Starting phenix.real_space_refine on Thu Jul 2 05:16:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10be_75039/07_2026/10be_75039.cif Found real_map, /net/cci-nas-00/data/ceres_data/10be_75039/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/10be_75039/07_2026/10be_75039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10be_75039/07_2026/10be_75039.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10be_75039/07_2026/10be_75039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10be_75039/07_2026/10be_75039.map" } 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): 0.01s 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: 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: 1.74, per 1000 atoms: 0.26 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: 0.43 Conformation dependent library (CDL) restraints added in 316.9 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: 0.45 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: 0.61 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=" 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 bond pdb=" N1 C C 12 " pdb=" C2 C C 12 " ideal model delta sigma weight residual 1.397 1.405 -0.008 1.00e-02 1.00e+04 6.14e-01 ... (remaining 6946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 9227 1.10 - 2.21: 178 2.21 - 3.31: 68 3.31 - 4.42: 14 4.42 - 5.52: 6 Bond angle restraints: 9493 Sorted by residual: 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=" CA LYS A 260 " pdb=" CB LYS A 260 " pdb=" CG LYS A 260 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.63e+00 angle pdb=" C3' U B 9 " pdb=" O3' U B 9 " pdb=" P U B 10 " ideal model delta sigma weight residual 120.20 124.14 -3.94 1.50e+00 4.44e-01 6.89e+00 angle pdb=" C1' C C 12 " pdb=" N1 C C 12 " pdb=" C6 C C 12 " ideal model delta sigma weight residual 120.80 117.87 2.93 1.20e+00 6.94e-01 5.97e+00 angle pdb=" C4' U B 9 " pdb=" C3' U B 9 " pdb=" O3' U B 9 " ideal model delta sigma weight residual 109.40 112.30 -2.90 1.50e+00 4.44e-01 3.73e+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: 659 0.027 - 0.054: 259 0.054 - 0.081: 73 0.081 - 0.108: 55 0.108 - 0.135: 26 Chirality restraints: 1072 Sorted by residual: chirality pdb=" CA ILE A 639 " pdb=" N ILE A 639 " pdb=" C ILE A 639 " pdb=" CB ILE A 639 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA PRO A 743 " pdb=" N PRO A 743 " pdb=" C PRO A 743 " pdb=" CB PRO A 743 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE A 269 " pdb=" N ILE A 269 " pdb=" C ILE A 269 " pdb=" CB ILE A 269 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-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: 8.590 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: 0.660 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.780 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.070 ------------------------------------------------------------------------------- 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= 0.104 Angle : 0.463 5.525 9493 Z= 0.256 Chirality : 0.040 0.135 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 0.00216 / 0.10 ( 6951) covalent geometry : angle 0.46286 / 0.26 ( 9493) hydrogen bonds : bond 0.18604 / 15.77 ( 277) hydrogen bonds : angle 7.58558 / 8.37 ( 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 : 0.164 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: 0.0794 time to fit residues: 9.5670 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 : 0.154 ------------------------------------------------------------------------------- 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 = 0.199502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.152744 restraints weight = 7115.862| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.33 r_work: 0.3588 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.0705 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= 0.121 Angle : 0.489 5.772 9493 Z= 0.255 Chirality : 0.042 0.150 1072 Planarity : 0.004 0.040 1152 Dihedral : 12.252 110.775 1147 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.33 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: 0.39 (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 0.004 0.000 ARG A 179 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 0.00270 / 0.12 ( 6951) covalent geometry : angle 0.48929 / 0.26 ( 9493) hydrogen bonds : bond 0.04251 / 3.67 ( 277) hydrogen bonds : angle 5.52759 / 6.47 ( 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 88 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.184 Fit side-chains REVERT: A 99 ASN cc_start: 0.7964 (m110) cc_final: 0.7267 (m-40) REVERT: A 279 TYR cc_start: 0.6828 (m-80) cc_final: 0.6570 (m-80) REVERT: A 355 LYS cc_start: 0.7231 (mptt) cc_final: 0.6821 (mttp) REVERT: A 694 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8103 (mp) outliers start: 3 outliers final: 1 residues processed: 86 average time/residue: 0.0781 time to fit residues: 8.7276 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 : 0.162 ------------------------------------------------------------------------------- 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: 30.0000 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.190065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.142908 restraints weight = 7037.071| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.26 r_work: 0.3462 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6951 Z= 0.212 Angle : 0.573 8.406 9493 Z= 0.296 Chirality : 0.045 0.191 1072 Planarity : 0.005 0.040 1152 Dihedral : 12.275 120.334 1147 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.28 % Allowed : 6.85 % Favored : 91.87 % 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: 0.18 (0.31), residues: 776 helix: 1.28 (0.34), residues: 245 sheet: -0.05 (0.36), residues: 191 loop : -0.54 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 370 TYR 0.021 0.002 TYR A 804 PHE 0.024 0.002 PHE A 704 TRP 0.009 0.002 TRP A 211 HIS 0.008 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 ( 6951) covalent geometry : angle 0.57269 / 0.30 ( 9493) hydrogen bonds : bond 0.05248 / 4.48 ( 277) hydrogen bonds : angle 5.25945 / 6.19 ( 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 99 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.157 Fit side-chains REVERT: A 47 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8610 (mtp) REVERT: A 99 ASN cc_start: 0.8192 (m110) cc_final: 0.7452 (m-40) REVERT: A 104 MET cc_start: 0.6489 (mmm) cc_final: 0.6076 (mmm) REVERT: A 355 LYS cc_start: 0.7428 (mptt) cc_final: 0.7000 (mttp) REVERT: A 429 THR cc_start: 0.9038 (m) cc_final: 0.8663 (p) REVERT: A 554 ARG cc_start: 0.7310 (ptm-80) cc_final: 0.6444 (mtm110) REVERT: A 694 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8117 (mp) outliers start: 9 outliers final: 6 residues processed: 95 average time/residue: 0.0785 time to fit residues: 9.5856 Evaluate side-chains 93 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 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 262 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 47 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.191442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144176 restraints weight = 7144.578| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.32 r_work: 0.3424 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6951 Z= 0.207 Angle : 0.539 7.288 9493 Z= 0.281 Chirality : 0.044 0.144 1072 Planarity : 0.005 0.043 1152 Dihedral : 12.429 125.776 1147 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.71 % Allowed : 8.27 % 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: 0.12 (0.31), residues: 776 helix: 1.29 (0.34), residues: 245 sheet: -0.14 (0.35), residues: 191 loop : -0.60 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 370 TYR 0.018 0.002 TYR A 804 PHE 0.019 0.002 PHE A 704 TRP 0.009 0.001 TRP A 435 HIS 0.007 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 ( 6951) covalent geometry : angle 0.53946 / 0.28 ( 9493) hydrogen bonds : bond 0.04533 / 4.01 ( 277) hydrogen bonds : angle 5.12117 / 6.08 ( 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: 12 poor density : 87 time to evaluate : 0.168 Fit side-chains REVERT: A 99 ASN cc_start: 0.8206 (m110) cc_final: 0.7474 (m-40) REVERT: A 104 MET cc_start: 0.6445 (mmm) cc_final: 0.6025 (mmm) REVERT: A 355 LYS cc_start: 0.7468 (mptt) cc_final: 0.7037 (mttp) REVERT: A 429 THR cc_start: 0.9035 (m) cc_final: 0.8713 (p) REVERT: A 554 ARG cc_start: 0.7335 (ptm-80) cc_final: 0.6536 (mtm110) REVERT: A 694 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8075 (mp) outliers start: 12 outliers final: 7 residues processed: 95 average time/residue: 0.0850 time to fit residues: 10.2007 Evaluate side-chains 89 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 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 180 SER 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 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: 1.9990 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.193727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.147036 restraints weight = 7157.858| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.31 r_work: 0.3455 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6951 Z= 0.123 Angle : 0.479 6.076 9493 Z= 0.250 Chirality : 0.042 0.156 1072 Planarity : 0.004 0.042 1152 Dihedral : 12.482 124.804 1147 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.57 % Allowed : 8.70 % Favored : 89.73 % 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: 0.27 (0.31), residues: 776 helix: 1.44 (0.35), residues: 245 sheet: -0.06 (0.36), residues: 191 loop : -0.54 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 370 TYR 0.009 0.001 TYR A 55 PHE 0.013 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.004 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 6951) covalent geometry : angle 0.47920 / 0.25 ( 9493) hydrogen bonds : bond 0.03822 / 3.38 ( 277) hydrogen bonds : angle 4.86975 / 5.85 ( 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 95 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.161 Fit side-chains REVERT: A 99 ASN cc_start: 0.8122 (m110) cc_final: 0.7381 (m-40) REVERT: A 104 MET cc_start: 0.6410 (mmm) cc_final: 0.5997 (mmm) REVERT: A 429 THR cc_start: 0.9039 (m) cc_final: 0.8736 (p) REVERT: A 554 ARG cc_start: 0.7263 (ptm-80) cc_final: 0.6449 (mtm110) REVERT: A 694 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8034 (mp) outliers start: 11 outliers final: 7 residues processed: 93 average time/residue: 0.0853 time to fit residues: 10.2157 Evaluate side-chains 88 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 412 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 694 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.195200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148635 restraints weight = 7176.053| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.37 r_work: 0.3476 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1753 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= 0.103 Angle : 0.462 4.986 9493 Z= 0.242 Chirality : 0.042 0.144 1072 Planarity : 0.004 0.042 1152 Dihedral : 12.484 123.727 1147 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.57 % Allowed : 9.13 % 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: 0.32 (0.31), residues: 776 helix: 1.49 (0.35), residues: 245 sheet: -0.04 (0.35), residues: 191 loop : -0.52 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 624 TYR 0.009 0.001 TYR A 55 PHE 0.010 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.013 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 6951) covalent geometry : angle 0.46218 / 0.24 ( 9493) hydrogen bonds : bond 0.03458 / 3.06 ( 277) hydrogen bonds : angle 4.72705 / 5.72 ( 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 97 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.262 Fit side-chains REVERT: A 99 ASN cc_start: 0.8071 (m110) cc_final: 0.7416 (m-40) REVERT: A 104 MET cc_start: 0.6381 (mmm) cc_final: 0.5965 (mmm) REVERT: A 429 THR cc_start: 0.9033 (m) cc_final: 0.8743 (p) REVERT: A 554 ARG cc_start: 0.7212 (ptm-80) cc_final: 0.6361 (mtm110) REVERT: A 694 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7974 (mp) outliers start: 11 outliers final: 6 residues processed: 94 average time/residue: 0.1113 time to fit residues: 13.3076 Evaluate side-chains 90 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 0.0870 chunk 61 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 316 HIS A 640 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.189468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142021 restraints weight = 7167.775| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.37 r_work: 0.3417 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 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 : 0.004 0.041 6951 Z= 0.191 Angle : 0.535 8.392 9493 Z= 0.278 Chirality : 0.044 0.153 1072 Planarity : 0.005 0.044 1152 Dihedral : 12.459 127.073 1147 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.85 % Allowed : 8.84 % 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: 0.21 (0.31), residues: 776 helix: 1.37 (0.35), residues: 245 sheet: -0.09 (0.35), residues: 191 loop : -0.56 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 370 TYR 0.011 0.001 TYR A 625 PHE 0.019 0.001 PHE A 704 TRP 0.007 0.001 TRP A 435 HIS 0.010 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 6951) covalent geometry : angle 0.53492 / 0.28 ( 9493) hydrogen bonds : bond 0.04291 / 3.78 ( 277) hydrogen bonds : angle 4.82040 / 5.81 ( 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 98 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.207 Fit side-chains REVERT: A 99 ASN cc_start: 0.8166 (m-40) cc_final: 0.7514 (m110) REVERT: A 104 MET cc_start: 0.6349 (mmm) cc_final: 0.5903 (mmm) REVERT: A 429 THR cc_start: 0.9039 (m) cc_final: 0.8703 (p) REVERT: A 554 ARG cc_start: 0.7374 (ptm-80) cc_final: 0.6480 (mtm110) REVERT: A 694 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7973 (mp) outliers start: 13 outliers final: 9 residues processed: 94 average time/residue: 0.0826 time to fit residues: 10.0151 Evaluate side-chains 94 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 180 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 718 THR 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: 9.9990 chunk 74 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 634 HIS A 640 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.194446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148083 restraints weight = 7151.603| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.32 r_work: 0.3488 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6951 Z= 0.100 Angle : 0.469 6.066 9493 Z= 0.246 Chirality : 0.042 0.140 1072 Planarity : 0.004 0.043 1152 Dihedral : 12.530 125.093 1147 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.23 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: 0.33 (0.31), residues: 776 helix: 1.53 (0.35), residues: 245 sheet: -0.05 (0.35), residues: 191 loop : -0.53 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 624 TYR 0.008 0.001 TYR A 393 PHE 0.010 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.010 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 6951) covalent geometry : angle 0.46927 / 0.25 ( 9493) hydrogen bonds : bond 0.03389 / 3.01 ( 277) hydrogen bonds : angle 4.62140 / 5.64 ( 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 95 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.207 Fit side-chains REVERT: A 47 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8479 (mtp) REVERT: A 99 ASN cc_start: 0.8043 (m-40) cc_final: 0.7337 (m-40) REVERT: A 104 MET cc_start: 0.6303 (mmm) cc_final: 0.5870 (mmm) REVERT: A 429 THR cc_start: 0.9032 (m) cc_final: 0.8753 (p) REVERT: A 554 ARG cc_start: 0.7281 (ptm-80) cc_final: 0.6427 (mtm110) REVERT: A 694 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7939 (mp) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 0.0879 time to fit residues: 10.3996 Evaluate side-chains 88 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 412 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 694 LEU 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: 4.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.192112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144990 restraints weight = 7234.587| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.42 r_work: 0.3455 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6951 Z= 0.129 Angle : 0.486 5.977 9493 Z= 0.253 Chirality : 0.042 0.146 1072 Planarity : 0.004 0.046 1152 Dihedral : 12.480 125.175 1147 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.43 % Allowed : 9.42 % 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: 0.30 (0.31), residues: 776 helix: 1.50 (0.35), residues: 245 sheet: -0.05 (0.35), residues: 191 loop : -0.54 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 624 TYR 0.007 0.001 TYR A 393 PHE 0.012 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 0.00301 / 0.13 ( 6951) covalent geometry : angle 0.48602 / 0.25 ( 9493) hydrogen bonds : bond 0.03579 / 3.18 ( 277) hydrogen bonds : angle 4.60965 / 5.64 ( 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 89 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.290 Fit side-chains REVERT: A 99 ASN cc_start: 0.8074 (m-40) cc_final: 0.7365 (m-40) REVERT: A 429 THR cc_start: 0.9040 (m) cc_final: 0.8768 (p) REVERT: A 554 ARG cc_start: 0.7321 (ptm-80) cc_final: 0.6463 (mtm110) REVERT: A 694 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7936 (mp) outliers start: 10 outliers final: 8 residues processed: 88 average time/residue: 0.0886 time to fit residues: 10.0193 Evaluate side-chains 88 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 412 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 694 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 558 GLN A 634 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.193664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.146653 restraints weight = 7198.725| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.48 r_work: 0.3479 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1950 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= 0.100 Angle : 0.464 5.380 9493 Z= 0.243 Chirality : 0.042 0.137 1072 Planarity : 0.004 0.044 1152 Dihedral : 12.511 123.699 1147 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.14 % Allowed : 9.84 % Favored : 89.02 % 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: 0.36 (0.31), residues: 776 helix: 1.57 (0.35), residues: 245 sheet: -0.05 (0.35), residues: 191 loop : -0.51 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 624 TYR 0.007 0.001 TYR A 174 PHE 0.009 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.015 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 6951) covalent geometry : angle 0.46384 / 0.24 ( 9493) hydrogen bonds : bond 0.03206 / 2.87 ( 277) hydrogen bonds : angle 4.49117 / 5.53 ( 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 90 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.279 Fit side-chains REVERT: A 47 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8411 (mtp) REVERT: A 99 ASN cc_start: 0.7920 (m-40) cc_final: 0.7183 (m-40) REVERT: A 173 ARG cc_start: 0.6520 (mtp180) cc_final: 0.5900 (tpt-90) REVERT: A 355 LYS cc_start: 0.7443 (mmtt) cc_final: 0.6851 (mttp) REVERT: A 429 THR cc_start: 0.8961 (m) cc_final: 0.8707 (p) REVERT: A 554 ARG cc_start: 0.7064 (ptm-80) cc_final: 0.6357 (mtm110) REVERT: A 694 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7969 (mp) outliers start: 8 outliers final: 6 residues processed: 89 average time/residue: 0.1094 time to fit residues: 12.4580 Evaluate side-chains 88 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 412 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 694 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 61 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.194851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.147873 restraints weight = 7208.407| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.38 r_work: 0.3498 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6951 Z= 0.098 Angle : 0.460 5.362 9493 Z= 0.240 Chirality : 0.042 0.145 1072 Planarity : 0.004 0.043 1152 Dihedral : 12.487 122.329 1147 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.14 % Allowed : 10.13 % Favored : 88.73 % 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: 0.40 (0.31), residues: 776 helix: 1.61 (0.35), residues: 245 sheet: -0.01 (0.36), residues: 191 loop : -0.50 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 624 TYR 0.007 0.001 TYR A 393 PHE 0.009 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.014 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 6951) covalent geometry : angle 0.46047 / 0.24 ( 9493) hydrogen bonds : bond 0.03119 / 2.80 ( 277) hydrogen bonds : angle 4.41999 / 5.45 ( 820) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2113.70 seconds wall clock time: 36 minutes 48.43 seconds (2208.43 seconds total)