Starting phenix.real_space_refine on Thu Jul 2 05:48:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmh_66091/07_2026/9wmh_66091.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmh_66091/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9wmh_66091/07_2026/9wmh_66091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmh_66091/07_2026/9wmh_66091.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wmh_66091/07_2026/9wmh_66091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmh_66091/07_2026/9wmh_66091.map" } 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-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 1.35, per 1000 atoms: 0.20 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: 0.55 Conformation dependent library (CDL) restraints added in 282.7 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: 0.72 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: 0.95 Time building geometry restraints manager: 0.69 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=" C5 DT B 18 " pdb=" C6 DT B 18 " ideal model delta sigma weight residual 1.339 1.386 -0.047 7.00e-03 2.04e+04 4.59e+01 bond pdb=" N3 DT B 18 " pdb=" C4 DT B 18 " ideal model delta sigma weight residual 1.382 1.334 0.048 8.00e-03 1.56e+04 3.53e+01 bond pdb=" N1 DT B 18 " pdb=" C6 DT B 18 " ideal model delta sigma weight residual 1.378 1.340 0.038 7.00e-03 2.04e+04 2.94e+01 bond pdb=" C2 DT B 18 " pdb=" N3 DT B 18 " ideal model delta sigma weight residual 1.373 1.333 0.040 8.00e-03 1.56e+04 2.48e+01 bond pdb=" N1 DT B 18 " pdb=" C2 DT B 18 " ideal model delta sigma weight residual 1.376 1.410 -0.034 8.00e-03 1.56e+04 1.81e+01 ... (remaining 7036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 9286 2.12 - 4.24: 357 4.24 - 6.37: 27 6.37 - 8.49: 7 8.49 - 10.61: 1 Bond angle restraints: 9678 Sorted by residual: angle pdb=" N1 DT B 18 " pdb=" C2 DT B 18 " pdb=" N3 DT B 18 " ideal model delta sigma weight residual 114.60 121.62 -7.02 6.00e-01 2.78e+00 1.37e+02 angle pdb=" C2 DT B 18 " pdb=" N3 DT B 18 " pdb=" C4 DT B 18 " ideal model delta sigma weight residual 127.20 120.98 6.22 6.00e-01 2.78e+00 1.08e+02 angle pdb=" O4 DT B 18 " pdb=" C4 DT B 18 " pdb=" C5 DT B 18 " ideal model delta sigma weight residual 124.90 119.93 4.97 7.00e-01 2.04e+00 5.04e+01 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=" N1 DT B 18 " pdb=" C6 DT B 18 " pdb=" C5 DT B 18 " ideal model delta sigma weight residual 123.70 119.67 4.03 6.00e-01 2.78e+00 4.50e+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: 926 0.073 - 0.146: 118 0.146 - 0.218: 26 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 2.34 -2.65 -0.31 2.00e-01 2.50e+01 2.47e+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 3.250 nonbonded pdb=" OP2 DT B 1 " pdb="CA CA B 801 " model vdw 1.985 3.250 nonbonded pdb=" OP1 U C 9 " pdb="CA CA A 801 " model vdw 2.060 3.250 nonbonded pdb=" OP1 DA B 3 " pdb="CA CA B 801 " model vdw 2.061 3.250 nonbonded pdb=" NE2 HIS A 568 " pdb="CA CA A 801 " model vdw 2.152 3.330 ... (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: 2.620 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.050 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:5.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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= 0.395 Angle : 0.863 10.610 9678 Z= 0.615 Chirality : 0.057 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 0.00559 / 0.40 ( 7041) covalent geometry : angle 0.86264 / 0.62 ( 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 : 0.166 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 133 average time/residue: 0.5022 time to fit residues: 70.3008 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 : 0.175 ------------------------------------------------------------------------------- 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: 0.7980 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: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 386 ASN A 406 ASN A 502 ASN A 674 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.107227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.076500 restraints weight = 10883.935| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.84 r_work: 0.2789 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7041 Z= 0.179 Angle : 0.644 7.117 9678 Z= 0.358 Chirality : 0.047 0.277 1075 Planarity : 0.005 0.059 1104 Dihedral : 20.159 176.458 1281 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.53 % Favored : 96.34 % Rotamer: Outliers : 2.57 % Allowed : 11.33 % Favored : 86.10 % 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: -0.05 (0.30), residues: 737 helix: 1.00 (0.35), residues: 198 sheet: -0.43 (0.38), residues: 168 loop : -0.31 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 205 TYR 0.018 0.002 TYR A 562 PHE 0.024 0.002 PHE A 577 TRP 0.010 0.002 TRP A 131 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 ( 7041) covalent geometry : angle 0.64395 / 0.36 ( 9678) hydrogen bonds : bond 0.04602 / 3.09 ( 286) hydrogen bonds : angle 5.90119 / 4.10 ( 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 91 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.169 Fit side-chains REVERT: A 38 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7954 (tm) REVERT: A 76 MET cc_start: 0.8676 (ppp) cc_final: 0.8300 (ppp) REVERT: A 142 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8566 (mp0) REVERT: A 706 GLU cc_start: 0.8390 (tt0) cc_final: 0.8157 (tt0) outliers start: 17 outliers final: 4 residues processed: 84 average time/residue: 0.4340 time to fit residues: 38.8451 Evaluate side-chains 69 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 216 THR Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 452 VAL 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: 1.9990 chunk 61 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 690 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.076427 restraints weight = 11148.083| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.79 r_work: 0.2867 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2077 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= 0.167 Angle : 0.586 6.503 9678 Z= 0.328 Chirality : 0.045 0.273 1075 Planarity : 0.005 0.084 1104 Dihedral : 19.879 175.522 1276 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.53 % Favored : 96.34 % Rotamer: Outliers : 1.81 % Allowed : 13.60 % Favored : 84.59 % 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: 0.12 (0.30), residues: 737 helix: 1.23 (0.34), residues: 198 sheet: -0.34 (0.39), residues: 163 loop : -0.26 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 273 TYR 0.013 0.001 TYR A 268 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 0.00353 / 0.17 ( 7041) covalent geometry : angle 0.58596 / 0.33 ( 9678) hydrogen bonds : bond 0.04253 / 2.86 ( 286) hydrogen bonds : angle 5.61907 / 3.91 ( 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 82 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7995 (tm) cc_final: 0.7763 (tm) REVERT: A 76 MET cc_start: 0.8728 (ppp) cc_final: 0.8277 (ppp) REVERT: A 273 ARG cc_start: 0.7618 (mtt-85) cc_final: 0.7323 (mtt-85) REVERT: A 290 ASN cc_start: 0.7850 (m110) cc_final: 0.7641 (m-40) outliers start: 12 outliers final: 6 residues processed: 76 average time/residue: 0.5490 time to fit residues: 44.2954 Evaluate side-chains 69 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 275 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN A 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.104838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.074785 restraints weight = 11039.819| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.79 r_work: 0.2764 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7041 Z= 0.170 Angle : 0.561 6.556 9678 Z= 0.314 Chirality : 0.044 0.273 1075 Planarity : 0.004 0.053 1104 Dihedral : 19.728 175.548 1276 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.66 % Favored : 96.20 % Rotamer: Outliers : 2.72 % Allowed : 13.75 % Favored : 83.53 % 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: 0.24 (0.30), residues: 737 helix: 1.43 (0.34), residues: 198 sheet: -0.37 (0.38), residues: 163 loop : -0.19 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 273 TYR 0.009 0.001 TYR A 113 PHE 0.019 0.001 PHE A 577 TRP 0.008 0.002 TRP A 131 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 ( 7041) covalent geometry : angle 0.56055 / 0.31 ( 9678) hydrogen bonds : bond 0.04006 / 2.69 ( 286) hydrogen bonds : angle 5.48425 / 3.80 ( 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 82 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7734 (tm) REVERT: A 77 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7838 (tm-30) REVERT: A 79 ARG cc_start: 0.6641 (mtp85) cc_final: 0.6439 (mmm160) REVERT: A 95 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: A 142 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8634 (mp0) REVERT: A 266 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7540 (ppp) REVERT: A 290 ASN cc_start: 0.7822 (m110) cc_final: 0.7597 (m110) REVERT: A 469 ASP cc_start: 0.8357 (t0) cc_final: 0.7978 (t0) outliers start: 18 outliers final: 6 residues processed: 72 average time/residue: 0.5589 time to fit residues: 42.6738 Evaluate side-chains 66 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 275 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.074436 restraints weight = 11187.212| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.82 r_work: 0.2760 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7041 Z= 0.162 Angle : 0.554 8.849 9678 Z= 0.307 Chirality : 0.043 0.274 1075 Planarity : 0.004 0.049 1104 Dihedral : 19.684 175.101 1276 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.39 % Favored : 96.47 % Rotamer: Outliers : 2.72 % Allowed : 14.20 % Favored : 83.08 % 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: 0.30 (0.30), residues: 737 helix: 1.49 (0.34), residues: 198 sheet: -0.31 (0.37), residues: 175 loop : -0.17 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 522 TYR 0.009 0.001 TYR A 113 PHE 0.019 0.001 PHE A 577 TRP 0.008 0.002 TRP A 214 HIS 0.002 0.001 HIS A 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 7041) covalent geometry : angle 0.55439 / 0.31 ( 9678) hydrogen bonds : bond 0.03938 / 2.65 ( 286) hydrogen bonds : angle 5.36928 / 3.71 ( 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 77 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7653 (tm) REVERT: A 79 ARG cc_start: 0.6599 (mtp85) cc_final: 0.6385 (mmm160) REVERT: A 142 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8645 (mp0) REVERT: A 144 MET cc_start: 0.9099 (mtp) cc_final: 0.8793 (mtt) REVERT: A 287 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7295 (tpt) REVERT: A 690 GLN cc_start: 0.8162 (pt0) cc_final: 0.7370 (pm20) outliers start: 18 outliers final: 8 residues processed: 69 average time/residue: 0.4375 time to fit residues: 32.0095 Evaluate side-chains 66 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 142 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 495 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 52 optimal weight: 0.0060 chunk 1 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 GLN A 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.076080 restraints weight = 11303.782| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.79 r_work: 0.2870 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7041 Z= 0.141 Angle : 0.539 6.907 9678 Z= 0.300 Chirality : 0.043 0.278 1075 Planarity : 0.004 0.050 1104 Dihedral : 19.612 174.742 1276 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 2.57 % Allowed : 13.75 % Favored : 83.69 % 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: 0.38 (0.30), residues: 737 helix: 1.61 (0.35), residues: 198 sheet: -0.26 (0.37), residues: 173 loop : -0.15 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 522 TYR 0.018 0.001 TYR A 113 PHE 0.019 0.001 PHE A 577 TRP 0.007 0.001 TRP A 131 HIS 0.002 0.000 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 7041) covalent geometry : angle 0.53854 / 0.30 ( 9678) hydrogen bonds : bond 0.03826 / 2.58 ( 286) hydrogen bonds : angle 5.27351 / 3.63 ( 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 75 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: A 38 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7718 (tm) REVERT: A 95 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8013 (tm-30) REVERT: A 142 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8647 (mp0) REVERT: A 690 GLN cc_start: 0.8158 (pt0) cc_final: 0.7403 (pm20) outliers start: 17 outliers final: 8 residues processed: 66 average time/residue: 0.5797 time to fit residues: 40.3622 Evaluate side-chains 68 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU 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 142 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 275 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 56 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 482 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.106787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.076325 restraints weight = 11156.429| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.84 r_work: 0.2847 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7041 Z= 0.150 Angle : 0.546 7.931 9678 Z= 0.302 Chirality : 0.043 0.275 1075 Planarity : 0.004 0.056 1104 Dihedral : 19.547 175.227 1276 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 2.42 % Allowed : 13.90 % Favored : 83.69 % 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: 0.38 (0.30), residues: 737 helix: 1.65 (0.34), residues: 198 sheet: -0.37 (0.36), residues: 178 loop : -0.11 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 522 TYR 0.013 0.001 TYR A 113 PHE 0.018 0.001 PHE A 577 TRP 0.012 0.002 TRP A 214 HIS 0.002 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 7041) covalent geometry : angle 0.54631 / 0.30 ( 9678) hydrogen bonds : bond 0.03794 / 2.57 ( 286) hydrogen bonds : angle 5.23871 / 3.60 ( 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: 16 poor density : 59 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7715 (tm) REVERT: A 144 MET cc_start: 0.9100 (mtp) cc_final: 0.8801 (mtt) REVERT: A 690 GLN cc_start: 0.8144 (pt0) cc_final: 0.7391 (pm20) outliers start: 16 outliers final: 8 residues processed: 65 average time/residue: 0.5863 time to fit residues: 40.3066 Evaluate side-chains 64 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 194 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 674 GLN Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.0470 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.105469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.075974 restraints weight = 11271.341| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.76 r_work: 0.2858 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2886 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 : 0.555 10.701 9678 Z= 0.304 Chirality : 0.043 0.274 1075 Planarity : 0.004 0.056 1104 Dihedral : 19.502 175.609 1276 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 2.57 % Allowed : 14.20 % Favored : 83.23 % 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: 0.40 (0.31), residues: 737 helix: 1.70 (0.35), residues: 199 sheet: -0.40 (0.36), residues: 178 loop : -0.10 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 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 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 7041) covalent geometry : angle 0.55509 / 0.30 ( 9678) hydrogen bonds : bond 0.03783 / 2.56 ( 286) hydrogen bonds : angle 5.21314 / 3.58 ( 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 72 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: A 38 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7705 (tm) REVERT: A 95 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: A 144 MET cc_start: 0.9090 (mtp) cc_final: 0.8795 (mtt) REVERT: A 690 GLN cc_start: 0.8139 (pt0) cc_final: 0.7418 (pm20) outliers start: 17 outliers final: 9 residues processed: 64 average time/residue: 0.5530 time to fit residues: 37.6327 Evaluate side-chains 64 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU 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 216 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 674 GLN Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 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: 0.8980 chunk 54 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 58 optimal weight: 0.0040 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.106074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.076396 restraints weight = 11281.364| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.78 r_work: 0.2885 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7041 Z= 0.140 Angle : 0.555 11.708 9678 Z= 0.302 Chirality : 0.042 0.277 1075 Planarity : 0.004 0.061 1104 Dihedral : 19.455 175.910 1276 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.39 % Favored : 96.47 % Rotamer: Outliers : 2.27 % Allowed : 14.35 % Favored : 83.38 % 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: 0.40 (0.31), residues: 737 helix: 1.71 (0.35), residues: 199 sheet: -0.43 (0.38), residues: 173 loop : -0.09 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 522 TYR 0.015 0.001 TYR A 113 PHE 0.018 0.001 PHE A 577 TRP 0.012 0.002 TRP A 214 HIS 0.002 0.001 HIS A 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 7041) covalent geometry : angle 0.55459 / 0.30 ( 9678) hydrogen bonds : bond 0.03731 / 2.52 ( 286) hydrogen bonds : angle 5.17481 / 3.54 ( 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 70 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: A 38 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7697 (tm) REVERT: A 95 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8043 (tm-30) REVERT: A 690 GLN cc_start: 0.8148 (pt0) cc_final: 0.7406 (pm20) outliers start: 15 outliers final: 10 residues processed: 65 average time/residue: 0.5774 time to fit residues: 39.7293 Evaluate side-chains 66 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU 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 216 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 56 optimal weight: 0.0030 chunk 2 optimal weight: 0.0070 chunk 62 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 overall best weight: 0.3208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.106390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.076784 restraints weight = 11286.425| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.79 r_work: 0.2877 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7041 Z= 0.127 Angle : 0.560 11.423 9678 Z= 0.303 Chirality : 0.042 0.281 1075 Planarity : 0.004 0.062 1104 Dihedral : 19.405 176.422 1276 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.53 % Favored : 96.34 % Rotamer: Outliers : 1.96 % Allowed : 14.50 % Favored : 83.53 % 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: 0.44 (0.31), residues: 737 helix: 1.77 (0.35), residues: 198 sheet: -0.41 (0.38), residues: 173 loop : -0.07 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 522 TYR 0.015 0.001 TYR A 113 PHE 0.018 0.001 PHE A 577 TRP 0.005 0.001 TRP A 214 HIS 0.001 0.000 HIS A 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 7041) covalent geometry : angle 0.55956 / 0.30 ( 9678) hydrogen bonds : bond 0.03660 / 2.46 ( 286) hydrogen bonds : angle 5.14448 / 3.52 ( 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 73 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: A 38 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7723 (tm) REVERT: A 95 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: A 690 GLN cc_start: 0.8125 (pt0) cc_final: 0.7395 (pm20) outliers start: 13 outliers final: 6 residues processed: 68 average time/residue: 0.5637 time to fit residues: 40.7345 Evaluate side-chains 64 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU 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 216 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 729 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 22 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3443 r_free = 0.3443 target = 0.104611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.074564 restraints weight = 11377.961| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.83 r_work: 0.2841 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7041 Z= 0.192 Angle : 0.584 11.383 9678 Z= 0.315 Chirality : 0.043 0.268 1075 Planarity : 0.004 0.062 1104 Dihedral : 19.405 176.545 1276 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.26 % Favored : 96.47 % Rotamer: Outliers : 2.27 % Allowed : 14.80 % 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: 0.49 (0.31), residues: 737 helix: 1.73 (0.35), residues: 199 sheet: -0.31 (0.38), residues: 178 loop : -0.03 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 522 TYR 0.015 0.001 TYR A 113 PHE 0.018 0.001 PHE A 577 TRP 0.006 0.001 TRP A 131 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 ( 7041) covalent geometry : angle 0.58422 / 0.32 ( 9678) hydrogen bonds : bond 0.03772 / 2.54 ( 286) hydrogen bonds : angle 5.15145 / 3.53 ( 769) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2376.89 seconds wall clock time: 41 minutes 24.73 seconds (2484.73 seconds total)