Starting phenix.real_space_refine on Tue Feb 3 17:16:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hji_52215/02_2026/9hji_52215.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hji_52215/02_2026/9hji_52215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hji_52215/02_2026/9hji_52215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hji_52215/02_2026/9hji_52215.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hji_52215/02_2026/9hji_52215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hji_52215/02_2026/9hji_52215.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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 22 5.16 5 C 3532 2.51 5 N 930 2.21 5 O 1048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5532 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5532 Classifications: {'peptide': 697} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 661} Time building chain proxies: 1.36, per 1000 atoms: 0.25 Number of scatterers: 5532 At special positions: 0 Unit cell: (89.216, 78.72, 83.968, 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 22 16.00 O 1048 8.00 N 930 7.00 C 3532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 364.3 milliseconds 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 10 sheets defined 24.0% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 26 through 30 Processing helix chain 'A' and resid 34 through 53 Processing helix chain 'A' and resid 55 through 71 Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.585A pdb=" N GLU A 221 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing helix chain 'A' and resid 516 through 534 removed outlier: 3.880A pdb=" N CYS A 520 " --> pdb=" O CYS A 516 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 562 through 565 Processing helix chain 'A' and resid 585 through 594 removed outlier: 3.745A pdb=" N TRP A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP A 592 " --> pdb=" O ALA A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.845A pdb=" N VAL A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 650 removed outlier: 3.599A pdb=" N LEU A 640 " --> pdb=" O PRO A 636 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 646 " --> pdb=" O TYR A 642 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N HIS A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 692 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 132 removed outlier: 5.697A pdb=" N LEU A 127 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER A 144 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A 157 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU A 162 " --> pdb=" O ARG A 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 179 removed outlier: 3.888A pdb=" N GLY A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE A 212 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL A 224 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 235 through 240 removed outlier: 7.040A pdb=" N VAL A 263 " --> pdb=" O LYS A 282 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LYS A 282 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 297 removed outlier: 5.272A pdb=" N TYR A 293 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL A 304 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 295 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 301 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE A 314 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 341 removed outlier: 6.096A pdb=" N LEU A 335 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU A 350 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE A 357 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 381 removed outlier: 6.742A pdb=" N LYS A 392 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE A 380 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N SER A 390 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE A 404 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL A 416 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 430 through 438 removed outlier: 6.112A pdb=" N LEU A 462 " --> pdb=" O ALA A 543 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N MET A 545 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU A 464 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 570 through 571 removed outlier: 6.550A pdb=" N VAL A 625 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLU A 662 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR A 627 " --> pdb=" O GLU A 662 " (cutoff:3.500A) 212 hydrogen bonds defined for protein. 570 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1808 1.34 - 1.46: 1388 1.46 - 1.58: 2446 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 5678 Sorted by residual: bond pdb=" C ARG A 660 " pdb=" N ILE A 661 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.25e-02 6.40e+03 2.07e+00 bond pdb=" CB GLU A 563 " pdb=" CG GLU A 563 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" CG1 ILE A 544 " pdb=" CD1 ILE A 544 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.06e+00 bond pdb=" CG ARG A 217 " pdb=" CD ARG A 217 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CB MET A 103 " pdb=" CG MET A 103 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.55e-01 ... (remaining 5673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 7541 2.31 - 4.61: 138 4.61 - 6.92: 25 6.92 - 9.22: 6 9.22 - 11.53: 1 Bond angle restraints: 7711 Sorted by residual: angle pdb=" C HIS A 180 " pdb=" CA HIS A 180 " pdb=" CB HIS A 180 " ideal model delta sigma weight residual 116.54 110.24 6.30 1.15e+00 7.56e-01 3.00e+01 angle pdb=" CB MET A 138 " pdb=" CG MET A 138 " pdb=" SD MET A 138 " ideal model delta sigma weight residual 112.70 124.23 -11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C SER A 76 " pdb=" N ASN A 77 " pdb=" CA ASN A 77 " ideal model delta sigma weight residual 120.49 125.77 -5.28 1.42e+00 4.96e-01 1.39e+01 angle pdb=" CA HIS A 180 " pdb=" C HIS A 180 " pdb=" N ASN A 181 " ideal model delta sigma weight residual 119.52 116.83 2.69 7.90e-01 1.60e+00 1.16e+01 angle pdb=" CA ILE A 544 " pdb=" CB ILE A 544 " pdb=" CG1 ILE A 544 " ideal model delta sigma weight residual 110.40 116.03 -5.63 1.70e+00 3.46e-01 1.10e+01 ... (remaining 7706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2860 17.95 - 35.89: 355 35.89 - 53.84: 105 53.84 - 71.78: 24 71.78 - 89.73: 8 Dihedral angle restraints: 3352 sinusoidal: 1327 harmonic: 2025 Sorted by residual: dihedral pdb=" CA LEU A 283 " pdb=" C LEU A 283 " pdb=" N VAL A 284 " pdb=" CA VAL A 284 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ARG A 157 " pdb=" C ARG A 157 " pdb=" N ALA A 158 " pdb=" CA ALA A 158 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ASN A 95 " pdb=" CB ASN A 95 " pdb=" CG ASN A 95 " pdb=" OD1 ASN A 95 " ideal model delta sinusoidal sigma weight residual 120.00 -168.79 -71.21 2 2.00e+01 2.50e-03 1.08e+01 ... (remaining 3349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 697 0.066 - 0.133: 125 0.133 - 0.199: 6 0.199 - 0.266: 0 0.266 - 0.332: 1 Chirality restraints: 829 Sorted by residual: chirality pdb=" CG LEU A 552 " pdb=" CB LEU A 552 " pdb=" CD1 LEU A 552 " pdb=" CD2 LEU A 552 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB ILE A 623 " pdb=" CA ILE A 623 " pdb=" CG1 ILE A 623 " pdb=" CG2 ILE A 623 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CG LEU A 283 " pdb=" CB LEU A 283 " pdb=" CD1 LEU A 283 " pdb=" CD2 LEU A 283 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.93e-01 ... (remaining 826 not shown) Planarity restraints: 1005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 553 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C LEU A 553 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU A 553 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 554 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 554 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C VAL A 554 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL A 554 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA A 555 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 132 " -0.012 2.00e-02 2.50e+03 1.24e-02 3.85e+00 pdb=" CG TRP A 132 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 132 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 132 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 132 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 132 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 132 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 132 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 132 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 132 " 0.000 2.00e-02 2.50e+03 ... (remaining 1002 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 3056 3.00 - 3.48: 5727 3.48 - 3.95: 8648 3.95 - 4.43: 9853 4.43 - 4.90: 15915 Nonbonded interactions: 43199 Sorted by model distance: nonbonded pdb=" N GLU A 563 " pdb=" OE1 GLU A 563 " model vdw 2.529 3.120 nonbonded pdb=" O ASN A 549 " pdb=" CB LEU A 552 " model vdw 2.548 3.440 nonbonded pdb=" N ASP A 159 " pdb=" OD1 ASP A 159 " model vdw 2.559 3.120 nonbonded pdb=" O VAL A 568 " pdb=" O ALA A 622 " model vdw 2.573 3.040 nonbonded pdb=" N ILE A 585 " pdb=" N GLY A 586 " model vdw 2.574 2.560 ... (remaining 43194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.310 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 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 : 0.003 0.040 5678 Z= 0.157 Angle : 0.810 11.528 7711 Z= 0.438 Chirality : 0.049 0.332 829 Planarity : 0.005 0.040 1005 Dihedral : 17.950 89.726 2056 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.51 % Allowed : 40.07 % Favored : 56.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.31), residues: 695 helix: -0.54 (0.42), residues: 144 sheet: -0.60 (0.36), residues: 184 loop : -0.80 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 217 TYR 0.020 0.002 TYR A 642 PHE 0.026 0.002 PHE A 388 TRP 0.033 0.004 TRP A 132 HIS 0.005 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 5678) covalent geometry : angle 0.80973 ( 7711) hydrogen bonds : bond 0.14516 ( 212) hydrogen bonds : angle 7.94059 ( 570) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 130 THR cc_start: 0.7050 (m) cc_final: 0.6676 (m) REVERT: A 349 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.5828 (m-80) REVERT: A 357 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6401 (t80) REVERT: A 444 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.5820 (mtp85) REVERT: A 504 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.6316 (m-80) REVERT: A 523 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7644 (m-30) outliers start: 21 outliers final: 9 residues processed: 125 average time/residue: 0.0663 time to fit residues: 11.2669 Evaluate side-chains 107 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 95 ASN A 181 ASN A 219 GLN A 581 HIS ** A 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.137504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125169 restraints weight = 12161.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.128532 restraints weight = 6449.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.130746 restraints weight = 3865.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.132240 restraints weight = 2499.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.133281 restraints weight = 1721.192| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5678 Z= 0.229 Angle : 0.703 6.058 7711 Z= 0.372 Chirality : 0.050 0.330 829 Planarity : 0.005 0.039 1005 Dihedral : 7.460 60.507 787 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 9.18 % Allowed : 30.55 % Favored : 60.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.31), residues: 695 helix: 0.14 (0.43), residues: 142 sheet: -0.91 (0.35), residues: 182 loop : -0.82 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 452 TYR 0.016 0.002 TYR A 291 PHE 0.023 0.002 PHE A 252 TRP 0.034 0.003 TRP A 234 HIS 0.010 0.002 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 5678) covalent geometry : angle 0.70254 ( 7711) hydrogen bonds : bond 0.05114 ( 212) hydrogen bonds : angle 6.41524 ( 570) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 106 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.6298 (mtm-85) cc_final: 0.5995 (mtm-85) REVERT: A 87 TYR cc_start: 0.7853 (p90) cc_final: 0.7585 (p90) REVERT: A 88 TYR cc_start: 0.7011 (m-80) cc_final: 0.6796 (m-80) REVERT: A 130 THR cc_start: 0.6786 (OUTLIER) cc_final: 0.6438 (m) REVERT: A 219 GLN cc_start: 0.7208 (mp10) cc_final: 0.6687 (mp10) REVERT: A 349 TYR cc_start: 0.7086 (OUTLIER) cc_final: 0.5598 (m-80) REVERT: A 357 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6634 (t80) REVERT: A 498 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7857 (pt) REVERT: A 523 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: A 564 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6999 (tt) REVERT: A 632 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7750 (m-30) outliers start: 55 outliers final: 26 residues processed: 144 average time/residue: 0.0564 time to fit residues: 11.1611 Evaluate side-chains 136 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 150 TRP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 0.0770 chunk 28 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN ** A 647 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 = 0.3953 r_free = 0.3953 target = 0.142306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.129764 restraints weight = 12067.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.133155 restraints weight = 6533.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.135413 restraints weight = 3965.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.136933 restraints weight = 2577.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.137939 restraints weight = 1778.517| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5678 Z= 0.109 Angle : 0.595 6.269 7711 Z= 0.303 Chirality : 0.045 0.180 829 Planarity : 0.004 0.032 1005 Dihedral : 6.228 57.807 778 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 6.34 % Allowed : 31.05 % Favored : 62.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.32), residues: 695 helix: 0.45 (0.44), residues: 145 sheet: -0.63 (0.36), residues: 183 loop : -0.65 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 633 TYR 0.013 0.001 TYR A 608 PHE 0.021 0.001 PHE A 388 TRP 0.049 0.003 TRP A 234 HIS 0.005 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 5678) covalent geometry : angle 0.59474 ( 7711) hydrogen bonds : bond 0.03821 ( 212) hydrogen bonds : angle 5.67629 ( 570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 THR cc_start: 0.6811 (OUTLIER) cc_final: 0.6371 (m) REVERT: A 141 TYR cc_start: 0.6670 (p90) cc_final: 0.6411 (p90) REVERT: A 260 LEU cc_start: 0.3628 (OUTLIER) cc_final: 0.3283 (pp) REVERT: A 317 ILE cc_start: 0.5653 (OUTLIER) cc_final: 0.5409 (pt) REVERT: A 349 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.5484 (m-80) REVERT: A 357 PHE cc_start: 0.7144 (OUTLIER) cc_final: 0.6669 (t80) REVERT: A 498 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7960 (pt) REVERT: A 559 ASN cc_start: 0.7010 (t0) cc_final: 0.6801 (t0) REVERT: A 564 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6767 (tt) outliers start: 38 outliers final: 22 residues processed: 136 average time/residue: 0.0659 time to fit residues: 12.0734 Evaluate side-chains 136 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 63 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN ** A 647 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 = 0.3916 r_free = 0.3916 target = 0.138855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.126505 restraints weight = 12197.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.129829 restraints weight = 6537.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.132026 restraints weight = 3940.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.133512 restraints weight = 2569.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.134563 restraints weight = 1784.504| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5678 Z= 0.168 Angle : 0.632 7.303 7711 Z= 0.329 Chirality : 0.047 0.171 829 Planarity : 0.005 0.034 1005 Dihedral : 5.950 56.449 776 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 8.85 % Allowed : 29.22 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.32), residues: 695 helix: 0.42 (0.44), residues: 145 sheet: -0.78 (0.35), residues: 185 loop : -0.73 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 452 TYR 0.012 0.002 TYR A 291 PHE 0.021 0.002 PHE A 252 TRP 0.047 0.003 TRP A 234 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5678) covalent geometry : angle 0.63212 ( 7711) hydrogen bonds : bond 0.04136 ( 212) hydrogen bonds : angle 5.79573 ( 570) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 107 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.6571 (mtm-85) cc_final: 0.6189 (mtm-85) REVERT: A 77 ASN cc_start: 0.6954 (m-40) cc_final: 0.6586 (m110) REVERT: A 87 TYR cc_start: 0.7809 (p90) cc_final: 0.7604 (p90) REVERT: A 101 ARG cc_start: 0.6923 (ttt-90) cc_final: 0.6675 (ttt-90) REVERT: A 150 TRP cc_start: 0.7382 (OUTLIER) cc_final: 0.6713 (m-90) REVERT: A 219 GLN cc_start: 0.7256 (mp10) cc_final: 0.6787 (mp10) REVERT: A 349 TYR cc_start: 0.7108 (OUTLIER) cc_final: 0.5634 (m-80) REVERT: A 357 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6702 (t80) REVERT: A 444 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.5968 (mtp85) REVERT: A 498 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7806 (pt) REVERT: A 504 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.6977 (m-80) REVERT: A 564 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6720 (tt) outliers start: 53 outliers final: 33 residues processed: 146 average time/residue: 0.0702 time to fit residues: 13.5203 Evaluate side-chains 145 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 105 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 150 TRP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.0060 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN A 559 ASN ** A 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.139346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.127060 restraints weight = 12376.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.130389 restraints weight = 6619.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.132562 restraints weight = 3994.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.134054 restraints weight = 2605.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.135018 restraints weight = 1810.484| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5678 Z= 0.142 Angle : 0.604 6.789 7711 Z= 0.313 Chirality : 0.046 0.148 829 Planarity : 0.004 0.033 1005 Dihedral : 5.834 56.746 775 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 9.35 % Allowed : 29.22 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.32), residues: 695 helix: 0.57 (0.44), residues: 145 sheet: -0.79 (0.35), residues: 185 loop : -0.76 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 452 TYR 0.016 0.002 TYR A 28 PHE 0.019 0.002 PHE A 388 TRP 0.060 0.003 TRP A 234 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5678) covalent geometry : angle 0.60413 ( 7711) hydrogen bonds : bond 0.03950 ( 212) hydrogen bonds : angle 5.58473 ( 570) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 111 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6887 (m-40) cc_final: 0.6547 (m110) REVERT: A 130 THR cc_start: 0.7200 (OUTLIER) cc_final: 0.6876 (m) REVERT: A 150 TRP cc_start: 0.7361 (OUTLIER) cc_final: 0.6688 (m-90) REVERT: A 233 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6302 (tp-100) REVERT: A 296 ASN cc_start: 0.8489 (p0) cc_final: 0.8218 (p0) REVERT: A 349 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.5626 (m-80) REVERT: A 357 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6768 (t80) REVERT: A 444 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6163 (mtp85) REVERT: A 498 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7712 (pt) REVERT: A 504 TYR cc_start: 0.7365 (OUTLIER) cc_final: 0.6996 (m-80) REVERT: A 523 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7039 (m-30) REVERT: A 564 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6686 (tt) REVERT: A 619 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.6593 (ptmm) outliers start: 56 outliers final: 31 residues processed: 152 average time/residue: 0.0593 time to fit residues: 11.8926 Evaluate side-chains 145 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 150 TRP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN A 233 GLN A 285 ASN A 559 ASN ** A 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.138995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.126675 restraints weight = 12294.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.129991 restraints weight = 6623.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.132211 restraints weight = 4013.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.133625 restraints weight = 2615.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.134687 restraints weight = 1840.937| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5678 Z= 0.147 Angle : 0.630 8.010 7711 Z= 0.322 Chirality : 0.046 0.155 829 Planarity : 0.004 0.035 1005 Dihedral : 5.825 56.684 775 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 9.18 % Allowed : 29.72 % Favored : 61.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.32), residues: 695 helix: 0.56 (0.44), residues: 146 sheet: -0.78 (0.34), residues: 185 loop : -0.75 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 101 TYR 0.022 0.002 TYR A 26 PHE 0.019 0.002 PHE A 388 TRP 0.065 0.003 TRP A 234 HIS 0.007 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 5678) covalent geometry : angle 0.63042 ( 7711) hydrogen bonds : bond 0.03919 ( 212) hydrogen bonds : angle 5.53042 ( 570) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 112 time to evaluate : 0.226 Fit side-chains REVERT: A 74 ARG cc_start: 0.6578 (mtm-85) cc_final: 0.6190 (mtm-85) REVERT: A 77 ASN cc_start: 0.6906 (m-40) cc_final: 0.6195 (m110) REVERT: A 130 THR cc_start: 0.6958 (OUTLIER) cc_final: 0.6617 (m) REVERT: A 150 TRP cc_start: 0.7363 (OUTLIER) cc_final: 0.6686 (m-90) REVERT: A 219 GLN cc_start: 0.7366 (mp-120) cc_final: 0.6885 (mp10) REVERT: A 233 GLN cc_start: 0.6702 (OUTLIER) cc_final: 0.6318 (tp-100) REVERT: A 260 LEU cc_start: 0.3619 (OUTLIER) cc_final: 0.3397 (pp) REVERT: A 296 ASN cc_start: 0.8482 (p0) cc_final: 0.8209 (p0) REVERT: A 349 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.5651 (m-80) REVERT: A 357 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6738 (t80) REVERT: A 379 SER cc_start: 0.8875 (m) cc_final: 0.8445 (t) REVERT: A 444 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6178 (mtp85) REVERT: A 450 VAL cc_start: 0.8008 (OUTLIER) cc_final: 0.7799 (m) REVERT: A 498 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7735 (pt) REVERT: A 504 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.7083 (m-80) REVERT: A 523 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7052 (m-30) REVERT: A 564 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6697 (tt) REVERT: A 619 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.6621 (ptmm) outliers start: 55 outliers final: 32 residues processed: 150 average time/residue: 0.0751 time to fit residues: 15.0128 Evaluate side-chains 152 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 107 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 150 TRP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 27 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 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 = 0.3894 r_free = 0.3894 target = 0.137419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125141 restraints weight = 12264.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.128447 restraints weight = 6589.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.130663 restraints weight = 3983.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.132157 restraints weight = 2597.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.133168 restraints weight = 1797.165| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5678 Z= 0.203 Angle : 0.674 7.330 7711 Z= 0.351 Chirality : 0.048 0.167 829 Planarity : 0.005 0.040 1005 Dihedral : 6.069 55.757 775 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 9.02 % Allowed : 30.38 % Favored : 60.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.31), residues: 695 helix: 0.38 (0.43), residues: 146 sheet: -0.74 (0.35), residues: 178 loop : -0.94 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 101 TYR 0.020 0.002 TYR A 26 PHE 0.020 0.002 PHE A 388 TRP 0.071 0.004 TRP A 234 HIS 0.011 0.002 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 5678) covalent geometry : angle 0.67397 ( 7711) hydrogen bonds : bond 0.04317 ( 212) hydrogen bonds : angle 5.73852 ( 570) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 106 time to evaluate : 0.226 Fit side-chains REVERT: A 74 ARG cc_start: 0.6696 (mtm-85) cc_final: 0.6321 (mtm-85) REVERT: A 77 ASN cc_start: 0.7010 (m-40) cc_final: 0.6321 (m-40) REVERT: A 88 TYR cc_start: 0.6973 (m-80) cc_final: 0.6750 (m-80) REVERT: A 130 THR cc_start: 0.6977 (OUTLIER) cc_final: 0.6652 (m) REVERT: A 150 TRP cc_start: 0.7486 (OUTLIER) cc_final: 0.6849 (m-90) REVERT: A 233 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6384 (tp-100) REVERT: A 234 TRP cc_start: 0.6454 (m-90) cc_final: 0.6212 (m-90) REVERT: A 260 LEU cc_start: 0.3658 (OUTLIER) cc_final: 0.3450 (pp) REVERT: A 296 ASN cc_start: 0.8485 (p0) cc_final: 0.8274 (p0) REVERT: A 349 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.5579 (m-80) REVERT: A 357 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6689 (t80) REVERT: A 379 SER cc_start: 0.8877 (m) cc_final: 0.8394 (t) REVERT: A 388 PHE cc_start: 0.7516 (t80) cc_final: 0.7300 (t80) REVERT: A 444 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6079 (mtp85) REVERT: A 498 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7827 (pt) REVERT: A 504 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: A 523 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7147 (m-30) REVERT: A 564 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6730 (tt) outliers start: 54 outliers final: 36 residues processed: 144 average time/residue: 0.0721 time to fit residues: 13.9901 Evaluate side-chains 151 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 104 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 150 TRP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN ** A 647 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 = 0.3942 r_free = 0.3942 target = 0.140727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.128456 restraints weight = 12069.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.131768 restraints weight = 6492.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.133962 restraints weight = 3920.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.135456 restraints weight = 2562.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.136479 restraints weight = 1776.596| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5678 Z= 0.112 Angle : 0.611 7.670 7711 Z= 0.309 Chirality : 0.046 0.174 829 Planarity : 0.004 0.036 1005 Dihedral : 5.642 56.623 775 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 6.84 % Allowed : 33.39 % Favored : 59.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.32), residues: 695 helix: 0.76 (0.44), residues: 145 sheet: -0.31 (0.38), residues: 152 loop : -0.93 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 101 TYR 0.017 0.001 TYR A 26 PHE 0.019 0.001 PHE A 388 TRP 0.062 0.003 TRP A 234 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 5678) covalent geometry : angle 0.61072 ( 7711) hydrogen bonds : bond 0.03619 ( 212) hydrogen bonds : angle 5.32226 ( 570) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.6593 (mtm-85) cc_final: 0.6224 (mtm-85) REVERT: A 77 ASN cc_start: 0.6837 (m-40) cc_final: 0.6222 (m-40) REVERT: A 88 TYR cc_start: 0.6837 (m-80) cc_final: 0.6588 (m-80) REVERT: A 130 THR cc_start: 0.6892 (OUTLIER) cc_final: 0.6579 (m) REVERT: A 150 TRP cc_start: 0.7392 (OUTLIER) cc_final: 0.6719 (m-90) REVERT: A 219 GLN cc_start: 0.7332 (mp-120) cc_final: 0.6879 (mp10) REVERT: A 296 ASN cc_start: 0.8519 (p0) cc_final: 0.8223 (p0) REVERT: A 349 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.5529 (m-80) REVERT: A 357 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6796 (t80) REVERT: A 379 SER cc_start: 0.8813 (m) cc_final: 0.8468 (t) REVERT: A 444 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6110 (mtp85) REVERT: A 470 PHE cc_start: 0.6943 (m-10) cc_final: 0.6640 (m-80) REVERT: A 498 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7806 (pt) REVERT: A 504 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.7052 (m-80) REVERT: A 523 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.6980 (m-30) REVERT: A 564 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6822 (tt) REVERT: A 619 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.6632 (ptmm) REVERT: A 650 ASN cc_start: 0.8299 (m-40) cc_final: 0.8061 (m110) outliers start: 41 outliers final: 25 residues processed: 144 average time/residue: 0.0776 time to fit residues: 14.7098 Evaluate side-chains 142 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 150 TRP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 3 optimal weight: 0.0370 chunk 58 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 0.1980 chunk 15 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN ** A 647 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 = 0.3925 r_free = 0.3925 target = 0.140525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.128273 restraints weight = 12115.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.131720 restraints weight = 6510.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.133895 restraints weight = 3917.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.135426 restraints weight = 2561.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.136438 restraints weight = 1765.862| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5678 Z= 0.124 Angle : 0.649 8.343 7711 Z= 0.329 Chirality : 0.046 0.173 829 Planarity : 0.004 0.044 1005 Dihedral : 5.504 56.918 773 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 6.68 % Allowed : 34.06 % Favored : 59.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.32), residues: 695 helix: 0.60 (0.43), residues: 151 sheet: -0.32 (0.38), residues: 152 loop : -1.00 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 101 TYR 0.016 0.002 TYR A 28 PHE 0.021 0.002 PHE A 388 TRP 0.065 0.003 TRP A 234 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 5678) covalent geometry : angle 0.64937 ( 7711) hydrogen bonds : bond 0.03628 ( 212) hydrogen bonds : angle 5.29889 ( 570) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.206 Fit side-chains REVERT: A 74 ARG cc_start: 0.6582 (mtm-85) cc_final: 0.6203 (mtm-85) REVERT: A 77 ASN cc_start: 0.6966 (m-40) cc_final: 0.6347 (m-40) REVERT: A 130 THR cc_start: 0.6831 (OUTLIER) cc_final: 0.6488 (m) REVERT: A 150 TRP cc_start: 0.7344 (OUTLIER) cc_final: 0.6670 (m-90) REVERT: A 219 GLN cc_start: 0.7406 (mp-120) cc_final: 0.6931 (mp10) REVERT: A 296 ASN cc_start: 0.8461 (p0) cc_final: 0.8166 (p0) REVERT: A 349 TYR cc_start: 0.6942 (OUTLIER) cc_final: 0.5501 (m-80) REVERT: A 357 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6827 (t80) REVERT: A 379 SER cc_start: 0.8845 (m) cc_final: 0.8510 (t) REVERT: A 444 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6113 (mtp85) REVERT: A 470 PHE cc_start: 0.6983 (m-10) cc_final: 0.6558 (m-80) REVERT: A 498 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7753 (pt) REVERT: A 504 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.6982 (m-80) REVERT: A 523 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7123 (m-30) REVERT: A 564 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6815 (tt) REVERT: A 577 MET cc_start: 0.7505 (mmt) cc_final: 0.6952 (mmt) REVERT: A 619 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.6632 (ptmm) REVERT: A 650 ASN cc_start: 0.8357 (m-40) cc_final: 0.8078 (m110) outliers start: 40 outliers final: 26 residues processed: 137 average time/residue: 0.0789 time to fit residues: 14.1664 Evaluate side-chains 145 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 150 TRP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 38 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 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 = 0.3908 r_free = 0.3908 target = 0.139260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.126992 restraints weight = 12251.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.130375 restraints weight = 6563.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.132577 restraints weight = 3955.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.134026 restraints weight = 2575.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.135055 restraints weight = 1801.015| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5678 Z= 0.159 Angle : 0.674 8.344 7711 Z= 0.344 Chirality : 0.048 0.208 829 Planarity : 0.005 0.043 1005 Dihedral : 5.679 56.543 773 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 6.34 % Allowed : 34.39 % Favored : 59.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.32), residues: 695 helix: 0.52 (0.43), residues: 151 sheet: -0.59 (0.36), residues: 173 loop : -1.00 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 101 TYR 0.016 0.002 TYR A 28 PHE 0.021 0.002 PHE A 388 TRP 0.066 0.004 TRP A 234 HIS 0.008 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 5678) covalent geometry : angle 0.67356 ( 7711) hydrogen bonds : bond 0.03963 ( 212) hydrogen bonds : angle 5.42137 ( 570) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.6630 (mtm-85) cc_final: 0.6169 (mtm-85) REVERT: A 77 ASN cc_start: 0.6859 (m-40) cc_final: 0.6221 (m-40) REVERT: A 130 THR cc_start: 0.6825 (OUTLIER) cc_final: 0.6507 (m) REVERT: A 150 TRP cc_start: 0.7493 (OUTLIER) cc_final: 0.6821 (m-90) REVERT: A 296 ASN cc_start: 0.8482 (p0) cc_final: 0.8191 (p0) REVERT: A 349 TYR cc_start: 0.6997 (OUTLIER) cc_final: 0.5552 (m-80) REVERT: A 357 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6738 (t80) REVERT: A 379 SER cc_start: 0.8902 (m) cc_final: 0.8564 (t) REVERT: A 444 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6149 (mtp85) REVERT: A 470 PHE cc_start: 0.7023 (m-10) cc_final: 0.6749 (m-10) REVERT: A 498 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7818 (pt) REVERT: A 504 TYR cc_start: 0.7420 (OUTLIER) cc_final: 0.7057 (m-80) REVERT: A 523 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7148 (m-30) REVERT: A 564 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6849 (tt) REVERT: A 577 MET cc_start: 0.7390 (mmt) cc_final: 0.6830 (mmt) outliers start: 38 outliers final: 27 residues processed: 136 average time/residue: 0.0835 time to fit residues: 14.9044 Evaluate side-chains 144 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 150 TRP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 GLN A 219 GLN ** A 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.137399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.125386 restraints weight = 12151.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.128728 restraints weight = 6477.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.130927 restraints weight = 3876.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.132379 restraints weight = 2504.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.133398 restraints weight = 1722.079| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5678 Z= 0.223 Angle : 0.739 9.081 7711 Z= 0.382 Chirality : 0.050 0.214 829 Planarity : 0.005 0.043 1005 Dihedral : 6.093 54.488 771 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 7.18 % Allowed : 33.22 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.32), residues: 695 helix: 0.45 (0.44), residues: 145 sheet: -0.88 (0.35), residues: 178 loop : -1.05 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 452 TYR 0.015 0.002 TYR A 26 PHE 0.021 0.002 PHE A 252 TRP 0.069 0.005 TRP A 234 HIS 0.010 0.002 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 5678) covalent geometry : angle 0.73866 ( 7711) hydrogen bonds : bond 0.04571 ( 212) hydrogen bonds : angle 5.83536 ( 570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 970.34 seconds wall clock time: 17 minutes 33.58 seconds (1053.58 seconds total)