Starting phenix.real_space_refine on Tue Aug 4 19:46:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymd_73103/08_2026/9ymd_73103.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymd_73103/08_2026/9ymd_73103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ymd_73103/08_2026/9ymd_73103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymd_73103/08_2026/9ymd_73103.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ymd_73103/08_2026/9ymd_73103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymd_73103/08_2026/9ymd_73103.map" } resolution = 3.45 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= 0.007 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: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 40 5.16 5 C 3964 2.51 5 N 1134 2.21 5 O 1150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6299 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 6061 Classifications: {'peptide': 758} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 44, 'TRANS': 709} Chain breaks: 6 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 238 Classifications: {'RNA': 11} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain breaks: 1 Time building chain proxies: 1.54, per 1000 atoms: 0.24 Number of scatterers: 6299 At special positions: 0 Unit cell: (74.315, 82.665, 106.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 11 15.00 O 1150 8.00 N 1134 7.00 C 3964 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: 0.42 Conformation dependent library (CDL) restraints added in 245.9 milliseconds 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 35.2% alpha, 22.0% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 67 through 82 removed outlier: 3.851A pdb=" N GLN A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 148 removed outlier: 3.559A pdb=" N LEU A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 174 removed outlier: 5.045A pdb=" N LEU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 229 through 238 Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.770A pdb=" N GLU A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 391 through 397 removed outlier: 3.629A pdb=" N PHE A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 526 through 539 removed outlier: 4.381A pdb=" N ALA A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.699A pdb=" N VAL A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.725A pdb=" N GLN A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 658 removed outlier: 3.532A pdb=" N MET A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 695 removed outlier: 3.879A pdb=" N LEU A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 787 Processing helix chain 'A' and resid 800 through 816 removed outlier: 3.504A pdb=" N TYR A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 846 removed outlier: 3.917A pdb=" N VAL A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 625 through 632 removed outlier: 3.636A pdb=" N ARG A 630 " --> pdb=" O ALA A 612 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 611 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER A 617 " --> pdb=" O PHE A 593 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 592 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N TYR A 667 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU A 594 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ASP A 669 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA A 596 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE A 702 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP A 770 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE A 704 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 734 " --> pdb=" O CYS A 751 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 177 removed outlier: 6.070A pdb=" N ARG A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 4.634A pdb=" N MET A 213 " --> pdb=" O MET A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.520A pdb=" N SER A 136 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLU A 58 " --> pdb=" O TRP A 134 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TRP A 134 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASP A 60 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE A 132 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LYS A 62 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL A 130 " --> pdb=" O LYS A 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA6, first strand: chain 'A' and resid 281 through 284 removed outlier: 6.718A pdb=" N GLN A 329 " --> pdb=" O CYS A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 428 Processing sheet with id=AA8, first strand: chain 'A' and resid 492 through 494 removed outlier: 6.590A pdb=" N ALA A 452 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ILE A 521 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA A 454 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL A 518 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL A 547 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 520 " --> pdb=" O VAL A 547 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1929 1.34 - 1.45: 964 1.45 - 1.57: 3493 1.57 - 1.69: 20 1.69 - 1.81: 59 Bond restraints: 6465 Sorted by residual: bond pdb=" C GLU A 186 " pdb=" N GLY A 187 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 7.27e-01 bond pdb=" N7 A B 4 " pdb=" C5 A B 4 " ideal model delta sigma weight residual 1.388 1.383 0.005 6.00e-03 2.78e+04 6.50e-01 bond pdb=" CA GLN A 228 " pdb=" CB GLN A 228 " ideal model delta sigma weight residual 1.538 1.527 0.011 1.40e-02 5.10e+03 6.07e-01 bond pdb=" N3 A B 4 " pdb=" C4 A B 4 " ideal model delta sigma weight residual 1.344 1.339 0.005 6.00e-03 2.78e+04 5.82e-01 bond pdb=" CA ASN A 43 " pdb=" CB ASN A 43 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.21e-02 6.83e+03 5.69e-01 ... (remaining 6460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 8666 2.04 - 4.09: 121 4.09 - 6.13: 8 6.13 - 8.18: 0 8.18 - 10.22: 1 Bond angle restraints: 8796 Sorted by residual: angle pdb=" O4' U B 21 " pdb=" C1' U B 21 " pdb=" N1 U B 21 " ideal model delta sigma weight residual 108.50 112.92 -4.42 7.00e-01 2.04e+00 3.99e+01 angle pdb=" O5' U B 21 " pdb=" C5' U B 21 " pdb=" C4' U B 21 " ideal model delta sigma weight residual 109.40 112.84 -3.44 8.00e-01 1.56e+00 1.84e+01 angle pdb=" N GLN A 228 " pdb=" CA GLN A 228 " pdb=" C GLN A 228 " ideal model delta sigma weight residual 108.13 111.60 -3.47 9.00e-01 1.23e+00 1.48e+01 angle pdb=" OP1 U B 21 " pdb=" P U B 21 " pdb=" OP2 U B 21 " ideal model delta sigma weight residual 119.60 109.38 10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" O5' G B 23 " pdb=" C5' G B 23 " pdb=" C4' G B 23 " ideal model delta sigma weight residual 109.40 112.12 -2.72 8.00e-01 1.56e+00 1.16e+01 ... (remaining 8791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.52: 3676 18.52 - 37.04: 183 37.04 - 55.56: 44 55.56 - 74.08: 22 74.08 - 92.60: 3 Dihedral angle restraints: 3928 sinusoidal: 1725 harmonic: 2203 Sorted by residual: dihedral pdb=" O4' U B 21 " pdb=" C1' U B 21 " pdb=" N1 U B 21 " pdb=" C2 U B 21 " ideal model delta sinusoidal sigma weight residual -160.00 -115.42 -44.58 1 1.50e+01 4.44e-03 1.23e+01 dihedral pdb=" CA ILE A 86 " pdb=" C ILE A 86 " pdb=" N PHE A 87 " pdb=" CA PHE A 87 " ideal model delta harmonic sigma weight residual -180.00 -164.13 -15.87 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CB LYS A 607 " pdb=" CG LYS A 607 " pdb=" CD LYS A 607 " pdb=" CE LYS A 607 " ideal model delta sinusoidal sigma weight residual 60.00 119.22 -59.22 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 792 0.051 - 0.103: 151 0.103 - 0.154: 39 0.154 - 0.205: 1 0.205 - 0.257: 2 Chirality restraints: 985 Sorted by residual: chirality pdb=" C1' U B 21 " pdb=" O4' U B 21 " pdb=" C2' U B 21 " pdb=" N1 U B 21 " both_signs ideal model delta sigma weight residual False 2.47 2.21 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" P U B 21 " pdb=" OP1 U B 21 " pdb=" OP2 U B 21 " pdb=" O5' U B 21 " both_signs ideal model delta sigma weight residual True 2.41 -2.66 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C3' U B 21 " pdb=" C4' U B 21 " pdb=" O3' U B 21 " pdb=" C2' U B 21 " both_signs ideal model delta sigma weight residual False -2.48 -2.63 0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 982 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 175 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.70e+00 pdb=" N PRO A 176 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 4 " -0.021 2.00e-02 2.50e+03 9.20e-03 2.33e+00 pdb=" N9 A B 4 " 0.021 2.00e-02 2.50e+03 pdb=" C8 A B 4 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A B 4 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 4 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A B 4 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B 4 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A B 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 4 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B 4 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 106 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO A 107 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " 0.020 5.00e-02 4.00e+02 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 209 2.71 - 3.26: 6281 3.26 - 3.81: 9910 3.81 - 4.35: 12251 4.35 - 4.90: 20786 Nonbonded interactions: 49437 Sorted by model distance: nonbonded pdb=" O HIS A 168 " pdb=" OG SER A 171 " model vdw 2.166 3.040 nonbonded pdb=" OG SER A 727 " pdb=" OD1 ASN A 729 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR A 357 " pdb=" OD1 ASN A 359 " model vdw 2.235 3.040 nonbonded pdb=" NH1 ARG A 668 " pdb=" O ASP A 669 " model vdw 2.310 3.120 nonbonded pdb=" NH2 ARG A 792 " pdb=" OP1 A B 3 " model vdw 2.318 3.120 ... (remaining 49432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.400 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6465 Z= 0.131 Angle : 0.557 10.222 8796 Z= 0.326 Chirality : 0.045 0.257 985 Planarity : 0.005 0.041 1092 Dihedral : 12.875 92.604 2500 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.80 % Allowed : 5.84 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.28 % 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 (0.31), residues: 744 helix: 0.76 (0.35), residues: 239 sheet: -0.59 (0.37), residues: 192 loop : -0.69 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.006 0.001 TYR A 55 PHE 0.009 0.001 PHE A 774 TRP 0.005 0.001 TRP A 211 HIS 0.006 0.001 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 6465) covalent geometry : angle 0.55717 / 0.33 ( 8796) hydrogen bonds : bond 0.21002 / 13.60 ( 253) hydrogen bonds : angle 8.27992 / 6.29 ( 726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 82 PHE cc_start: 0.7019 (m-10) cc_final: 0.6335 (m-10) REVERT: A 549 MET cc_start: 0.7548 (ttm) cc_final: 0.7182 (tpt) REVERT: A 623 ASN cc_start: 0.8200 (t0) cc_final: 0.7980 (t0) REVERT: A 804 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7173 (m-80) outliers start: 12 outliers final: 5 residues processed: 103 average time/residue: 0.0594 time to fit residues: 8.3241 Evaluate side-chains 82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 848 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN A 764 HIS A 772 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.189444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.152930 restraints weight = 10759.396| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 3.44 r_work: 0.3940 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6465 Z= 0.178 Angle : 0.616 8.172 8796 Z= 0.323 Chirality : 0.046 0.190 985 Planarity : 0.006 0.066 1092 Dihedral : 11.492 80.118 997 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.54 % Allowed : 9.43 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.28 % 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: -0.45 (0.31), residues: 744 helix: 0.77 (0.34), residues: 251 sheet: -0.86 (0.36), residues: 189 loop : -0.69 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 167 TYR 0.009 0.002 TYR A 815 PHE 0.011 0.002 PHE A 82 TRP 0.008 0.002 TRP A 211 HIS 0.009 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 ( 6465) covalent geometry : angle 0.61577 / 0.32 ( 8796) hydrogen bonds : bond 0.05398 / 3.51 ( 253) hydrogen bonds : angle 6.52975 / 5.00 ( 726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 538 THR cc_start: 0.7773 (p) cc_final: 0.7485 (p) REVERT: A 549 MET cc_start: 0.7320 (ttm) cc_final: 0.7080 (tpt) outliers start: 17 outliers final: 13 residues processed: 91 average time/residue: 0.0534 time to fit residues: 6.7203 Evaluate side-chains 87 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 848 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 chunk 75 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.190831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.155995 restraints weight = 10859.469| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 3.47 r_work: 0.3931 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6465 Z= 0.151 Angle : 0.579 7.734 8796 Z= 0.303 Chirality : 0.045 0.190 985 Planarity : 0.005 0.076 1092 Dihedral : 11.406 77.968 994 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.14 % Allowed : 10.03 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.28 % 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: -0.54 (0.31), residues: 744 helix: 0.78 (0.34), residues: 255 sheet: -0.82 (0.36), residues: 190 loop : -0.92 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.010 0.001 TYR A 815 PHE 0.016 0.002 PHE A 233 TRP 0.008 0.001 TRP A 211 HIS 0.005 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 6465) covalent geometry : angle 0.57869 / 0.30 ( 8796) hydrogen bonds : bond 0.04624 / 3.06 ( 253) hydrogen bonds : angle 6.02112 / 4.60 ( 726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 396 GLU cc_start: 0.5689 (OUTLIER) cc_final: 0.5475 (tt0) REVERT: A 483 MET cc_start: 0.7429 (ppp) cc_final: 0.7178 (ppp) REVERT: A 538 THR cc_start: 0.7800 (p) cc_final: 0.7520 (p) REVERT: A 804 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7491 (m-80) outliers start: 21 outliers final: 14 residues processed: 94 average time/residue: 0.0527 time to fit residues: 6.9319 Evaluate side-chains 89 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 848 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.0470 chunk 3 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN A 623 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.188984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.151093 restraints weight = 10596.774| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 3.85 r_work: 0.3919 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6465 Z= 0.138 Angle : 0.570 8.075 8796 Z= 0.296 Chirality : 0.045 0.198 985 Planarity : 0.005 0.069 1092 Dihedral : 11.398 77.375 994 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.14 % Allowed : 10.78 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.28 % 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: 744 helix: 0.84 (0.34), residues: 249 sheet: -0.80 (0.37), residues: 184 loop : -0.94 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.008 0.001 TYR A 815 PHE 0.013 0.001 PHE A 233 TRP 0.007 0.001 TRP A 211 HIS 0.004 0.001 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6465) covalent geometry : angle 0.57027 / 0.30 ( 8796) hydrogen bonds : bond 0.04197 / 2.77 ( 253) hydrogen bonds : angle 5.81022 / 4.45 ( 726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 82 PHE cc_start: 0.9137 (m-10) cc_final: 0.8869 (m-10) REVERT: A 538 THR cc_start: 0.7792 (p) cc_final: 0.7528 (p) REVERT: A 804 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7555 (m-80) outliers start: 21 outliers final: 14 residues processed: 93 average time/residue: 0.0595 time to fit residues: 7.8337 Evaluate side-chains 86 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 848 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.188675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.152233 restraints weight = 10716.636| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 3.45 r_work: 0.3934 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6465 Z= 0.145 Angle : 0.583 7.855 8796 Z= 0.301 Chirality : 0.045 0.197 985 Planarity : 0.006 0.085 1092 Dihedral : 11.424 75.930 994 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.69 % Allowed : 11.38 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.30), residues: 744 helix: 0.73 (0.34), residues: 250 sheet: -0.83 (0.37), residues: 184 loop : -1.06 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.007 0.001 TYR A 815 PHE 0.021 0.002 PHE A 182 TRP 0.009 0.001 TRP A 211 HIS 0.004 0.001 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 6465) covalent geometry : angle 0.58253 / 0.30 ( 8796) hydrogen bonds : bond 0.04162 / 2.74 ( 253) hydrogen bonds : angle 5.62465 / 4.29 ( 726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 82 PHE cc_start: 0.9185 (m-10) cc_final: 0.8851 (m-10) REVERT: A 538 THR cc_start: 0.7784 (p) cc_final: 0.7539 (p) REVERT: A 623 ASN cc_start: 0.8255 (t0) cc_final: 0.7881 (t0) REVERT: A 768 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8010 (tp) REVERT: A 804 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7536 (m-80) outliers start: 18 outliers final: 12 residues processed: 89 average time/residue: 0.0719 time to fit residues: 9.3652 Evaluate side-chains 88 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 848 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 27 optimal weight: 0.1980 chunk 54 optimal weight: 0.1980 chunk 43 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN A 623 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.186996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.148279 restraints weight = 10753.386| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 3.85 r_work: 0.3867 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6465 Z= 0.182 Angle : 0.621 7.540 8796 Z= 0.320 Chirality : 0.046 0.194 985 Planarity : 0.006 0.079 1092 Dihedral : 11.521 75.214 994 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.99 % Allowed : 10.93 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.28 % 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: -0.72 (0.30), residues: 744 helix: 0.66 (0.34), residues: 248 sheet: -0.85 (0.36), residues: 189 loop : -1.07 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 438 TYR 0.008 0.001 TYR A 765 PHE 0.027 0.002 PHE A 23 TRP 0.006 0.001 TRP A 769 HIS 0.005 0.001 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 6465) covalent geometry : angle 0.62105 / 0.32 ( 8796) hydrogen bonds : bond 0.04414 / 2.92 ( 253) hydrogen bonds : angle 5.66336 / 4.30 ( 726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7331 (m-10) REVERT: A 82 PHE cc_start: 0.9184 (m-10) cc_final: 0.8941 (m-10) REVERT: A 399 ILE cc_start: 0.8650 (mm) cc_final: 0.8367 (mp) REVERT: A 437 MET cc_start: 0.6288 (OUTLIER) cc_final: 0.5097 (ttm) REVERT: A 538 THR cc_start: 0.7831 (p) cc_final: 0.7607 (p) REVERT: A 768 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8112 (tp) outliers start: 20 outliers final: 15 residues processed: 94 average time/residue: 0.0712 time to fit residues: 9.4001 Evaluate side-chains 88 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 848 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 0.0570 chunk 41 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 0.0570 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN A 623 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.190182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.153200 restraints weight = 10709.419| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 3.63 r_work: 0.3953 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6465 Z= 0.112 Angle : 0.578 8.227 8796 Z= 0.296 Chirality : 0.044 0.174 985 Planarity : 0.006 0.075 1092 Dihedral : 11.450 74.579 994 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.99 % Allowed : 11.98 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.28 % 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: 744 helix: 0.89 (0.34), residues: 249 sheet: -0.66 (0.38), residues: 185 loop : -1.00 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 438 TYR 0.011 0.001 TYR A 494 PHE 0.024 0.001 PHE A 23 TRP 0.008 0.001 TRP A 769 HIS 0.010 0.001 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 6465) covalent geometry : angle 0.57850 / 0.30 ( 8796) hydrogen bonds : bond 0.03741 / 2.46 ( 253) hydrogen bonds : angle 5.45392 / 4.14 ( 726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 PHE cc_start: 0.9131 (m-10) cc_final: 0.8820 (m-10) REVERT: A 213 MET cc_start: 0.6189 (tpp) cc_final: 0.5492 (ttm) REVERT: A 354 LYS cc_start: 0.7158 (mmtt) cc_final: 0.6280 (mmtm) REVERT: A 437 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.5048 (ttm) REVERT: A 538 THR cc_start: 0.7763 (p) cc_final: 0.7536 (p) REVERT: A 804 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7591 (m-80) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 0.0643 time to fit residues: 8.7434 Evaluate side-chains 91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 848 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 50 optimal weight: 0.0370 chunk 71 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 0.0980 chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 0.0970 chunk 31 optimal weight: 3.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.194292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.159350 restraints weight = 10760.910| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 3.60 r_work: 0.3965 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 6465 Z= 0.109 Angle : 0.577 8.521 8796 Z= 0.295 Chirality : 0.044 0.162 985 Planarity : 0.005 0.071 1092 Dihedral : 11.381 74.310 993 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.69 % Allowed : 13.02 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.28 % 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 (0.31), residues: 744 helix: 1.02 (0.34), residues: 251 sheet: -0.64 (0.38), residues: 187 loop : -0.98 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 635 TYR 0.011 0.001 TYR A 494 PHE 0.021 0.001 PHE A 23 TRP 0.010 0.001 TRP A 769 HIS 0.008 0.001 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 6465) covalent geometry : angle 0.57720 / 0.29 ( 8796) hydrogen bonds : bond 0.03472 / 2.29 ( 253) hydrogen bonds : angle 5.27151 / 3.98 ( 726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 82 PHE cc_start: 0.9170 (m-10) cc_final: 0.8901 (m-10) REVERT: A 354 LYS cc_start: 0.7078 (mmtt) cc_final: 0.6223 (mmtm) REVERT: A 399 ILE cc_start: 0.8613 (mm) cc_final: 0.8385 (tp) REVERT: A 437 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.5033 (ttm) REVERT: A 538 THR cc_start: 0.7762 (p) cc_final: 0.7527 (p) REVERT: A 618 MET cc_start: 0.6142 (mmm) cc_final: 0.5913 (mmt) REVERT: A 623 ASN cc_start: 0.8127 (t0) cc_final: 0.7762 (t0) REVERT: A 804 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7579 (m-80) outliers start: 18 outliers final: 11 residues processed: 101 average time/residue: 0.0733 time to fit residues: 10.3494 Evaluate side-chains 92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 199 TRP Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 848 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.191355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.156262 restraints weight = 10750.727| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 3.44 r_work: 0.3930 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6465 Z= 0.171 Angle : 0.634 9.815 8796 Z= 0.324 Chirality : 0.046 0.155 985 Planarity : 0.006 0.091 1092 Dihedral : 11.489 76.308 993 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.69 % Allowed : 12.72 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.28 % 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: 744 helix: 0.91 (0.34), residues: 250 sheet: -0.65 (0.38), residues: 181 loop : -1.07 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.009 0.001 TYR A 494 PHE 0.019 0.002 PHE A 23 TRP 0.007 0.001 TRP A 769 HIS 0.008 0.001 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 6465) covalent geometry : angle 0.63364 / 0.32 ( 8796) hydrogen bonds : bond 0.04069 / 2.68 ( 253) hydrogen bonds : angle 5.38199 / 4.07 ( 726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7423 (m-10) REVERT: A 82 PHE cc_start: 0.9189 (m-10) cc_final: 0.8536 (m-10) REVERT: A 213 MET cc_start: 0.5920 (tpp) cc_final: 0.5348 (ttm) REVERT: A 354 LYS cc_start: 0.7107 (mmtt) cc_final: 0.6231 (mptt) REVERT: A 399 ILE cc_start: 0.8645 (mm) cc_final: 0.8398 (tp) REVERT: A 437 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5012 (ttm) REVERT: A 618 MET cc_start: 0.6150 (mmm) cc_final: 0.5928 (mmt) REVERT: A 768 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8177 (tp) REVERT: A 804 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: A 856 MET cc_start: 0.7849 (mmm) cc_final: 0.7460 (mmt) outliers start: 18 outliers final: 13 residues processed: 91 average time/residue: 0.0629 time to fit residues: 8.2071 Evaluate side-chains 91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 199 TRP Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 848 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.189785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.152503 restraints weight = 10534.401| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 3.76 r_work: 0.3946 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6465 Z= 0.136 Angle : 0.614 10.381 8796 Z= 0.312 Chirality : 0.045 0.149 985 Planarity : 0.006 0.085 1092 Dihedral : 11.461 76.388 993 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.54 % Allowed : 13.62 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.28 % 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: -0.45 (0.31), residues: 744 helix: 0.94 (0.34), residues: 250 sheet: -0.60 (0.38), residues: 181 loop : -1.05 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.010 0.001 TYR A 494 PHE 0.018 0.002 PHE A 23 TRP 0.024 0.002 TRP A 769 HIS 0.009 0.001 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 6465) covalent geometry : angle 0.61388 / 0.31 ( 8796) hydrogen bonds : bond 0.03803 / 2.50 ( 253) hydrogen bonds : angle 5.32995 / 4.03 ( 726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 PHE cc_start: 0.9193 (m-10) cc_final: 0.8572 (m-10) REVERT: A 213 MET cc_start: 0.5842 (tpp) cc_final: 0.5407 (ttm) REVERT: A 354 LYS cc_start: 0.7077 (mmtt) cc_final: 0.6203 (mptt) REVERT: A 399 ILE cc_start: 0.8626 (mm) cc_final: 0.8404 (tp) REVERT: A 437 MET cc_start: 0.6229 (OUTLIER) cc_final: 0.5008 (ttm) REVERT: A 538 THR cc_start: 0.7758 (p) cc_final: 0.7468 (p) REVERT: A 804 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7498 (m-80) outliers start: 17 outliers final: 13 residues processed: 90 average time/residue: 0.0659 time to fit residues: 8.5803 Evaluate side-chains 91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 199 TRP Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 848 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.191768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.156992 restraints weight = 10648.630| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 3.37 r_work: 0.3931 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6465 Z= 0.162 Angle : 0.643 10.165 8796 Z= 0.326 Chirality : 0.046 0.153 985 Planarity : 0.006 0.084 1092 Dihedral : 11.538 77.352 993 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.69 % Allowed : 13.62 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.28 % 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: -0.54 (0.31), residues: 744 helix: 0.83 (0.34), residues: 250 sheet: -0.63 (0.39), residues: 181 loop : -1.10 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.010 0.001 TYR A 749 PHE 0.015 0.002 PHE A 182 TRP 0.021 0.002 TRP A 769 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 6465) covalent geometry : angle 0.64304 / 0.33 ( 8796) hydrogen bonds : bond 0.04018 / 2.66 ( 253) hydrogen bonds : angle 5.37166 / 4.05 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1494.50 seconds wall clock time: 26 minutes 21.21 seconds (1581.21 seconds total)