Starting phenix.real_space_refine on Thu Jul 2 03:51:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymd_73103/07_2026/9ymd_73103.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymd_73103/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ymd_73103/07_2026/9ymd_73103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymd_73103/07_2026/9ymd_73103.map" model { file = "/net/cci-nas-00/data/ceres_data/9ymd_73103/07_2026/9ymd_73103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymd_73103/07_2026/9ymd_73103.cif" } 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-dev-6108/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: 1.58, per 1000 atoms: 0.25 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: 0.63 Conformation dependent library (CDL) restraints added in 338.8 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: 0.70 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: 1.02 Time building geometry restraints manager: 0.81 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: 8691 2.04 - 4.09: 96 4.09 - 6.13: 8 6.13 - 8.18: 0 8.18 - 10.22: 1 Bond angle restraints: 8796 Sorted by residual: 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=" C GLU A 186 " pdb=" N GLY A 187 " pdb=" CA GLY A 187 " ideal model delta sigma weight residual 121.70 127.46 -5.76 1.80e+00 3.09e-01 1.03e+01 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 1.50e+00 4.44e-01 8.70e+00 angle pdb=" C HIS A 336 " pdb=" N THR A 337 " pdb=" CA THR A 337 " ideal model delta sigma weight residual 121.54 127.07 -5.53 1.91e+00 2.74e-01 8.37e+00 ... (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 - 0.050: 798 0.050 - 0.101: 149 0.101 - 0.151: 35 0.151 - 0.201: 1 0.201 - 0.252: 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 0.25 2.00e-01 2.50e+01 1.58e+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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.230 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: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.950 ------------------------------------------------------------------------------- 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= 0.128 Angle : 0.538 10.222 8796 Z= 0.298 Chirality : 0.043 0.252 985 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 0.00261 / 0.13 ( 6465) covalent geometry : angle 0.53802 / 0.30 ( 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 : 0.234 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: 0.0819 time to fit residues: 11.2912 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 : 0.233 ------------------------------------------------------------------------------- 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 = 0.4473 r_free = 0.4473 target = 0.189251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.152050 restraints weight = 10746.507| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 3.57 r_work: 0.3917 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.0984 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= 0.176 Angle : 0.611 8.102 8796 Z= 0.321 Chirality : 0.045 0.179 985 Planarity : 0.006 0.069 1092 Dihedral : 11.584 78.869 997 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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: -0.48 (0.31), residues: 744 helix: 0.76 (0.34), residues: 251 sheet: -0.84 (0.36), residues: 194 loop : -0.74 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 167 TYR 0.009 0.001 TYR A 101 PHE 0.011 0.002 PHE A 774 TRP 0.008 0.001 TRP A 211 HIS 0.007 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 ( 6465) covalent geometry : angle 0.61110 / 0.32 ( 8796) hydrogen bonds : bond 0.05416 / 3.53 ( 253) hydrogen bonds : angle 6.51322 / 4.99 ( 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 : 0.198 Fit side-chains revert: symmetry clash REVERT: A 538 THR cc_start: 0.7793 (p) cc_final: 0.7504 (p) REVERT: A 549 MET cc_start: 0.7313 (ttm) cc_final: 0.6994 (tpt) outliers start: 17 outliers final: 13 residues processed: 91 average time/residue: 0.0717 time to fit residues: 9.0377 Evaluate side-chains 89 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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: 0.1980 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: 1.9990 chunk 27 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 74 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.188563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.151724 restraints weight = 10507.948| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 3.56 r_work: 0.3924 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1326 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= 0.152 Angle : 0.580 7.789 8796 Z= 0.304 Chirality : 0.045 0.190 985 Planarity : 0.006 0.079 1092 Dihedral : 11.511 77.574 994 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.14 % Allowed : 9.88 % Favored : 86.98 % 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: 0.79 (0.34), residues: 254 sheet: -0.84 (0.36), residues: 190 loop : -0.89 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.011 0.001 TYR A 815 PHE 0.013 0.002 PHE A 233 TRP 0.008 0.001 TRP A 211 HIS 0.005 0.001 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 6465) covalent geometry : angle 0.57970 / 0.30 ( 8796) hydrogen bonds : bond 0.04679 / 3.09 ( 253) hydrogen bonds : angle 6.05553 / 4.63 ( 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 102 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 396 GLU cc_start: 0.5678 (OUTLIER) cc_final: 0.5454 (tm-30) REVERT: A 483 MET cc_start: 0.7398 (ppp) cc_final: 0.7163 (ppp) REVERT: A 538 THR cc_start: 0.7791 (p) cc_final: 0.7510 (p) REVERT: A 804 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7489 (m-80) outliers start: 21 outliers final: 14 residues processed: 93 average time/residue: 0.0745 time to fit residues: 9.5762 Evaluate side-chains 87 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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: 9.9990 chunk 17 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.4457 r_free = 0.4457 target = 0.187905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.149855 restraints weight = 10525.701| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.81 r_work: 0.3883 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6465 Z= 0.159 Angle : 0.585 7.856 8796 Z= 0.306 Chirality : 0.045 0.198 985 Planarity : 0.005 0.071 1092 Dihedral : 11.543 76.930 994 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.14 % Allowed : 10.63 % Favored : 86.23 % 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: -0.63 (0.31), residues: 744 helix: 0.74 (0.34), residues: 249 sheet: -0.89 (0.36), residues: 188 loop : -0.95 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 167 TYR 0.009 0.001 TYR A 815 PHE 0.015 0.002 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 0.00364 / 0.16 ( 6465) covalent geometry : angle 0.58527 / 0.31 ( 8796) hydrogen bonds : bond 0.04391 / 2.90 ( 253) hydrogen bonds : angle 5.86222 / 4.48 ( 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 101 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 82 PHE cc_start: 0.9148 (m-10) cc_final: 0.8906 (m-10) REVERT: A 538 THR cc_start: 0.7805 (p) cc_final: 0.7546 (p) REVERT: A 768 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8090 (tp) REVERT: A 804 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7550 (m-80) outliers start: 21 outliers final: 14 residues processed: 93 average time/residue: 0.0648 time to fit residues: 8.5676 Evaluate side-chains 88 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 34 optimal weight: 0.3980 chunk 5 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 = 0.4441 r_free = 0.4441 target = 0.186163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.148236 restraints weight = 10727.637| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 3.77 r_work: 0.3864 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6465 Z= 0.196 Angle : 0.626 7.769 8796 Z= 0.327 Chirality : 0.046 0.197 985 Planarity : 0.006 0.063 1092 Dihedral : 11.648 75.755 994 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.59 % Allowed : 11.08 % Favored : 85.33 % 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: -0.83 (0.30), residues: 744 helix: 0.53 (0.33), residues: 248 sheet: -0.96 (0.36), residues: 185 loop : -1.07 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 167 TYR 0.009 0.002 TYR A 765 PHE 0.021 0.002 PHE A 182 TRP 0.009 0.001 TRP A 211 HIS 0.006 0.001 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 ( 6465) covalent geometry : angle 0.62643 / 0.33 ( 8796) hydrogen bonds : bond 0.04666 / 3.09 ( 253) hydrogen bonds : angle 5.78294 / 4.39 ( 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 102 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 PHE cc_start: 0.9197 (m-10) cc_final: 0.8871 (m-10) REVERT: A 191 PRO cc_start: 0.8413 (Cg_exo) cc_final: 0.8213 (Cg_exo) REVERT: A 213 MET cc_start: 0.6349 (tpp) cc_final: 0.5570 (tpp) REVERT: A 399 ILE cc_start: 0.8638 (mm) cc_final: 0.8353 (mp) REVERT: A 538 THR cc_start: 0.7832 (p) cc_final: 0.7599 (p) REVERT: A 618 MET cc_start: 0.6363 (mmm) cc_final: 0.6060 (mmt) outliers start: 24 outliers final: 14 residues processed: 93 average time/residue: 0.0726 time to fit residues: 9.4394 Evaluate side-chains 83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 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 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 724 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 791 VAL 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: 0.8980 chunk 38 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 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: 0.9990 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4510 r_free = 0.4510 target = 0.190965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.155923 restraints weight = 11116.659| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 3.51 r_work: 0.3939 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6465 Z= 0.120 Angle : 0.570 8.499 8796 Z= 0.294 Chirality : 0.044 0.199 985 Planarity : 0.005 0.062 1092 Dihedral : 11.570 74.925 993 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.40 % Allowed : 12.28 % Favored : 85.33 % 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: -0.59 (0.31), residues: 744 helix: 0.73 (0.34), residues: 249 sheet: -0.71 (0.37), residues: 185 loop : -1.01 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 438 TYR 0.008 0.001 TYR A 815 PHE 0.025 0.002 PHE A 23 TRP 0.007 0.001 TRP A 769 HIS 0.009 0.001 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 6465) covalent geometry : angle 0.56953 / 0.29 ( 8796) hydrogen bonds : bond 0.03862 / 2.53 ( 253) hydrogen bonds : angle 5.54897 / 4.22 ( 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 97 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7144 (m-10) REVERT: A 82 PHE cc_start: 0.9167 (m-10) cc_final: 0.8906 (m-10) REVERT: A 213 MET cc_start: 0.6195 (tpp) cc_final: 0.5381 (tpp) REVERT: A 354 LYS cc_start: 0.7155 (mmtt) cc_final: 0.6270 (mmtm) REVERT: A 399 ILE cc_start: 0.8635 (mm) cc_final: 0.8308 (mp) REVERT: A 437 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.5035 (ttm) REVERT: A 538 THR cc_start: 0.7784 (p) cc_final: 0.7553 (p) REVERT: A 618 MET cc_start: 0.6300 (mmm) cc_final: 0.6088 (mmm) REVERT: A 804 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7535 (m-80) outliers start: 16 outliers final: 10 residues processed: 91 average time/residue: 0.0722 time to fit residues: 9.0701 Evaluate side-chains 85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 0.0050 chunk 24 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN A 486 GLN A 623 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.190439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.154165 restraints weight = 10679.065| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 3.88 r_work: 0.3955 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6465 Z= 0.111 Angle : 0.573 8.951 8796 Z= 0.292 Chirality : 0.044 0.257 985 Planarity : 0.005 0.081 1092 Dihedral : 11.446 74.500 993 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.99 % Allowed : 12.72 % 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: -0.39 (0.31), residues: 744 helix: 0.98 (0.34), residues: 249 sheet: -0.56 (0.38), residues: 189 loop : -1.01 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 438 TYR 0.013 0.001 TYR A 494 PHE 0.020 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 0.00243 / 0.11 ( 6465) covalent geometry : angle 0.57256 / 0.29 ( 8796) hydrogen bonds : bond 0.03565 / 2.33 ( 253) hydrogen bonds : angle 5.34063 / 4.03 ( 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 103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 PHE cc_start: 0.9218 (m-10) cc_final: 0.8941 (m-10) REVERT: A 213 MET cc_start: 0.6141 (tpp) cc_final: 0.5368 (tpp) REVERT: A 214 MET cc_start: 0.5683 (mmt) cc_final: 0.5456 (mmt) REVERT: A 354 LYS cc_start: 0.7084 (mmtt) cc_final: 0.6192 (mptt) REVERT: A 399 ILE cc_start: 0.8631 (mm) cc_final: 0.8398 (tp) REVERT: A 437 MET cc_start: 0.6206 (OUTLIER) cc_final: 0.5018 (ttm) REVERT: A 538 THR cc_start: 0.7784 (p) cc_final: 0.7560 (p) REVERT: A 804 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7511 (m-80) outliers start: 20 outliers final: 13 residues processed: 96 average time/residue: 0.0704 time to fit residues: 9.4435 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 : 0.232 ------------------------------------------------------------------------------- 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 494 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 50 optimal weight: 0.0370 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 0.0020 chunk 61 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.8868 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.190004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.152360 restraints weight = 10651.370| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 3.68 r_work: 0.3932 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 : 0.003 0.044 6465 Z= 0.123 Angle : 0.586 8.647 8796 Z= 0.299 Chirality : 0.044 0.252 985 Planarity : 0.005 0.077 1092 Dihedral : 11.452 74.989 993 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % 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: -0.45 (0.31), residues: 744 helix: 0.97 (0.34), residues: 250 sheet: -0.58 (0.37), residues: 186 loop : -1.10 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 635 TYR 0.011 0.001 TYR A 494 PHE 0.020 0.001 PHE A 23 TRP 0.008 0.001 TRP A 769 HIS 0.008 0.001 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 6465) covalent geometry : angle 0.58630 / 0.30 ( 8796) hydrogen bonds : bond 0.03652 / 2.39 ( 253) hydrogen bonds : angle 5.29528 / 3.97 ( 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 101 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 PHE cc_start: 0.9241 (m-10) cc_final: 0.8572 (m-10) REVERT: A 191 PRO cc_start: 0.8396 (Cg_exo) cc_final: 0.8191 (Cg_exo) REVERT: A 213 MET cc_start: 0.6122 (tpp) cc_final: 0.5388 (tpp) REVERT: A 214 MET cc_start: 0.5716 (mmt) cc_final: 0.5462 (mmt) REVERT: A 354 LYS cc_start: 0.7059 (mmtt) cc_final: 0.6161 (mptt) REVERT: A 399 ILE cc_start: 0.8641 (mm) cc_final: 0.8404 (tp) REVERT: A 437 MET cc_start: 0.6220 (OUTLIER) cc_final: 0.5026 (ttm) REVERT: A 538 THR cc_start: 0.7767 (p) cc_final: 0.7539 (p) REVERT: A 623 ASN cc_start: 0.8204 (t0) cc_final: 0.8000 (t0) REVERT: A 804 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7511 (m-80) REVERT: A 856 MET cc_start: 0.7777 (mmm) cc_final: 0.7403 (mmt) outliers start: 18 outliers final: 13 residues processed: 96 average time/residue: 0.0675 time to fit residues: 9.1643 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 : 0.249 ------------------------------------------------------------------------------- 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 199 TRP Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 494 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 = 0.4500 r_free = 0.4500 target = 0.189568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.153673 restraints weight = 10703.498| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 3.49 r_work: 0.3893 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6465 Z= 0.204 Angle : 0.671 9.461 8796 Z= 0.343 Chirality : 0.047 0.234 985 Planarity : 0.006 0.082 1092 Dihedral : 11.688 78.151 993 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.25 % Allowed : 13.77 % Favored : 83.98 % 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: -0.69 (0.30), residues: 744 helix: 0.73 (0.34), residues: 249 sheet: -0.68 (0.38), residues: 171 loop : -1.21 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 167 TYR 0.011 0.002 TYR A 765 PHE 0.019 0.002 PHE A 23 TRP 0.009 0.002 TRP A 435 HIS 0.008 0.002 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 ( 6465) covalent geometry : angle 0.67092 / 0.34 ( 8796) hydrogen bonds : bond 0.04453 / 2.94 ( 253) hydrogen bonds : angle 5.53436 / 4.14 ( 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 93 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 PHE cc_start: 0.9244 (m-10) cc_final: 0.8557 (m-10) REVERT: A 191 PRO cc_start: 0.8469 (Cg_exo) cc_final: 0.8266 (Cg_exo) REVERT: A 213 MET cc_start: 0.6187 (tpp) cc_final: 0.5442 (tpp) REVERT: A 214 MET cc_start: 0.5669 (mmt) cc_final: 0.5411 (mmt) REVERT: A 354 LYS cc_start: 0.7200 (mmtt) cc_final: 0.6228 (mptt) REVERT: A 399 ILE cc_start: 0.8637 (mm) cc_final: 0.8398 (tp) REVERT: A 437 MET cc_start: 0.6287 (OUTLIER) cc_final: 0.5091 (ttm) outliers start: 15 outliers final: 13 residues processed: 88 average time/residue: 0.0669 time to fit residues: 8.4076 Evaluate side-chains 89 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 205 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 494 TYR 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 3 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4522 r_free = 0.4522 target = 0.191685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.156735 restraints weight = 10579.388| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 3.68 r_work: 0.3855 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6465 Z= 0.137 Angle : 0.615 10.049 8796 Z= 0.313 Chirality : 0.045 0.244 985 Planarity : 0.006 0.076 1092 Dihedral : 11.563 77.117 993 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.69 % Allowed : 13.77 % Favored : 83.53 % 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: -0.52 (0.31), residues: 744 helix: 0.91 (0.34), residues: 249 sheet: -0.65 (0.38), residues: 186 loop : -1.10 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.011 0.001 TYR A 494 PHE 0.018 0.002 PHE A 23 TRP 0.019 0.002 TRP A 769 HIS 0.009 0.001 HIS A 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6465) covalent geometry : angle 0.61506 / 0.31 ( 8796) hydrogen bonds : bond 0.03843 / 2.50 ( 253) hydrogen bonds : angle 5.41841 / 4.06 ( 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 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 PHE cc_start: 0.9249 (m-10) cc_final: 0.8587 (m-10) REVERT: A 191 PRO cc_start: 0.8452 (Cg_exo) cc_final: 0.8250 (Cg_exo) REVERT: A 213 MET cc_start: 0.6098 (tpp) cc_final: 0.5376 (tpp) REVERT: A 214 MET cc_start: 0.5628 (mmt) cc_final: 0.5393 (mmt) REVERT: A 399 ILE cc_start: 0.8656 (mm) cc_final: 0.8422 (tp) REVERT: A 437 MET cc_start: 0.6271 (OUTLIER) cc_final: 0.5028 (ttm) REVERT: A 538 THR cc_start: 0.7783 (p) cc_final: 0.7497 (p) REVERT: A 769 TRP cc_start: 0.7346 (t-100) cc_final: 0.7133 (t-100) REVERT: A 804 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7528 (m-80) outliers start: 18 outliers final: 14 residues processed: 92 average time/residue: 0.0683 time to fit residues: 8.9319 Evaluate side-chains 91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 210 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 494 TYR 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: 1.9990 chunk 3 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 = 0.4506 r_free = 0.4506 target = 0.190064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.154879 restraints weight = 10581.178| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 3.71 r_work: 0.3831 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6465 Z= 0.172 Angle : 0.645 9.949 8796 Z= 0.329 Chirality : 0.046 0.237 985 Planarity : 0.006 0.079 1092 Dihedral : 11.647 78.629 993 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.40 % Allowed : 14.22 % Favored : 83.38 % 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: -0.64 (0.30), residues: 744 helix: 0.79 (0.34), residues: 249 sheet: -0.59 (0.38), residues: 176 loop : -1.24 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.011 0.001 TYR A 494 PHE 0.015 0.002 PHE A 182 TRP 0.026 0.002 TRP A 769 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 6465) covalent geometry : angle 0.64504 / 0.33 ( 8796) hydrogen bonds : bond 0.04124 / 2.71 ( 253) hydrogen bonds : angle 5.47784 / 4.09 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1700.14 seconds wall clock time: 29 minutes 59.75 seconds (1799.75 seconds total)