Starting phenix.real_space_refine on Tue Aug 4 21:19:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10be_75039/08_2026/10be_75039.cif Found real_map, /net/cci-nas-00/data/ceres_data/10be_75039/08_2026/10be_75039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10be_75039/08_2026/10be_75039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10be_75039/08_2026/10be_75039.map" model { file = "/net/cci-nas-00/data/ceres_data/10be_75039/08_2026/10be_75039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10be_75039/08_2026/10be_75039.cif" } resolution = 3.02 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= 0.005 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 19 5.49 5 S 40 5.16 5 C 4230 2.51 5 N 1214 2.21 5 O 1254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s 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: 6757 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 213 Classifications: {'RNA': 10} Modifications used: {'p5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 7} Chain: "C" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "A" Number of atoms: 6355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6355 Classifications: {'peptide': 792} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 741} Chain breaks: 7 Time building chain proxies: 1.97, per 1000 atoms: 0.29 Number of scatterers: 6757 At special positions: 0 Unit cell: (73.6896, 93.3888, 110.534, 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 19 15.00 O 1254 8.00 N 1214 7.00 C 4230 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: 0.71 Conformation dependent library (CDL) restraints added in 452.5 milliseconds 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 6 sheets defined 34.8% alpha, 24.5% beta 7 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 139 through 148 removed outlier: 3.804A pdb=" N LEU A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 174 removed outlier: 3.701A pdb=" N ILE A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 4.866A 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 239 removed outlier: 3.845A pdb=" N CYS A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 263 removed outlier: 3.691A pdb=" N GLU A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 357 through 367 Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.532A pdb=" N SER A 387 " --> pdb=" O MET A 383 " (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: 3.727A 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 500 through 512 Processing helix chain 'A' and resid 526 through 539 removed outlier: 4.326A 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 Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.515A pdb=" N GLN A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 658 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 693 removed outlier: 3.815A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 787 Processing helix chain 'A' and resid 800 through 818 removed outlier: 3.717A pdb=" N TYR A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 846 removed outlier: 3.906A pdb=" N VAL A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 removed outlier: 4.129A pdb=" N ARG A 854 " --> pdb=" O GLN A 850 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.809A pdb=" N MET A 213 " --> pdb=" O MET A 47 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 217 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASN A 43 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 11.908A pdb=" N VAL A 219 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 16.613A pdb=" N GLN A 41 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 25.191A pdb=" N ALA A 221 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 29.820A pdb=" N LYS A 39 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 38.230A pdb=" N ALA A 223 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 42.152A pdb=" N THR A 37 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE A 44 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU A 404 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU A 46 " --> pdb=" O LYS A 402 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE A 704 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP A 770 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 702 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A 664 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE A 705 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE A 666 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL A 707 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG A 668 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL A 598 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 610 " --> pdb=" O GLN A 632 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.809A pdb=" N MET A 213 " --> pdb=" O MET A 47 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 217 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASN A 43 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 11.908A pdb=" N VAL A 219 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 16.613A pdb=" N GLN A 41 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 25.191A pdb=" N ALA A 221 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 29.820A pdb=" N LYS A 39 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 38.230A pdb=" N ALA A 223 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 42.152A pdb=" N THR A 37 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.660A pdb=" N SER A 136 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU A 58 " --> pdb=" O TRP A 134 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N TRP A 134 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 117 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 130 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.650A pdb=" N ASN A 283 " --> pdb=" O GLN A 329 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR A 285 " --> pdb=" O CYS A 327 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N CYS A 327 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 427 through 428 Processing sheet with id=AA6, first strand: chain 'A' and resid 492 through 494 removed outlier: 3.707A pdb=" N LYS A 493 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 455 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA A 452 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE A 521 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA A 454 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL A 518 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL A 547 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL A 520 " --> pdb=" O VAL A 547 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 281 hydrogen bonds defined for protein. 786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 0.85 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1920 1.33 - 1.45: 1204 1.45 - 1.57: 3732 1.57 - 1.69: 36 1.69 - 1.81: 59 Bond restraints: 6951 Sorted by residual: bond pdb=" CG1 ILE A 638 " pdb=" CD1 ILE A 638 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.58e+00 bond pdb=" C3' U B 9 " pdb=" O3' U B 9 " ideal model delta sigma weight residual 1.427 1.439 -0.012 1.20e-02 6.94e+03 9.38e-01 bond pdb=" C2 U C 14 " pdb=" N3 U C 14 " ideal model delta sigma weight residual 1.373 1.379 -0.006 7.00e-03 2.04e+04 6.80e-01 bond pdb=" CB ASP A 30 " pdb=" CG ASP A 30 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.59e-01 bond pdb=" CB LYS A 260 " pdb=" CG LYS A 260 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.36e-01 ... (remaining 6946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 9169 1.10 - 2.21: 200 2.21 - 3.31: 104 3.31 - 4.42: 13 4.42 - 5.52: 7 Bond angle restraints: 9493 Sorted by residual: angle pdb=" C3' U B 9 " pdb=" O3' U B 9 " pdb=" P U B 10 " ideal model delta sigma weight residual 119.70 124.14 -4.44 1.20e+00 6.94e-01 1.37e+01 angle pdb=" O5' A C 16 " pdb=" C5' A C 16 " pdb=" C4' A C 16 " ideal model delta sigma weight residual 109.40 112.10 -2.70 8.00e-01 1.56e+00 1.14e+01 angle pdb=" O5' U B 10 " pdb=" C5' U B 10 " pdb=" C4' U B 10 " ideal model delta sigma weight residual 109.40 112.09 -2.69 8.00e-01 1.56e+00 1.13e+01 angle pdb=" C1' C C 12 " pdb=" N1 C C 12 " pdb=" C2 C C 12 " ideal model delta sigma weight residual 118.80 122.31 -3.51 1.10e+00 8.26e-01 1.02e+01 angle pdb=" O5' U B 9 " pdb=" C5' U B 9 " pdb=" C4' U B 9 " ideal model delta sigma weight residual 109.40 111.88 -2.48 8.00e-01 1.56e+00 9.58e+00 ... (remaining 9488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 3979 21.16 - 42.32: 197 42.32 - 63.49: 41 63.49 - 84.65: 16 84.65 - 105.81: 2 Dihedral angle restraints: 4235 sinusoidal: 1925 harmonic: 2310 Sorted by residual: dihedral pdb=" C4' U B 9 " pdb=" C3' U B 9 " pdb=" O3' U B 9 " pdb=" P U B 10 " ideal model delta sinusoidal sigma weight residual -110.00 -4.19 -105.81 1 3.50e+01 8.16e-04 9.97e+00 dihedral pdb=" CB MET A 213 " pdb=" CG MET A 213 " pdb=" SD MET A 213 " pdb=" CE MET A 213 " ideal model delta sinusoidal sigma weight residual 180.00 127.69 52.31 3 1.50e+01 4.44e-03 9.10e+00 dihedral pdb=" CG ARG A 179 " pdb=" CD ARG A 179 " pdb=" NE ARG A 179 " pdb=" CZ ARG A 179 " ideal model delta sinusoidal sigma weight residual -180.00 -139.39 -40.61 2 1.50e+01 4.44e-03 9.04e+00 ... (remaining 4232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 646 0.027 - 0.055: 260 0.055 - 0.082: 69 0.082 - 0.110: 62 0.110 - 0.137: 35 Chirality restraints: 1072 Sorted by residual: chirality pdb=" C2' U C 14 " pdb=" C3' U C 14 " pdb=" O2' U C 14 " pdb=" C1' U C 14 " both_signs ideal model delta sigma weight residual False -2.62 -2.75 0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" C2' A B 2 " pdb=" C3' A B 2 " pdb=" O2' A B 2 " pdb=" C1' A B 2 " both_signs ideal model delta sigma weight residual False -2.62 -2.75 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" C2' C C 10 " pdb=" C3' C C 10 " pdb=" O2' C C 10 " pdb=" C1' C C 10 " both_signs ideal model delta sigma weight residual False -2.62 -2.75 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 1069 not shown) Planarity restraints: 1152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 228 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 229 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 62 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 63 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 63 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 63 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C C 12 " -0.014 2.00e-02 2.50e+03 8.71e-03 1.71e+00 pdb=" N1 C C 12 " 0.021 2.00e-02 2.50e+03 pdb=" C2 C C 12 " -0.005 2.00e-02 2.50e+03 pdb=" O2 C C 12 " 0.002 2.00e-02 2.50e+03 pdb=" N3 C C 12 " -0.000 2.00e-02 2.50e+03 pdb=" C4 C C 12 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C C 12 " -0.003 2.00e-02 2.50e+03 pdb=" C5 C C 12 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C C 12 " 0.001 2.00e-02 2.50e+03 ... (remaining 1149 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1743 2.81 - 3.33: 5958 3.33 - 3.86: 11012 3.86 - 4.38: 12770 4.38 - 4.90: 22304 Nonbonded interactions: 53787 Sorted by model distance: nonbonded pdb=" NE2 HIS A 600 " pdb=" OE2 GLU A 637 " model vdw 2.291 3.120 nonbonded pdb=" OP2 C B 8 " pdb=" O2' U B 9 " model vdw 2.317 3.040 nonbonded pdb=" O2' U C 15 " pdb=" OE1 GLN A 558 " model vdw 2.348 3.040 nonbonded pdb=" NE2 GLN A 632 " pdb=" O ILE A 638 " model vdw 2.365 3.120 nonbonded pdb=" O GLU A 73 " pdb=" ND1 HIS A 77 " model vdw 2.368 3.120 ... (remaining 53782 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: 13.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.460 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.640 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.002 0.049 6951 Z= 0.108 Angle : 0.495 5.525 9493 Z= 0.292 Chirality : 0.043 0.137 1072 Planarity : 0.004 0.040 1152 Dihedral : 13.584 105.809 2735 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.31), residues: 776 helix: 1.56 (0.35), residues: 245 sheet: 0.31 (0.39), residues: 178 loop : -0.49 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 624 TYR 0.011 0.001 TYR A 393 PHE 0.011 0.001 PHE A 746 TRP 0.008 0.001 TRP A 211 HIS 0.007 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 6951) covalent geometry : angle 0.49465 / 0.29 ( 9493) hydrogen bonds : bond 0.18604 / 18.08 ( 277) hydrogen bonds : angle 7.58558 / 8.57 ( 820) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.265 Fit side-chains REVERT: A 99 ASN cc_start: 0.7803 (m110) cc_final: 0.7061 (m-40) REVERT: A 355 LYS cc_start: 0.7171 (mptt) cc_final: 0.6838 (mttp) REVERT: A 450 VAL cc_start: 0.8961 (t) cc_final: 0.8734 (p) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0982 time to fit residues: 11.8710 Evaluate side-chains 79 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.199553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.152776 restraints weight = 7119.639| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.36 r_work: 0.3581 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6951 Z= 0.119 Angle : 0.494 6.492 9493 Z= 0.255 Chirality : 0.042 0.203 1072 Planarity : 0.004 0.040 1152 Dihedral : 12.308 112.244 1147 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.43 % Allowed : 4.28 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.31), residues: 776 helix: 1.51 (0.35), residues: 246 sheet: 0.02 (0.37), residues: 193 loop : -0.46 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 370 TYR 0.011 0.001 TYR A 804 PHE 0.011 0.001 PHE A 704 TRP 0.006 0.001 TRP A 211 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 6951) covalent geometry : angle 0.49366 / 0.25 ( 9493) hydrogen bonds : bond 0.04264 / 4.10 ( 277) hydrogen bonds : angle 5.51573 / 6.61 ( 820) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.265 Fit side-chains REVERT: A 99 ASN cc_start: 0.7858 (m110) cc_final: 0.7141 (m-40) REVERT: A 279 TYR cc_start: 0.6698 (m-80) cc_final: 0.6449 (m-80) REVERT: A 355 LYS cc_start: 0.7183 (mptt) cc_final: 0.6852 (mttp) REVERT: A 694 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8128 (mp) outliers start: 3 outliers final: 1 residues processed: 85 average time/residue: 0.1061 time to fit residues: 11.5971 Evaluate side-chains 81 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 694 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 25 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.197153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.148910 restraints weight = 6983.010| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.60 r_work: 0.3530 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6951 Z= 0.124 Angle : 0.484 6.536 9493 Z= 0.246 Chirality : 0.042 0.181 1072 Planarity : 0.004 0.039 1152 Dihedral : 12.244 115.136 1147 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.00 % Allowed : 6.70 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.31), residues: 776 helix: 1.55 (0.35), residues: 245 sheet: 0.07 (0.36), residues: 193 loop : -0.46 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 854 TYR 0.015 0.001 TYR A 804 PHE 0.011 0.001 PHE A 704 TRP 0.007 0.001 TRP A 211 HIS 0.008 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 6951) covalent geometry : angle 0.48444 / 0.25 ( 9493) hydrogen bonds : bond 0.04119 / 3.95 ( 277) hydrogen bonds : angle 5.09237 / 6.15 ( 820) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.216 Fit side-chains REVERT: A 99 ASN cc_start: 0.7958 (m110) cc_final: 0.7213 (m-40) REVERT: A 104 MET cc_start: 0.6514 (mmm) cc_final: 0.6088 (mmm) REVERT: A 355 LYS cc_start: 0.7261 (mptt) cc_final: 0.6891 (mttp) REVERT: A 429 THR cc_start: 0.8948 (m) cc_final: 0.8544 (p) REVERT: A 694 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8116 (mp) outliers start: 7 outliers final: 5 residues processed: 88 average time/residue: 0.0885 time to fit residues: 10.2050 Evaluate side-chains 85 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 694 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 47 optimal weight: 6.9990 chunk 56 optimal weight: 0.0570 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 ASN A 634 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.194031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.147142 restraints weight = 7077.588| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.27 r_work: 0.3479 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6951 Z= 0.177 Angle : 0.523 7.014 9493 Z= 0.266 Chirality : 0.044 0.231 1072 Planarity : 0.004 0.040 1152 Dihedral : 12.333 122.048 1147 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.43 % Allowed : 7.70 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.31), residues: 776 helix: 1.45 (0.35), residues: 245 sheet: 0.09 (0.36), residues: 191 loop : -0.52 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 370 TYR 0.021 0.001 TYR A 804 PHE 0.018 0.001 PHE A 704 TRP 0.007 0.001 TRP A 435 HIS 0.009 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 6951) covalent geometry : angle 0.52336 / 0.27 ( 9493) hydrogen bonds : bond 0.04294 / 4.11 ( 277) hydrogen bonds : angle 4.94710 / 6.04 ( 820) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.186 Fit side-chains REVERT: A 99 ASN cc_start: 0.8142 (m110) cc_final: 0.7396 (m-40) REVERT: A 104 MET cc_start: 0.6477 (mmm) cc_final: 0.6040 (mmm) REVERT: A 355 LYS cc_start: 0.7401 (mptt) cc_final: 0.6978 (mttp) REVERT: A 429 THR cc_start: 0.9027 (m) cc_final: 0.8651 (p) REVERT: A 554 ARG cc_start: 0.7235 (ptm-80) cc_final: 0.6373 (mtm110) REVERT: A 694 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8069 (mp) outliers start: 10 outliers final: 7 residues processed: 95 average time/residue: 0.0801 time to fit residues: 9.7080 Evaluate side-chains 90 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 31 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 0.0170 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.194482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.148897 restraints weight = 7128.967| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.23 r_work: 0.3519 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6951 Z= 0.095 Angle : 0.460 6.075 9493 Z= 0.237 Chirality : 0.042 0.204 1072 Planarity : 0.004 0.041 1152 Dihedral : 12.379 120.869 1147 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.28 % Allowed : 8.56 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.31), residues: 776 helix: 1.60 (0.35), residues: 245 sheet: 0.11 (0.35), residues: 191 loop : -0.49 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 854 TYR 0.010 0.001 TYR A 55 PHE 0.008 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.007 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 ( 6951) covalent geometry : angle 0.45973 / 0.24 ( 9493) hydrogen bonds : bond 0.03439 / 3.32 ( 277) hydrogen bonds : angle 4.73376 / 5.84 ( 820) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.254 Fit side-chains REVERT: A 99 ASN cc_start: 0.8032 (m110) cc_final: 0.7298 (m-40) REVERT: A 104 MET cc_start: 0.6452 (mmm) cc_final: 0.6018 (mmm) REVERT: A 355 LYS cc_start: 0.7350 (mptt) cc_final: 0.6934 (mttp) REVERT: A 429 THR cc_start: 0.9012 (m) cc_final: 0.8649 (p) REVERT: A 694 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8052 (mp) REVERT: A 804 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.7563 (m-80) outliers start: 9 outliers final: 5 residues processed: 91 average time/residue: 0.0822 time to fit residues: 9.6921 Evaluate side-chains 86 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 804 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 0.0060 chunk 56 optimal weight: 0.4980 chunk 67 optimal weight: 0.8980 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.195372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.149119 restraints weight = 7124.047| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.29 r_work: 0.3499 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6951 Z= 0.128 Angle : 0.481 6.976 9493 Z= 0.245 Chirality : 0.042 0.224 1072 Planarity : 0.004 0.042 1152 Dihedral : 12.364 122.781 1147 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.28 % Allowed : 8.70 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.31), residues: 776 helix: 1.53 (0.35), residues: 245 sheet: 0.10 (0.35), residues: 191 loop : -0.49 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 854 TYR 0.009 0.001 TYR A 55 PHE 0.012 0.001 PHE A 704 TRP 0.007 0.001 TRP A 435 HIS 0.007 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 6951) covalent geometry : angle 0.48062 / 0.25 ( 9493) hydrogen bonds : bond 0.03699 / 3.55 ( 277) hydrogen bonds : angle 4.69697 / 5.81 ( 820) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.251 Fit side-chains REVERT: A 99 ASN cc_start: 0.8078 (m110) cc_final: 0.7325 (m-40) REVERT: A 104 MET cc_start: 0.6409 (mmm) cc_final: 0.5956 (mmm) REVERT: A 355 LYS cc_start: 0.7373 (mptt) cc_final: 0.6952 (mttp) REVERT: A 429 THR cc_start: 0.9022 (m) cc_final: 0.8678 (p) REVERT: A 554 ARG cc_start: 0.7230 (ptm-80) cc_final: 0.6339 (mtm110) REVERT: A 694 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8045 (mp) outliers start: 9 outliers final: 6 residues processed: 88 average time/residue: 0.0792 time to fit residues: 9.1355 Evaluate side-chains 88 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 694 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.197173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151122 restraints weight = 7010.099| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.55 r_work: 0.3512 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6951 Z= 0.097 Angle : 0.457 6.155 9493 Z= 0.234 Chirality : 0.042 0.212 1072 Planarity : 0.004 0.041 1152 Dihedral : 12.385 122.190 1147 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.43 % Allowed : 8.56 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.31), residues: 776 helix: 1.61 (0.35), residues: 245 sheet: 0.09 (0.35), residues: 189 loop : -0.47 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 854 TYR 0.009 0.001 TYR A 55 PHE 0.010 0.001 PHE A 491 TRP 0.008 0.001 TRP A 435 HIS 0.010 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 6951) covalent geometry : angle 0.45726 / 0.23 ( 9493) hydrogen bonds : bond 0.03301 / 3.19 ( 277) hydrogen bonds : angle 4.57296 / 5.71 ( 820) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.267 Fit side-chains REVERT: A 47 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8465 (mtp) REVERT: A 99 ASN cc_start: 0.8034 (m110) cc_final: 0.7296 (m-40) REVERT: A 104 MET cc_start: 0.6367 (mmm) cc_final: 0.5944 (mmm) REVERT: A 355 LYS cc_start: 0.7371 (mptt) cc_final: 0.6930 (mttp) REVERT: A 429 THR cc_start: 0.9026 (m) cc_final: 0.8740 (p) REVERT: A 554 ARG cc_start: 0.7241 (ptm-80) cc_final: 0.6339 (mtm110) REVERT: A 694 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8020 (mp) REVERT: A 804 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.7821 (m-80) outliers start: 10 outliers final: 5 residues processed: 90 average time/residue: 0.0730 time to fit residues: 8.5924 Evaluate side-chains 87 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 804 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.197150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.150381 restraints weight = 7120.110| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.32 r_work: 0.3521 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6951 Z= 0.100 Angle : 0.462 6.170 9493 Z= 0.236 Chirality : 0.042 0.215 1072 Planarity : 0.004 0.042 1152 Dihedral : 12.374 122.373 1147 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.28 % Allowed : 9.13 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.31), residues: 776 helix: 1.59 (0.35), residues: 245 sheet: 0.08 (0.35), residues: 189 loop : -0.47 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 854 TYR 0.008 0.001 TYR A 55 PHE 0.010 0.001 PHE A 491 TRP 0.008 0.001 TRP A 435 HIS 0.008 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 6951) covalent geometry : angle 0.46159 / 0.24 ( 9493) hydrogen bonds : bond 0.03283 / 3.17 ( 277) hydrogen bonds : angle 4.51400 / 5.65 ( 820) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.177 Fit side-chains REVERT: A 47 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8471 (mtp) REVERT: A 99 ASN cc_start: 0.8034 (m110) cc_final: 0.7295 (m-40) REVERT: A 104 MET cc_start: 0.6327 (mmm) cc_final: 0.5885 (mmm) REVERT: A 280 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7453 (ttt180) REVERT: A 355 LYS cc_start: 0.7367 (mptt) cc_final: 0.6927 (mttp) REVERT: A 429 THR cc_start: 0.9021 (m) cc_final: 0.8730 (p) REVERT: A 554 ARG cc_start: 0.7208 (ptm-80) cc_final: 0.6296 (mtm110) REVERT: A 638 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7483 (mt) REVERT: A 694 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8021 (mp) REVERT: A 804 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.7824 (m-80) outliers start: 9 outliers final: 4 residues processed: 87 average time/residue: 0.0893 time to fit residues: 9.9465 Evaluate side-chains 86 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 804 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 634 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.196710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.149795 restraints weight = 7100.682| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.32 r_work: 0.3513 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6951 Z= 0.108 Angle : 0.470 6.497 9493 Z= 0.240 Chirality : 0.042 0.220 1072 Planarity : 0.004 0.042 1152 Dihedral : 12.374 123.080 1147 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.43 % Allowed : 9.27 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.31), residues: 776 helix: 1.60 (0.35), residues: 245 sheet: 0.06 (0.35), residues: 189 loop : -0.48 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 854 TYR 0.007 0.001 TYR A 749 PHE 0.010 0.001 PHE A 491 TRP 0.007 0.001 TRP A 435 HIS 0.008 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 6951) covalent geometry : angle 0.47002 / 0.24 ( 9493) hydrogen bonds : bond 0.03360 / 3.25 ( 277) hydrogen bonds : angle 4.48444 / 5.62 ( 820) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.195 Fit side-chains REVERT: A 47 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8481 (mtp) REVERT: A 99 ASN cc_start: 0.8047 (m110) cc_final: 0.7304 (m-40) REVERT: A 355 LYS cc_start: 0.7377 (mptt) cc_final: 0.6944 (mttp) REVERT: A 429 THR cc_start: 0.9020 (m) cc_final: 0.8739 (p) REVERT: A 494 TYR cc_start: 0.8605 (m-80) cc_final: 0.8288 (m-80) REVERT: A 554 ARG cc_start: 0.7233 (ptm-80) cc_final: 0.6324 (mtm110) REVERT: A 638 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7456 (mt) REVERT: A 694 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8000 (mp) REVERT: A 804 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.7861 (m-80) outliers start: 10 outliers final: 6 residues processed: 88 average time/residue: 0.0978 time to fit residues: 10.9750 Evaluate side-chains 89 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 804 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.0060 chunk 72 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.195375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.150119 restraints weight = 7075.026| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.29 r_work: 0.3533 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6951 Z= 0.090 Angle : 0.458 6.255 9493 Z= 0.233 Chirality : 0.041 0.211 1072 Planarity : 0.004 0.044 1152 Dihedral : 12.378 122.297 1147 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.00 % Allowed : 9.84 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.31), residues: 776 helix: 1.65 (0.35), residues: 245 sheet: 0.06 (0.35), residues: 189 loop : -0.47 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 854 TYR 0.009 0.001 TYR A 393 PHE 0.009 0.001 PHE A 491 TRP 0.008 0.001 TRP A 435 HIS 0.007 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 6951) covalent geometry : angle 0.45776 / 0.23 ( 9493) hydrogen bonds : bond 0.03102 / 3.01 ( 277) hydrogen bonds : angle 4.40986 / 5.55 ( 820) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.172 Fit side-chains REVERT: A 47 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8483 (mtp) REVERT: A 99 ASN cc_start: 0.8023 (m110) cc_final: 0.7288 (m-40) REVERT: A 280 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7437 (ttt180) REVERT: A 355 LYS cc_start: 0.7366 (mptt) cc_final: 0.6931 (mttp) REVERT: A 429 THR cc_start: 0.9014 (m) cc_final: 0.8743 (p) REVERT: A 638 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7519 (mt) REVERT: A 694 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7990 (mp) REVERT: A 804 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.7936 (m-80) outliers start: 7 outliers final: 3 residues processed: 84 average time/residue: 0.0970 time to fit residues: 10.3272 Evaluate side-chains 85 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 804 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 61 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 634 HIS A 788 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.196068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.149555 restraints weight = 7011.419| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.54 r_work: 0.3525 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6951 Z= 0.096 Angle : 0.463 6.349 9493 Z= 0.236 Chirality : 0.042 0.213 1072 Planarity : 0.004 0.045 1152 Dihedral : 12.367 122.276 1147 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.00 % Allowed : 10.13 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.31), residues: 776 helix: 1.61 (0.34), residues: 245 sheet: 0.06 (0.35), residues: 189 loop : -0.50 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 854 TYR 0.008 0.001 TYR A 393 PHE 0.009 0.001 PHE A 491 TRP 0.008 0.001 TRP A 435 HIS 0.007 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 6951) covalent geometry : angle 0.46343 / 0.24 ( 9493) hydrogen bonds : bond 0.03148 / 3.05 ( 277) hydrogen bonds : angle 4.37659 / 5.52 ( 820) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2152.36 seconds wall clock time: 37 minutes 20.49 seconds (2240.49 seconds total)