxj_37909_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wxj_37909/07_2025/8wxj_37909_neut.cif" } resolution = 2.68 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 4794 2.51 5 N 1140 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7188 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3585 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain breaks: 1 Chain: "B" Number of atoms: 3585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3585 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Unusual residues: {'SCN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Unusual residues: {'SCN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 12.31, per 1000 atoms: 1.71 Number of scatterers: 7188 At special positions: 0 Unit cell: (73.15, 105.35, 69.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1190 8.00 N 1140 7.00 C 4794 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: 1.97 Conformation dependent library (CDL) restraints added in 1.3 seconds 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 3 sheets defined 75.3% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 115 through 153 removed outlier: 3.585A pdb=" N ILE A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 183 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 190 through 199 Processing helix chain 'A' and resid 208 through 224 Processing helix chain 'A' and resid 231 through 251 Processing helix chain 'A' and resid 263 through 280 Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 299 through 324 Processing helix chain 'A' and resid 347 through 379 removed outlier: 3.967A pdb=" N ARG A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 391 through 405 Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 443 through 449 removed outlier: 3.571A pdb=" N SER A 446 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 448 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP A 449 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 475 removed outlier: 3.527A pdb=" N TRP A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 506 Processing helix chain 'A' and resid 520 through 537 Processing helix chain 'A' and resid 541 through 550 Processing helix chain 'A' and resid 555 through 574 Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'B' and resid 116 through 153 Processing helix chain 'B' and resid 156 through 183 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 208 through 224 Processing helix chain 'B' and resid 231 through 251 Processing helix chain 'B' and resid 263 through 280 Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 299 through 324 Processing helix chain 'B' and resid 347 through 379 removed outlier: 3.967A pdb=" N ARG B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 Processing helix chain 'B' and resid 391 through 405 Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 443 through 449 removed outlier: 3.571A pdb=" N SER B 446 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 448 " --> pdb=" O GLN B 445 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP B 449 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 475 removed outlier: 3.527A pdb=" N TRP B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 506 Processing helix chain 'B' and resid 520 through 537 Processing helix chain 'B' and resid 541 through 550 Processing helix chain 'B' and resid 555 through 574 Processing helix chain 'B' and resid 576 through 585 Processing sheet with id=AA1, first strand: chain 'A' and resid 296 through 298 Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 511 Processing sheet with id=AA3, first strand: chain 'B' and resid 510 through 511 542 hydrogen bonds defined for protein. 1614 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: 2.37 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1068 1.28 - 1.42: 1966 1.42 - 1.55: 4222 1.55 - 1.68: 22 1.68 - 1.81: 104 Bond restraints: 7382 Sorted by residual: bond pdb=" CA PRO A 407 " pdb=" C PRO A 407 " ideal model delta sigma weight residual 1.517 1.538 -0.021 9.30e-03 1.16e+04 5.27e+00 bond pdb=" CA PRO B 407 " pdb=" C PRO B 407 " ideal model delta sigma weight residual 1.517 1.538 -0.021 9.30e-03 1.16e+04 5.27e+00 bond pdb=" C MET B 485 " pdb=" O MET B 485 " ideal model delta sigma weight residual 1.244 1.221 0.023 1.00e-02 1.00e+04 5.10e+00 bond pdb=" C MET A 485 " pdb=" O MET A 485 " ideal model delta sigma weight residual 1.244 1.221 0.023 1.00e-02 1.00e+04 5.10e+00 bond pdb=" C SCN A1003 " pdb=" S SCN A1003 " ideal model delta sigma weight residual 1.645 1.689 -0.044 2.00e-02 2.50e+03 4.77e+00 ... (remaining 7377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 9334 1.96 - 3.92: 587 3.92 - 5.89: 82 5.89 - 7.85: 23 7.85 - 9.81: 6 Bond angle restraints: 10032 Sorted by residual: angle pdb=" N VAL A 269 " pdb=" CA VAL A 269 " pdb=" C VAL A 269 " ideal model delta sigma weight residual 111.00 104.47 6.53 1.09e+00 8.42e-01 3.59e+01 angle pdb=" N PRO A 407 " pdb=" CA PRO A 407 " pdb=" C PRO A 407 " ideal model delta sigma weight residual 110.70 117.26 -6.56 1.22e+00 6.72e-01 2.89e+01 angle pdb=" N PRO B 407 " pdb=" CA PRO B 407 " pdb=" C PRO B 407 " ideal model delta sigma weight residual 110.70 117.26 -6.56 1.22e+00 6.72e-01 2.89e+01 angle pdb=" CA PHE A 512 " pdb=" C PHE A 512 " pdb=" N ASP A 513 " ideal model delta sigma weight residual 119.56 116.89 2.67 5.80e-01 2.97e+00 2.11e+01 angle pdb=" CA PHE B 512 " pdb=" C PHE B 512 " pdb=" N ASP B 513 " ideal model delta sigma weight residual 119.56 116.89 2.67 5.80e-01 2.97e+00 2.11e+01 ... (remaining 10027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 3418 17.37 - 34.73: 423 34.73 - 52.10: 287 52.10 - 69.47: 118 69.47 - 86.83: 6 Dihedral angle restraints: 4252 sinusoidal: 1586 harmonic: 2666 Sorted by residual: dihedral pdb=" C PHE B 343 " pdb=" N PHE B 343 " pdb=" CA PHE B 343 " pdb=" CB PHE B 343 " ideal model delta harmonic sigma weight residual -122.60 -133.17 10.57 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" C PHE A 343 " pdb=" N PHE A 343 " pdb=" CA PHE A 343 " pdb=" CB PHE A 343 " ideal model delta harmonic sigma weight residual -122.60 -133.17 10.57 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" N PHE B 343 " pdb=" C PHE B 343 " pdb=" CA PHE B 343 " pdb=" CB PHE B 343 " ideal model delta harmonic sigma weight residual 122.80 132.25 -9.45 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 4249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 924 0.076 - 0.151: 196 0.151 - 0.227: 36 0.227 - 0.303: 8 0.303 - 0.378: 6 Chirality restraints: 1170 Sorted by residual: chirality pdb=" CA GLN B 154 " pdb=" N GLN B 154 " pdb=" C GLN B 154 " pdb=" CB GLN B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA GLN A 154 " pdb=" N GLN A 154 " pdb=" C GLN A 154 " pdb=" CB GLN A 154 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA PHE B 343 " pdb=" N PHE B 343 " pdb=" C PHE B 343 " pdb=" CB PHE B 343 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 1167 not shown) Planarity restraints: 1226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 407 " 0.037 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO A 408 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 408 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 408 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 407 " 0.037 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO B 408 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 408 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 408 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 348 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO A 349 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 349 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 349 " -0.032 5.00e-02 4.00e+02 ... (remaining 1223 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1868 2.77 - 3.30: 6954 3.30 - 3.84: 13846 3.84 - 4.37: 16809 4.37 - 4.90: 26734 Nonbonded interactions: 66211 Sorted by model distance: nonbonded pdb=" O THR A 550 " pdb=" CD1 ILE B 553 " model vdw 2.242 3.460 nonbonded pdb=" CD1 ILE A 553 " pdb=" O THR B 550 " model vdw 2.242 3.460 nonbonded pdb=" CZ PHE A 306 " pdb=" CE MET B 560 " model vdw 2.334 3.760 nonbonded pdb=" CE MET A 560 " pdb=" CZ PHE B 306 " model vdw 2.334 3.760 nonbonded pdb=" OE2 GLU A 291 " pdb=" CE2 TYR B 302 " model vdw 2.363 3.340 ... (remaining 66206 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1272.720 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 29.820 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 1316.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3863 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 0.044 7382 Z= 0.514 Angle : 1.097 9.812 10032 Z= 0.749 Chirality : 0.071 0.378 1170 Planarity : 0.006 0.055 1226 Dihedral : 22.791 86.834 2544 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 1.51 % Allowed : 7.13 % Favored : 91.36 % Rotamer: Outliers : 31.50 % Allowed : 11.81 % Favored : 56.69 % Cbeta Deviations : 0.23 % 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: -2.38 (0.25), residues: 926 helix: -0.97 (0.18), residues: 686 sheet: None (None), residues: 0 loop : -3.08 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 469 HIS 0.003 0.001 HIS A 436 PHE 0.019 0.002 PHE A 297 TYR 0.009 0.001 TYR B 578 ARG 0.002 0.000 ARG B 370 Details of bonding type rmsd hydrogen bonds : bond 0.14834 ( 542) hydrogen bonds : angle 6.45624 ( 1614) covalent geometry : bond 0.00692 ( 7382) covalent geometry : angle 1.09689 (10032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 167 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.6015 (OUTLIER) cc_final: 0.5733 (mtp) REVERT: A 283 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6066 (mp) REVERT: A 294 SER cc_start: 0.5756 (t) cc_final: 0.5347 (p) REVERT: A 419 MET cc_start: 0.5150 (OUTLIER) cc_final: 0.4687 (mmt) REVERT: A 439 ASP cc_start: 0.4728 (t0) cc_final: 0.4477 (p0) REVERT: B 250 MET cc_start: 0.6007 (OUTLIER) cc_final: 0.5728 (mtp) REVERT: B 283 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6069 (mp) REVERT: B 294 SER cc_start: 0.5791 (t) cc_final: 0.5305 (p) REVERT: B 419 MET cc_start: 0.5153 (OUTLIER) cc_final: 0.4687 (mmt) REVERT: B 439 ASP cc_start: 0.4724 (t0) cc_final: 0.4475 (p0) outliers start: 240 outliers final: 48 residues processed: 326 average time/residue: 1.0696 time to fit residues: 369.3076 Evaluate side-chains 161 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 107 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 384 GLN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 552 GLN Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 555 HIS Chi-restraints excluded: chain B residue 580 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.0570 chunk 83 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN A 431 ASN A 451 HIS A 552 GLN A 574 GLN B 384 GLN B 431 ASN B 451 HIS ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116787 restraints weight = 8087.345| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.98 r_work: 0.3247 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7382 Z= 0.154 Angle : 0.620 5.974 10032 Z= 0.328 Chirality : 0.043 0.172 1170 Planarity : 0.006 0.051 1226 Dihedral : 11.887 79.230 1078 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.54 % Favored : 95.25 % Rotamer: Outliers : 9.19 % Allowed : 24.28 % Favored : 66.54 % 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: -0.02 (0.27), residues: 926 helix: 0.86 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -2.62 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 469 HIS 0.002 0.000 HIS A 369 PHE 0.015 0.001 PHE A 306 TYR 0.009 0.001 TYR B 578 ARG 0.003 0.000 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.04737 ( 542) hydrogen bonds : angle 4.52092 ( 1614) covalent geometry : bond 0.00341 ( 7382) covalent geometry : angle 0.62007 (10032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 117 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 LYS cc_start: 0.7938 (tptt) cc_final: 0.7622 (tttm) REVERT: A 248 LYS cc_start: 0.6647 (OUTLIER) cc_final: 0.6390 (mttt) REVERT: A 317 ARG cc_start: 0.6449 (mmt90) cc_final: 0.5805 (tpt170) REVERT: B 204 LYS cc_start: 0.7941 (tptt) cc_final: 0.7622 (tttm) REVERT: B 248 LYS cc_start: 0.6657 (OUTLIER) cc_final: 0.6400 (mttt) REVERT: B 304 ARG cc_start: 0.7795 (mtp85) cc_final: 0.7592 (mtm110) REVERT: B 306 PHE cc_start: 0.7067 (t80) cc_final: 0.6843 (t80) REVERT: B 317 ARG cc_start: 0.6467 (mmt90) cc_final: 0.5822 (tpt170) outliers start: 70 outliers final: 36 residues processed: 171 average time/residue: 1.1657 time to fit residues: 210.6622 Evaluate side-chains 143 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 384 GLN Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 555 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 62 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN B 431 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115579 restraints weight = 8240.320| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.01 r_work: 0.3232 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7382 Z= 0.148 Angle : 0.583 7.236 10032 Z= 0.302 Chirality : 0.042 0.142 1170 Planarity : 0.006 0.045 1226 Dihedral : 9.483 78.678 1034 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.32 % Favored : 95.46 % Rotamer: Outliers : 8.40 % Allowed : 23.23 % Favored : 68.37 % 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: 0.84 (0.27), residues: 926 helix: 1.43 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -2.13 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 303 HIS 0.002 0.001 HIS B 451 PHE 0.024 0.001 PHE A 547 TYR 0.009 0.001 TYR A 578 ARG 0.002 0.000 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 542) hydrogen bonds : angle 4.25133 ( 1614) covalent geometry : bond 0.00334 ( 7382) covalent geometry : angle 0.58309 (10032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 116 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 139 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7409 (m) REVERT: A 173 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7717 (mp) REVERT: A 203 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6850 (mm) REVERT: A 204 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7402 (tttm) REVERT: A 248 LYS cc_start: 0.6655 (OUTLIER) cc_final: 0.6393 (mttt) REVERT: A 317 ARG cc_start: 0.6495 (mmt90) cc_final: 0.5866 (tpt170) REVERT: A 338 ARG cc_start: 0.6518 (mmp-170) cc_final: 0.6287 (mmt180) REVERT: A 431 ASN cc_start: 0.8129 (m-40) cc_final: 0.7840 (m110) REVERT: B 139 SER cc_start: 0.7756 (OUTLIER) cc_final: 0.7380 (m) REVERT: B 173 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7740 (mp) REVERT: B 204 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7384 (tttm) REVERT: B 248 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.6418 (mttt) REVERT: B 317 ARG cc_start: 0.6511 (mmt90) cc_final: 0.5887 (tpt170) REVERT: B 338 ARG cc_start: 0.6549 (mmp-170) cc_final: 0.6306 (mmt180) REVERT: B 431 ASN cc_start: 0.8099 (m-40) cc_final: 0.7813 (m110) outliers start: 64 outliers final: 32 residues processed: 161 average time/residue: 1.2152 time to fit residues: 206.3563 Evaluate side-chains 147 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 555 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 0.0050 chunk 39 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.144095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114920 restraints weight = 8363.483| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.07 r_work: 0.3162 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7382 Z= 0.136 Angle : 0.559 7.999 10032 Z= 0.288 Chirality : 0.041 0.139 1170 Planarity : 0.005 0.050 1226 Dihedral : 8.573 76.789 1016 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.43 % Favored : 95.36 % Rotamer: Outliers : 8.01 % Allowed : 23.10 % Favored : 68.90 % 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: 1.27 (0.27), residues: 926 helix: 1.73 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -1.90 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 303 HIS 0.002 0.000 HIS A 555 PHE 0.015 0.001 PHE B 306 TYR 0.009 0.001 TYR A 578 ARG 0.004 0.000 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 542) hydrogen bonds : angle 4.12896 ( 1614) covalent geometry : bond 0.00306 ( 7382) covalent geometry : angle 0.55903 (10032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 105 time to evaluate : 0.865 Fit side-chains REVERT: A 139 SER cc_start: 0.7712 (OUTLIER) cc_final: 0.7363 (m) REVERT: A 173 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7713 (mp) REVERT: A 203 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6636 (mm) REVERT: A 204 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7273 (tttm) REVERT: A 248 LYS cc_start: 0.6580 (OUTLIER) cc_final: 0.6308 (mttt) REVERT: A 317 ARG cc_start: 0.6457 (mmt90) cc_final: 0.5871 (tpt170) REVERT: A 334 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7520 (mpt180) REVERT: A 421 ARG cc_start: 0.7584 (mtt-85) cc_final: 0.7208 (mmm160) REVERT: A 425 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.7984 (m) REVERT: A 431 ASN cc_start: 0.8067 (m-40) cc_final: 0.7646 (m110) REVERT: A 515 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6945 (tp) REVERT: A 560 MET cc_start: 0.7714 (mmm) cc_final: 0.7188 (mtm) REVERT: B 139 SER cc_start: 0.7700 (OUTLIER) cc_final: 0.7355 (m) REVERT: B 173 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7715 (mp) REVERT: B 204 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7242 (tttm) REVERT: B 248 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.6306 (mttt) REVERT: B 317 ARG cc_start: 0.6461 (mmt90) cc_final: 0.5862 (tpt170) REVERT: B 334 ARG cc_start: 0.7942 (mpt180) cc_final: 0.7572 (mpt180) REVERT: B 421 ARG cc_start: 0.7594 (mtt-85) cc_final: 0.7221 (mmm160) REVERT: B 425 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.7984 (m) REVERT: B 431 ASN cc_start: 0.8035 (m-40) cc_final: 0.7619 (m110) REVERT: B 515 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.6950 (tp) outliers start: 61 outliers final: 28 residues processed: 151 average time/residue: 1.3534 time to fit residues: 216.8300 Evaluate side-chains 141 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 555 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112964 restraints weight = 8389.500| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.06 r_work: 0.3213 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7382 Z= 0.159 Angle : 0.571 8.715 10032 Z= 0.292 Chirality : 0.042 0.139 1170 Planarity : 0.005 0.049 1226 Dihedral : 8.185 73.497 1012 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.64 % Favored : 95.14 % Rotamer: Outliers : 7.48 % Allowed : 23.10 % Favored : 69.42 % 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: 1.44 (0.27), residues: 926 helix: 1.82 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -1.72 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 469 HIS 0.003 0.001 HIS A 555 PHE 0.015 0.001 PHE B 547 TYR 0.009 0.001 TYR B 578 ARG 0.004 0.000 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 542) hydrogen bonds : angle 4.12588 ( 1614) covalent geometry : bond 0.00377 ( 7382) covalent geometry : angle 0.57077 (10032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 93 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 139 SER cc_start: 0.7857 (OUTLIER) cc_final: 0.7514 (m) REVERT: A 203 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6621 (mm) REVERT: A 204 LYS cc_start: 0.7380 (tptt) cc_final: 0.7100 (tttm) REVERT: A 248 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6507 (mttt) REVERT: A 317 ARG cc_start: 0.6629 (mmt90) cc_final: 0.6003 (tpt170) REVERT: A 421 ARG cc_start: 0.7744 (mtt-85) cc_final: 0.7412 (mtm180) REVERT: A 425 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.8151 (m) REVERT: A 431 ASN cc_start: 0.8200 (m-40) cc_final: 0.7933 (m110) REVERT: A 515 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7123 (tp) REVERT: A 560 MET cc_start: 0.7965 (mmm) cc_final: 0.7542 (mtm) REVERT: B 139 SER cc_start: 0.7863 (OUTLIER) cc_final: 0.7519 (m) REVERT: B 204 LYS cc_start: 0.7359 (tptt) cc_final: 0.7118 (tttm) REVERT: B 248 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6521 (mttt) REVERT: B 317 ARG cc_start: 0.6591 (mmt90) cc_final: 0.5998 (tpt170) REVERT: B 334 ARG cc_start: 0.7971 (mpt180) cc_final: 0.7694 (mpt180) REVERT: B 421 ARG cc_start: 0.7752 (mtt-85) cc_final: 0.7420 (mtm180) REVERT: B 425 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8141 (m) REVERT: B 431 ASN cc_start: 0.8184 (m-40) cc_final: 0.7923 (m110) REVERT: B 515 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7121 (tp) outliers start: 57 outliers final: 30 residues processed: 136 average time/residue: 1.1664 time to fit residues: 167.8758 Evaluate side-chains 125 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 555 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113112 restraints weight = 8377.835| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.03 r_work: 0.3258 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7382 Z= 0.192 Angle : 0.584 6.351 10032 Z= 0.303 Chirality : 0.044 0.138 1170 Planarity : 0.005 0.046 1226 Dihedral : 7.826 67.914 1008 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.43 % Favored : 95.36 % Rotamer: Outliers : 8.79 % Allowed : 22.18 % Favored : 69.03 % 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: 1.45 (0.27), residues: 926 helix: 1.88 (0.19), residues: 678 sheet: None (None), residues: 0 loop : -1.71 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 469 HIS 0.003 0.001 HIS A 555 PHE 0.017 0.002 PHE B 547 TYR 0.010 0.001 TYR B 206 ARG 0.002 0.000 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 542) hydrogen bonds : angle 4.18809 ( 1614) covalent geometry : bond 0.00461 ( 7382) covalent geometry : angle 0.58388 (10032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 91 time to evaluate : 0.723 Fit side-chains REVERT: A 139 SER cc_start: 0.7923 (OUTLIER) cc_final: 0.7566 (m) REVERT: A 173 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7996 (mp) REVERT: A 203 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6651 (mm) REVERT: A 204 LYS cc_start: 0.7291 (tptt) cc_final: 0.7044 (tttm) REVERT: A 248 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6589 (mttt) REVERT: A 317 ARG cc_start: 0.6621 (mmt90) cc_final: 0.5997 (tpt170) REVERT: A 334 ARG cc_start: 0.8093 (mpt180) cc_final: 0.7842 (mpt180) REVERT: A 421 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7637 (mtm180) REVERT: A 425 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8319 (m) REVERT: A 431 ASN cc_start: 0.8346 (m-40) cc_final: 0.8063 (m110) REVERT: A 515 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7165 (tp) REVERT: A 516 ILE cc_start: 0.8195 (pp) cc_final: 0.7987 (pp) REVERT: A 560 MET cc_start: 0.8121 (mmm) cc_final: 0.7843 (mtm) REVERT: B 139 SER cc_start: 0.7959 (OUTLIER) cc_final: 0.7595 (m) REVERT: B 173 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7990 (mp) REVERT: B 204 LYS cc_start: 0.7271 (tptt) cc_final: 0.7025 (tttm) REVERT: B 248 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6623 (mttt) REVERT: B 317 ARG cc_start: 0.6637 (mmt90) cc_final: 0.6051 (tpt170) REVERT: B 334 ARG cc_start: 0.8074 (mpt180) cc_final: 0.7678 (mpt180) REVERT: B 421 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.7611 (mtm180) REVERT: B 425 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.8304 (m) REVERT: B 431 ASN cc_start: 0.8356 (m-40) cc_final: 0.8074 (m110) REVERT: B 515 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7177 (tp) REVERT: B 516 ILE cc_start: 0.8208 (pp) cc_final: 0.8001 (pp) outliers start: 67 outliers final: 27 residues processed: 143 average time/residue: 1.1303 time to fit residues: 170.8880 Evaluate side-chains 121 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 83 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 555 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** 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 = 0.3686 r_free = 0.3686 target = 0.143388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115182 restraints weight = 8307.812| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.04 r_work: 0.3285 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7382 Z= 0.150 Angle : 0.563 5.926 10032 Z= 0.289 Chirality : 0.042 0.138 1170 Planarity : 0.005 0.045 1226 Dihedral : 7.708 68.916 1008 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.10 % Favored : 95.68 % Rotamer: Outliers : 6.56 % Allowed : 24.15 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.27), residues: 926 helix: 1.87 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -1.63 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 469 HIS 0.001 0.000 HIS A 555 PHE 0.016 0.001 PHE B 547 TYR 0.009 0.001 TYR B 578 ARG 0.002 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 542) hydrogen bonds : angle 4.13017 ( 1614) covalent geometry : bond 0.00351 ( 7382) covalent geometry : angle 0.56292 (10032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 86 time to evaluate : 0.778 Fit side-chains REVERT: A 139 SER cc_start: 0.7910 (OUTLIER) cc_final: 0.7566 (m) REVERT: A 248 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6593 (mttt) REVERT: A 317 ARG cc_start: 0.6627 (mmt90) cc_final: 0.6043 (tpt170) REVERT: A 334 ARG cc_start: 0.8060 (mpt180) cc_final: 0.7764 (mpt180) REVERT: A 343 PHE cc_start: 0.6236 (OUTLIER) cc_final: 0.4996 (t80) REVERT: A 421 ARG cc_start: 0.7918 (mtt-85) cc_final: 0.7620 (mtm180) REVERT: A 425 SER cc_start: 0.8521 (OUTLIER) cc_final: 0.8296 (m) REVERT: A 431 ASN cc_start: 0.8319 (m-40) cc_final: 0.8011 (m110) REVERT: A 516 ILE cc_start: 0.8208 (pp) cc_final: 0.7975 (pp) REVERT: B 139 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.7584 (m) REVERT: B 248 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6639 (mttt) REVERT: B 317 ARG cc_start: 0.6611 (mmt90) cc_final: 0.6039 (tpt170) REVERT: B 334 ARG cc_start: 0.8083 (mpt180) cc_final: 0.7707 (mpt180) REVERT: B 343 PHE cc_start: 0.6202 (OUTLIER) cc_final: 0.4983 (t80) REVERT: B 421 ARG cc_start: 0.7899 (mtt-85) cc_final: 0.7605 (mtm180) REVERT: B 425 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.8300 (m) REVERT: B 431 ASN cc_start: 0.8331 (m-40) cc_final: 0.8018 (m110) REVERT: B 516 ILE cc_start: 0.8211 (pp) cc_final: 0.7979 (pp) outliers start: 50 outliers final: 23 residues processed: 123 average time/residue: 1.2198 time to fit residues: 158.5148 Evaluate side-chains 114 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 343 PHE Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 555 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 75 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.0570 chunk 30 optimal weight: 0.5980 overall best weight: 0.2498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** 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 = 0.3702 r_free = 0.3702 target = 0.144925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116925 restraints weight = 8383.423| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.02 r_work: 0.3307 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7382 Z= 0.120 Angle : 0.544 6.343 10032 Z= 0.276 Chirality : 0.041 0.138 1170 Planarity : 0.005 0.043 1226 Dihedral : 7.249 71.848 1002 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.32 % Favored : 95.46 % Rotamer: Outliers : 5.91 % Allowed : 24.54 % Favored : 69.55 % 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 (0.28), residues: 926 helix: 2.04 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -1.43 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 469 HIS 0.002 0.000 HIS A 555 PHE 0.019 0.001 PHE B 279 TYR 0.010 0.001 TYR A 517 ARG 0.002 0.000 ARG B 370 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 542) hydrogen bonds : angle 4.02656 ( 1614) covalent geometry : bond 0.00257 ( 7382) covalent geometry : angle 0.54367 (10032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 88 time to evaluate : 0.817 Fit side-chains REVERT: A 204 LYS cc_start: 0.7084 (tttm) cc_final: 0.6738 (tttm) REVERT: A 248 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6562 (mttt) REVERT: A 317 ARG cc_start: 0.6542 (mmt90) cc_final: 0.6012 (tpt170) REVERT: A 334 ARG cc_start: 0.8065 (mpt180) cc_final: 0.7766 (mpt180) REVERT: A 421 ARG cc_start: 0.7806 (mtt-85) cc_final: 0.7471 (mtm180) REVERT: A 431 ASN cc_start: 0.8173 (m-40) cc_final: 0.7902 (m110) REVERT: B 204 LYS cc_start: 0.7073 (tttm) cc_final: 0.6848 (tttm) REVERT: B 248 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6558 (mttt) REVERT: B 317 ARG cc_start: 0.6497 (mmt90) cc_final: 0.5996 (tpt170) REVERT: B 334 ARG cc_start: 0.8078 (mpt180) cc_final: 0.7709 (mpt180) REVERT: B 421 ARG cc_start: 0.7816 (mtt-85) cc_final: 0.7484 (mtm180) REVERT: B 431 ASN cc_start: 0.8178 (m-40) cc_final: 0.7903 (m110) outliers start: 45 outliers final: 31 residues processed: 119 average time/residue: 1.1907 time to fit residues: 149.7980 Evaluate side-chains 116 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 555 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 78 optimal weight: 0.9990 chunk 53 optimal weight: 0.0040 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** 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 = 0.3680 r_free = 0.3680 target = 0.143331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115287 restraints weight = 8533.227| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.03 r_work: 0.3287 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7382 Z= 0.135 Angle : 0.558 6.621 10032 Z= 0.285 Chirality : 0.042 0.138 1170 Planarity : 0.005 0.043 1226 Dihedral : 7.157 70.961 1002 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.10 % Favored : 95.68 % Rotamer: Outliers : 5.38 % Allowed : 25.59 % Favored : 69.03 % 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: 1.90 (0.28), residues: 926 helix: 2.07 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -1.29 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 469 HIS 0.001 0.000 HIS A 555 PHE 0.025 0.001 PHE A 306 TYR 0.009 0.001 TYR A 206 ARG 0.001 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 542) hydrogen bonds : angle 4.02744 ( 1614) covalent geometry : bond 0.00307 ( 7382) covalent geometry : angle 0.55807 (10032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 85 time to evaluate : 0.725 Fit side-chains REVERT: A 248 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6610 (mttt) REVERT: A 317 ARG cc_start: 0.6576 (mmt90) cc_final: 0.6029 (tpt170) REVERT: A 334 ARG cc_start: 0.8071 (mpt180) cc_final: 0.7748 (mpt180) REVERT: A 431 ASN cc_start: 0.8200 (m-40) cc_final: 0.7907 (m110) REVERT: B 248 LYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6592 (mttt) REVERT: B 317 ARG cc_start: 0.6566 (mmt90) cc_final: 0.6049 (tpt170) REVERT: B 334 ARG cc_start: 0.8079 (mpt180) cc_final: 0.7681 (mpt180) REVERT: B 431 ASN cc_start: 0.8202 (m-40) cc_final: 0.7904 (m110) outliers start: 41 outliers final: 28 residues processed: 115 average time/residue: 1.2645 time to fit residues: 153.2144 Evaluate side-chains 111 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 443 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 18 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 0.0170 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** 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 = 0.3682 r_free = 0.3682 target = 0.143602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.115506 restraints weight = 8631.456| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.04 r_work: 0.3288 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7382 Z= 0.136 Angle : 0.565 6.665 10032 Z= 0.289 Chirality : 0.042 0.138 1170 Planarity : 0.005 0.043 1226 Dihedral : 7.041 70.067 1000 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.32 % Favored : 95.46 % Rotamer: Outliers : 4.86 % Allowed : 26.51 % Favored : 68.64 % 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: 1.92 (0.27), residues: 926 helix: 2.07 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -1.23 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 322 HIS 0.002 0.000 HIS B 555 PHE 0.028 0.001 PHE A 306 TYR 0.012 0.001 TYR B 206 ARG 0.002 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 542) hydrogen bonds : angle 4.04326 ( 1614) covalent geometry : bond 0.00310 ( 7382) covalent geometry : angle 0.56523 (10032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 0.723 Fit side-chains REVERT: A 248 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6599 (mttt) REVERT: A 297 PHE cc_start: 0.7216 (t80) cc_final: 0.7004 (t80) REVERT: A 317 ARG cc_start: 0.6565 (mmt90) cc_final: 0.6027 (tpt170) REVERT: A 334 ARG cc_start: 0.8051 (mpt180) cc_final: 0.7726 (mpt180) REVERT: A 431 ASN cc_start: 0.8208 (m-40) cc_final: 0.7909 (m110) REVERT: B 248 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6599 (mttt) REVERT: B 297 PHE cc_start: 0.7225 (t80) cc_final: 0.7009 (t80) REVERT: B 317 ARG cc_start: 0.6552 (mmt90) cc_final: 0.6037 (tpt170) REVERT: B 334 ARG cc_start: 0.8066 (mpt180) cc_final: 0.7833 (mpt180) REVERT: B 431 ASN cc_start: 0.8209 (m-40) cc_final: 0.7907 (m110) outliers start: 37 outliers final: 30 residues processed: 106 average time/residue: 1.2637 time to fit residues: 141.1803 Evaluate side-chains 113 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 555 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 66 optimal weight: 0.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** 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 = 0.3689 r_free = 0.3689 target = 0.144355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116261 restraints weight = 8495.894| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.03 r_work: 0.3302 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7382 Z= 0.131 Angle : 0.563 7.119 10032 Z= 0.288 Chirality : 0.042 0.138 1170 Planarity : 0.005 0.043 1226 Dihedral : 6.931 69.707 1000 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.32 % Favored : 95.46 % Rotamer: Outliers : 4.86 % Allowed : 26.64 % Favored : 68.50 % 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: 1.95 (0.28), residues: 926 helix: 2.09 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -1.18 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 469 HIS 0.001 0.000 HIS B 555 PHE 0.027 0.001 PHE A 306 TYR 0.008 0.001 TYR B 578 ARG 0.002 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 542) hydrogen bonds : angle 4.03544 ( 1614) covalent geometry : bond 0.00295 ( 7382) covalent geometry : angle 0.56254 (10032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9546.53 seconds wall clock time: 167 minutes 5.03 seconds (10025.03 seconds total)