Starting phenix.real_space_refine on Wed Jun 3 15:40:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmh_66091/06_2026/9wmh_66091.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmh_66091/06_2026/9wmh_66091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wmh_66091/06_2026/9wmh_66091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmh_66091/06_2026/9wmh_66091.map" model { file = "/net/cci-nas-00/data/ceres_data/9wmh_66091/06_2026/9wmh_66091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmh_66091/06_2026/9wmh_66091.cif" } resolution = 2.55 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= 0.011 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 36 5.49 5 S 16 5.16 5 C 4277 2.51 5 N 1153 2.21 5 O 1324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6809 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6036 Classifications: {'peptide': 741} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 707} Chain breaks: 1 Chain: "B" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 379 Classifications: {'DNA': 18} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.80, per 1000 atoms: 0.26 Number of scatterers: 6809 At special positions: 0 Unit cell: (76.26, 90.2, 107.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 16 16.00 P 36 15.00 O 1324 8.00 N 1153 7.00 C 4277 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: 0.73 Conformation dependent library (CDL) restraints added in 299.7 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 33.9% alpha, 23.6% beta 8 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 107 through 126 removed outlier: 4.454A pdb=" N VAL A 111 " --> pdb=" O HIS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.650A pdb=" N PHE A 197 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 4.021A pdb=" N SER A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 370 through 383 removed outlier: 3.886A pdb=" N ILE A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 423 Processing helix chain 'A' and resid 441 through 456 removed outlier: 3.626A pdb=" N GLN A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 489 removed outlier: 4.165A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.691A pdb=" N PHE A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 546 removed outlier: 3.539A pdb=" N TYR A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 604 through 624 removed outlier: 3.622A pdb=" N LEU A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 640 through 656 Processing helix chain 'A' and resid 735 through 748 Processing helix chain 'A' and resid 761 through 771 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 removed outlier: 3.550A pdb=" N LEU A 339 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 10 removed outlier: 5.423A pdb=" N GLU A 155 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 62 removed outlier: 7.248A pdb=" N PHE A 66 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE A 26 " --> pdb=" O PHE A 66 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 68 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR A 21 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLU A 95 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU A 23 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 278 through 281 removed outlier: 4.927A pdb=" N LYS A 224 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER A 267 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE A 222 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N THR A 269 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 220 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 359 Processing sheet with id=AA7, first strand: chain 'A' and resid 429 through 434 removed outlier: 6.422A pdb=" N TYR A 394 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL A 466 " --> pdb=" O TYR A 394 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 396 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 507 through 510 Processing sheet with id=AA9, first strand: chain 'A' and resid 583 through 590 removed outlier: 4.330A pdb=" N GLN A 583 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL A 567 " --> pdb=" O ASP A 635 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 630 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL A 669 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 632 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU A 671 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG A 634 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR A 666 " --> pdb=" O GLY A 732 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY A 732 " --> pdb=" O TYR A 666 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 668 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER A 698 " --> pdb=" O PHE A 710 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1032 1.31 - 1.44: 2103 1.44 - 1.56: 3809 1.56 - 1.69: 69 1.69 - 1.81: 28 Bond restraints: 7041 Sorted by residual: bond pdb=" O3' DT B 1 " pdb=" P DG B 2 " ideal model delta sigma weight residual 1.607 1.549 0.058 1.50e-02 4.44e+03 1.47e+01 bond pdb=" CA SER A 499 " pdb=" CB SER A 499 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.58e-02 4.01e+03 1.45e+01 bond pdb=" C LEU A 540 " pdb=" O LEU A 540 " ideal model delta sigma weight residual 1.237 1.192 0.044 1.17e-02 7.31e+03 1.44e+01 bond pdb=" O3' C C 8 " pdb=" P U C 9 " ideal model delta sigma weight residual 1.607 1.554 0.053 1.50e-02 4.44e+03 1.27e+01 bond pdb=" C PRO A 773 " pdb=" O PRO A 773 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.30e-02 5.92e+03 1.21e+01 ... (remaining 7036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 9302 2.12 - 4.24: 341 4.24 - 6.37: 27 6.37 - 8.49: 7 8.49 - 10.61: 1 Bond angle restraints: 9678 Sorted by residual: angle pdb=" C TYR A 270 " pdb=" CA TYR A 270 " pdb=" CB TYR A 270 " ideal model delta sigma weight residual 109.42 120.03 -10.61 1.57e+00 4.06e-01 4.57e+01 angle pdb=" N LEU A 771 " pdb=" CA LEU A 771 " pdb=" C LEU A 771 " ideal model delta sigma weight residual 113.28 107.27 6.01 1.22e+00 6.72e-01 2.43e+01 angle pdb=" C LYS A 494 " pdb=" CA LYS A 494 " pdb=" CB LYS A 494 " ideal model delta sigma weight residual 109.53 117.46 -7.93 1.65e+00 3.67e-01 2.31e+01 angle pdb=" C4' C C 8 " pdb=" C3' C C 8 " pdb=" O3' C C 8 " ideal model delta sigma weight residual 113.00 106.00 7.00 1.50e+00 4.44e-01 2.18e+01 angle pdb=" N1 DT B 18 " pdb=" C2 DT B 18 " pdb=" N3 DT B 18 " ideal model delta sigma weight residual 114.80 121.62 -6.82 1.50e+00 4.44e-01 2.07e+01 ... (remaining 9673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 4016 34.77 - 69.54: 143 69.54 - 104.31: 19 104.31 - 139.08: 0 139.08 - 173.85: 5 Dihedral angle restraints: 4183 sinusoidal: 2003 harmonic: 2180 Sorted by residual: dihedral pdb=" O4' C C 8 " pdb=" C1' C C 8 " pdb=" N1 C C 8 " pdb=" C2 C C 8 " ideal model delta sinusoidal sigma weight residual 200.00 26.15 173.85 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U C 12 " pdb=" C1' U C 12 " pdb=" N1 U C 12 " pdb=" C2 U C 12 " ideal model delta sinusoidal sigma weight residual 200.00 26.74 173.26 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C C 15 " pdb=" C1' C C 15 " pdb=" N1 C C 15 " pdb=" C2 C C 15 " ideal model delta sinusoidal sigma weight residual 200.00 36.20 163.80 1 1.50e+01 4.44e-03 8.36e+01 ... (remaining 4180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 935 0.073 - 0.146: 112 0.146 - 0.218: 23 0.218 - 0.291: 2 0.291 - 0.364: 3 Chirality restraints: 1075 Sorted by residual: chirality pdb=" CB VAL A 495 " pdb=" CA VAL A 495 " pdb=" CG1 VAL A 495 " pdb=" CG2 VAL A 495 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" P DG B 15 " pdb=" OP1 DG B 15 " pdb=" OP2 DG B 15 " pdb=" O5' DG B 15 " both_signs ideal model delta sigma weight residual True 2.35 -2.65 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA TYR A 270 " pdb=" N TYR A 270 " pdb=" C TYR A 270 " pdb=" CB TYR A 270 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 1072 not shown) Planarity restraints: 1104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 39 " -0.016 2.00e-02 2.50e+03 3.10e-02 9.64e+00 pdb=" C ASN A 39 " 0.054 2.00e-02 2.50e+03 pdb=" O ASN A 39 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS A 40 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 490 " -0.043 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO A 491 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 45 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C ILE A 45 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE A 45 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A 46 " 0.012 2.00e-02 2.50e+03 ... (remaining 1101 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 27 2.45 - 3.06: 4340 3.06 - 3.67: 11022 3.67 - 4.29: 17718 4.29 - 4.90: 27416 Nonbonded interactions: 60523 Sorted by model distance: nonbonded pdb=" OD2 ASP A 566 " pdb="CA CA A 801 " model vdw 1.835 2.510 nonbonded pdb=" OP2 DT B 1 " pdb="CA CA B 801 " model vdw 1.985 2.510 nonbonded pdb=" OP1 U C 9 " pdb="CA CA A 801 " model vdw 2.060 2.510 nonbonded pdb=" OP1 DA B 3 " pdb="CA CA B 801 " model vdw 2.061 2.510 nonbonded pdb=" NE2 HIS A 568 " pdb="CA CA A 801 " model vdw 2.152 2.590 ... (remaining 60518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.070 Find NCS groups from input model: 0.030 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 : 0.006 0.060 7041 Z= 0.328 Angle : 0.854 10.610 9678 Z= 0.537 Chirality : 0.056 0.364 1075 Planarity : 0.005 0.066 1104 Dihedral : 18.147 173.854 2779 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.12 % Favored : 96.74 % Rotamer: Outliers : 0.60 % Allowed : 1.06 % Favored : 98.34 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 9.38 % 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: -0.43 (0.30), residues: 737 helix: 0.31 (0.35), residues: 195 sheet: -0.26 (0.41), residues: 153 loop : -0.52 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 295 TYR 0.022 0.002 TYR A 113 PHE 0.016 0.002 PHE A 426 TRP 0.012 0.002 TRP A 131 HIS 0.006 0.002 HIS A 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.33 ( 7041) covalent geometry : angle 0.85391 / 0.54 ( 9678) hydrogen bonds : bond 0.14101 / 8.32 ( 286) hydrogen bonds : angle 7.75279 / 5.43 ( 769) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.266 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 133 average time/residue: 0.6036 time to fit residues: 84.2611 Evaluate side-chains 70 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 386 ASN A 406 ASN A 502 ASN A 746 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.107642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.077058 restraints weight = 11163.336| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.82 r_work: 0.2865 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7041 Z= 0.173 Angle : 0.639 6.328 9678 Z= 0.336 Chirality : 0.044 0.221 1075 Planarity : 0.004 0.038 1104 Dihedral : 19.970 179.142 1281 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 2.57 % Allowed : 12.08 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.09 (0.31), residues: 737 helix: 1.07 (0.35), residues: 198 sheet: -0.22 (0.39), residues: 163 loop : -0.27 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 205 TYR 0.017 0.002 TYR A 268 PHE 0.021 0.001 PHE A 577 TRP 0.009 0.002 TRP A 131 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 7041) covalent geometry : angle 0.63920 / 0.34 ( 9678) hydrogen bonds : bond 0.04320 / 2.89 ( 286) hydrogen bonds : angle 5.74000 / 3.99 ( 769) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.257 Fit side-chains REVERT: A 38 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7966 (tm) REVERT: A 76 MET cc_start: 0.8676 (ppp) cc_final: 0.8408 (ppp) REVERT: A 273 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6738 (mtt-85) outliers start: 17 outliers final: 3 residues processed: 81 average time/residue: 0.5284 time to fit residues: 45.3902 Evaluate side-chains 67 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 711 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 46 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 45 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 290 ASN A 690 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.077810 restraints weight = 11206.289| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.80 r_work: 0.2902 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7041 Z= 0.144 Angle : 0.586 6.829 9678 Z= 0.307 Chirality : 0.042 0.222 1075 Planarity : 0.004 0.033 1104 Dihedral : 19.748 179.827 1280 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.99 % Favored : 96.88 % Rotamer: Outliers : 2.57 % Allowed : 12.99 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.25 (0.31), residues: 737 helix: 1.35 (0.35), residues: 198 sheet: -0.17 (0.39), residues: 161 loop : -0.23 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 522 TYR 0.011 0.001 TYR A 113 PHE 0.020 0.001 PHE A 577 TRP 0.009 0.002 TRP A 214 HIS 0.002 0.001 HIS A 672 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 7041) covalent geometry : angle 0.58611 / 0.31 ( 9678) hydrogen bonds : bond 0.03916 / 2.62 ( 286) hydrogen bonds : angle 5.45969 / 3.79 ( 769) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.264 Fit side-chains REVERT: A 38 LEU cc_start: 0.7974 (tm) cc_final: 0.7738 (tm) REVERT: A 76 MET cc_start: 0.8733 (ppp) cc_final: 0.8408 (ppp) REVERT: A 142 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8626 (mp0) REVERT: A 144 MET cc_start: 0.9058 (mtp) cc_final: 0.8768 (mtt) REVERT: A 690 GLN cc_start: 0.8251 (pt0) cc_final: 0.7934 (pt0) outliers start: 17 outliers final: 6 residues processed: 76 average time/residue: 0.5363 time to fit residues: 43.0720 Evaluate side-chains 66 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 711 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 377 GLN A 406 ASN A 482 HIS A 690 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.074468 restraints weight = 11079.100| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.79 r_work: 0.2753 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7041 Z= 0.188 Angle : 0.587 6.848 9678 Z= 0.305 Chirality : 0.042 0.207 1075 Planarity : 0.004 0.045 1104 Dihedral : 19.541 178.703 1276 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.39 % Favored : 96.47 % Rotamer: Outliers : 2.87 % Allowed : 14.20 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.37 (0.30), residues: 737 helix: 1.52 (0.35), residues: 198 sheet: -0.10 (0.38), residues: 168 loop : -0.21 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 522 TYR 0.014 0.001 TYR A 113 PHE 0.019 0.001 PHE A 577 TRP 0.009 0.002 TRP A 131 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 7041) covalent geometry : angle 0.58729 / 0.31 ( 9678) hydrogen bonds : bond 0.03843 / 2.58 ( 286) hydrogen bonds : angle 5.33801 / 3.68 ( 769) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.249 Fit side-chains REVERT: A 38 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7699 (tm) REVERT: A 142 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8655 (mp0) REVERT: A 144 MET cc_start: 0.9007 (mtp) cc_final: 0.8736 (mtt) REVERT: A 207 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8850 (mp) outliers start: 19 outliers final: 7 residues processed: 67 average time/residue: 0.5931 time to fit residues: 41.9012 Evaluate side-chains 68 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 737 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.104880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.075042 restraints weight = 11140.689| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.80 r_work: 0.2774 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7041 Z= 0.163 Angle : 0.582 8.893 9678 Z= 0.299 Chirality : 0.042 0.216 1075 Planarity : 0.004 0.037 1104 Dihedral : 19.463 178.995 1276 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 2.42 % Allowed : 14.65 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.39 (0.30), residues: 737 helix: 1.61 (0.35), residues: 198 sheet: -0.23 (0.37), residues: 173 loop : -0.16 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 522 TYR 0.014 0.001 TYR A 113 PHE 0.019 0.001 PHE A 577 TRP 0.009 0.002 TRP A 131 HIS 0.002 0.001 HIS A 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 7041) covalent geometry : angle 0.58183 / 0.30 ( 9678) hydrogen bonds : bond 0.03741 / 2.51 ( 286) hydrogen bonds : angle 5.24647 / 3.61 ( 769) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7744 (tm) REVERT: A 77 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 79 ARG cc_start: 0.6664 (mtp85) cc_final: 0.6379 (mmm160) REVERT: A 142 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8674 (mp0) REVERT: A 144 MET cc_start: 0.9023 (mtp) cc_final: 0.8751 (mtt) REVERT: A 690 GLN cc_start: 0.8032 (pt0) cc_final: 0.7356 (pm20) outliers start: 16 outliers final: 6 residues processed: 66 average time/residue: 0.6075 time to fit residues: 42.3034 Evaluate side-chains 63 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 728 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 0.6980 chunk 71 optimal weight: 0.0970 chunk 53 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.075249 restraints weight = 11089.961| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.81 r_work: 0.2787 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7041 Z= 0.154 Angle : 0.578 6.917 9678 Z= 0.298 Chirality : 0.041 0.216 1075 Planarity : 0.004 0.043 1104 Dihedral : 19.356 179.074 1276 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.39 % Favored : 96.47 % Rotamer: Outliers : 2.57 % Allowed : 14.80 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.43 (0.30), residues: 737 helix: 1.65 (0.35), residues: 199 sheet: -0.27 (0.37), residues: 173 loop : -0.10 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 522 TYR 0.013 0.001 TYR A 113 PHE 0.019 0.001 PHE A 577 TRP 0.007 0.001 TRP A 131 HIS 0.002 0.001 HIS A 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 7041) covalent geometry : angle 0.57757 / 0.30 ( 9678) hydrogen bonds : bond 0.03644 / 2.44 ( 286) hydrogen bonds : angle 5.19908 / 3.57 ( 769) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7677 (tm) REVERT: A 77 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 79 ARG cc_start: 0.6697 (mtp85) cc_final: 0.6443 (mmm160) REVERT: A 95 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: A 144 MET cc_start: 0.8997 (mtp) cc_final: 0.8723 (mtt) REVERT: A 207 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8825 (mp) REVERT: A 690 GLN cc_start: 0.7957 (pt0) cc_final: 0.7295 (pm20) outliers start: 17 outliers final: 8 residues processed: 68 average time/residue: 0.5936 time to fit residues: 42.6201 Evaluate side-chains 64 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 728 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 0.0870 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** 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 = 0.3430 r_free = 0.3430 target = 0.104614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.074625 restraints weight = 11021.773| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.79 r_work: 0.2775 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7041 Z= 0.164 Angle : 0.585 9.690 9678 Z= 0.299 Chirality : 0.041 0.214 1075 Planarity : 0.004 0.047 1104 Dihedral : 19.313 179.145 1276 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.53 % Favored : 96.34 % Rotamer: Outliers : 2.57 % Allowed : 15.11 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.42 (0.31), residues: 737 helix: 1.68 (0.35), residues: 199 sheet: -0.37 (0.37), residues: 178 loop : -0.06 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 522 TYR 0.013 0.001 TYR A 113 PHE 0.019 0.001 PHE A 577 TRP 0.010 0.002 TRP A 214 HIS 0.002 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 7041) covalent geometry : angle 0.58477 / 0.30 ( 9678) hydrogen bonds : bond 0.03648 / 2.44 ( 286) hydrogen bonds : angle 5.17916 / 3.55 ( 769) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7704 (tm) REVERT: A 79 ARG cc_start: 0.6753 (mtp85) cc_final: 0.6471 (mmm160) REVERT: A 95 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: A 144 MET cc_start: 0.9003 (mtp) cc_final: 0.8739 (mtt) REVERT: A 207 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8856 (mp) REVERT: A 690 GLN cc_start: 0.7961 (pt0) cc_final: 0.7344 (pm20) outliers start: 17 outliers final: 9 residues processed: 68 average time/residue: 0.6051 time to fit residues: 43.4801 Evaluate side-chains 69 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 728 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 30 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.0470 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** A 300 HIS ** 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 = 0.3425 r_free = 0.3425 target = 0.104347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.074447 restraints weight = 11026.086| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.78 r_work: 0.2771 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7041 Z= 0.165 Angle : 0.585 7.907 9678 Z= 0.300 Chirality : 0.041 0.213 1075 Planarity : 0.004 0.051 1104 Dihedral : 19.281 179.274 1276 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.53 % Favored : 96.34 % Rotamer: Outliers : 2.42 % Allowed : 15.11 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.47 (0.31), residues: 737 helix: 1.75 (0.35), residues: 199 sheet: -0.40 (0.37), residues: 178 loop : -0.02 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 522 TYR 0.012 0.001 TYR A 113 PHE 0.019 0.001 PHE A 577 TRP 0.009 0.001 TRP A 214 HIS 0.002 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 ( 7041) covalent geometry : angle 0.58501 / 0.30 ( 9678) hydrogen bonds : bond 0.03615 / 2.42 ( 286) hydrogen bonds : angle 5.16148 / 3.53 ( 769) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7727 (tm) REVERT: A 79 ARG cc_start: 0.6759 (mtp85) cc_final: 0.6489 (mmm160) REVERT: A 95 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: A 144 MET cc_start: 0.8966 (mtp) cc_final: 0.8721 (mtt) REVERT: A 207 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8878 (mp) REVERT: A 690 GLN cc_start: 0.7965 (pt0) cc_final: 0.7293 (pm20) outliers start: 16 outliers final: 9 residues processed: 71 average time/residue: 0.5691 time to fit residues: 42.5493 Evaluate side-chains 73 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 728 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 0.0170 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** 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 = 0.3428 r_free = 0.3428 target = 0.104531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.074728 restraints weight = 11042.375| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.78 r_work: 0.2774 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7041 Z= 0.157 Angle : 0.603 11.773 9678 Z= 0.305 Chirality : 0.041 0.211 1075 Planarity : 0.004 0.058 1104 Dihedral : 19.254 179.389 1276 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.39 % Favored : 96.47 % Rotamer: Outliers : 2.27 % Allowed : 15.11 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.48 (0.31), residues: 737 helix: 1.74 (0.35), residues: 199 sheet: -0.41 (0.37), residues: 178 loop : -0.00 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 522 TYR 0.014 0.001 TYR A 113 PHE 0.018 0.001 PHE A 577 TRP 0.008 0.001 TRP A 131 HIS 0.002 0.000 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 7041) covalent geometry : angle 0.60311 / 0.31 ( 9678) hydrogen bonds : bond 0.03581 / 2.39 ( 286) hydrogen bonds : angle 5.11615 / 3.51 ( 769) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7766 (tm) REVERT: A 95 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: A 144 MET cc_start: 0.8955 (mtp) cc_final: 0.8708 (mtt) REVERT: A 207 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8845 (mp) REVERT: A 690 GLN cc_start: 0.7972 (pt0) cc_final: 0.7340 (pm20) outliers start: 15 outliers final: 9 residues processed: 69 average time/residue: 0.5471 time to fit residues: 39.9303 Evaluate side-chains 71 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 728 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 2 optimal weight: 0.0010 chunk 62 optimal weight: 0.9980 chunk 52 optimal weight: 0.0870 overall best weight: 0.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** A 300 HIS ** 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 = 0.3451 r_free = 0.3451 target = 0.105917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.076052 restraints weight = 11028.575| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.81 r_work: 0.2805 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7041 Z= 0.134 Angle : 0.602 12.280 9678 Z= 0.302 Chirality : 0.041 0.211 1075 Planarity : 0.004 0.058 1104 Dihedral : 19.201 179.497 1276 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.66 % Favored : 96.07 % Rotamer: Outliers : 1.51 % Allowed : 16.16 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.49 (0.31), residues: 737 helix: 1.76 (0.35), residues: 199 sheet: -0.41 (0.38), residues: 173 loop : 0.00 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 522 TYR 0.012 0.001 TYR A 113 PHE 0.018 0.001 PHE A 577 TRP 0.010 0.001 TRP A 214 HIS 0.002 0.000 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 7041) covalent geometry : angle 0.60170 / 0.30 ( 9678) hydrogen bonds : bond 0.03508 / 2.33 ( 286) hydrogen bonds : angle 5.06198 / 3.47 ( 769) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7742 (tm) REVERT: A 97 TYR cc_start: 0.8098 (m-80) cc_final: 0.7892 (m-80) REVERT: A 144 MET cc_start: 0.8937 (mtp) cc_final: 0.8694 (mtt) REVERT: A 690 GLN cc_start: 0.7936 (pt0) cc_final: 0.7318 (pm20) outliers start: 10 outliers final: 9 residues processed: 67 average time/residue: 0.5647 time to fit residues: 40.0608 Evaluate side-chains 70 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 52 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** 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 = 0.3441 r_free = 0.3441 target = 0.105239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.075251 restraints weight = 11028.302| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.81 r_work: 0.2788 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7041 Z= 0.151 Angle : 0.600 11.854 9678 Z= 0.302 Chirality : 0.041 0.196 1075 Planarity : 0.004 0.058 1104 Dihedral : 19.185 179.423 1276 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.66 % Favored : 96.07 % Rotamer: Outliers : 1.81 % Allowed : 15.86 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.53 (0.31), residues: 737 helix: 1.78 (0.35), residues: 199 sheet: -0.33 (0.38), residues: 178 loop : 0.00 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 522 TYR 0.012 0.001 TYR A 113 PHE 0.018 0.001 PHE A 577 TRP 0.010 0.001 TRP A 214 HIS 0.002 0.000 HIS A 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 7041) covalent geometry : angle 0.59989 / 0.30 ( 9678) hydrogen bonds : bond 0.03516 / 2.34 ( 286) hydrogen bonds : angle 5.04630 / 3.46 ( 769) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.04 seconds wall clock time: 42 minutes 27.62 seconds (2547.62 seconds total)