Starting phenix.real_space_refine on Thu Jul 2 03:50:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dvu_27745/07_2026/8dvu_27745.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvu_27745/07_2026/8dvu_27745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dvu_27745/07_2026/8dvu_27745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvu_27745/07_2026/8dvu_27745.map" model { file = "/net/cci-nas-00/data/ceres_data/8dvu_27745/07_2026/8dvu_27745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvu_27745/07_2026/8dvu_27745.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dvu_27745/07_2026/8dvu_27745.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dvu_27745/07_2026/8dvu_27745.cif" } resolution = 2.9 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= 0.015 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 38 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3784 2.51 5 N 1059 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 47 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: 6170 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5375 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 25, 'TRANS': 643} Chain breaks: 1 Chain: "B" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 766 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 18} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4570 SG CYS A 810 36.881 19.714 31.150 1.00 7.69 S ATOM 4596 SG CYS A 813 34.935 16.553 31.282 1.00 10.45 S ATOM 4899 SG CYS A 864 36.768 16.868 27.740 1.00 13.54 S ATOM 4938 SG CYS A 869 33.961 19.186 29.142 1.00 16.27 S Time building chain proxies: 1.44, per 1000 atoms: 0.23 Number of scatterers: 6170 At special positions: 0 Unit cell: (94.218, 94.218, 71.238, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 33 16.00 P 38 15.00 Mg 1 11.99 O 1254 8.00 N 1059 7.00 C 3784 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: 0.62 Conformation dependent library (CDL) restraints added in 392.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 813 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " Number of angles added : 6 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1274 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 6 sheets defined 49.2% alpha, 9.1% beta 18 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.673A pdb=" N GLU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.629A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.792A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 381 through 395 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 469 through 491 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 506 through 522 removed outlier: 3.705A pdb=" N VAL A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 558 removed outlier: 3.650A pdb=" N GLU A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 578 removed outlier: 3.632A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 602 removed outlier: 3.929A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 649 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 746 through 769 Processing helix chain 'A' and resid 772 through 792 Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.750A pdb=" N THR A 260 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 294 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASP A 372 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE A 296 " --> pdb=" O ASP A 372 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR A 322 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 462 Processing sheet with id=AA3, first strand: chain 'A' and resid 658 through 661 removed outlier: 6.381A pdb=" N GLY A 659 " --> pdb=" O ILE A 695 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 6.821A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 832 through 833 removed outlier: 4.532A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 844 removed outlier: 6.277A pdb=" N CYS A 864 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP A 872 " --> pdb=" O CYS A 864 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1358 1.33 - 1.45: 1471 1.45 - 1.57: 3416 1.57 - 1.69: 73 1.69 - 1.81: 46 Bond restraints: 6364 Sorted by residual: bond pdb=" C GLU A 716 " pdb=" O GLU A 716 " ideal model delta sigma weight residual 1.233 1.212 0.021 1.30e-02 5.92e+03 2.59e+00 bond pdb=" C ASN A 625 " pdb=" O ASN A 625 " ideal model delta sigma weight residual 1.249 1.239 0.010 8.50e-03 1.38e+04 1.26e+00 bond pdb=" C4 ADP A1003 " pdb=" C5 ADP A1003 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.69e-01 bond pdb=" N GLU A 716 " pdb=" CA GLU A 716 " ideal model delta sigma weight residual 1.462 1.475 -0.013 1.46e-02 4.69e+03 7.81e-01 bond pdb=" CB PRO A 797 " pdb=" CG PRO A 797 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.35e-01 ... (remaining 6359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 8539 1.35 - 2.70: 176 2.70 - 4.06: 30 4.06 - 5.41: 12 5.41 - 6.76: 3 Bond angle restraints: 8760 Sorted by residual: angle pdb=" C GLY A 689 " pdb=" N ASP A 690 " pdb=" CA ASP A 690 " ideal model delta sigma weight residual 121.54 128.30 -6.76 1.91e+00 2.74e-01 1.25e+01 angle pdb=" C GLU A 716 " pdb=" CA GLU A 716 " pdb=" CB GLU A 716 " ideal model delta sigma weight residual 111.86 108.41 3.45 1.34e+00 5.57e-01 6.62e+00 angle pdb=" N ALA A 440 " pdb=" CA ALA A 440 " pdb=" C ALA A 440 " ideal model delta sigma weight residual 110.64 114.09 -3.45 1.48e+00 4.57e-01 5.44e+00 angle pdb=" CA PRO A 797 " pdb=" C PRO A 797 " pdb=" O PRO A 797 " ideal model delta sigma weight residual 121.38 119.63 1.75 7.70e-01 1.69e+00 5.17e+00 angle pdb=" CA VAL A 332 " pdb=" CB VAL A 332 " pdb=" CG1 VAL A 332 " ideal model delta sigma weight residual 110.40 114.15 -3.75 1.70e+00 3.46e-01 4.87e+00 ... (remaining 8755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 3459 16.62 - 33.23: 238 33.23 - 49.85: 70 49.85 - 66.46: 16 66.46 - 83.08: 11 Dihedral angle restraints: 3794 sinusoidal: 1832 harmonic: 1962 Sorted by residual: dihedral pdb=" O2A ADP A1003 " pdb=" O3A ADP A1003 " pdb=" PA ADP A1003 " pdb=" PB ADP A1003 " ideal model delta sinusoidal sigma weight residual -60.00 7.39 -67.39 1 2.00e+01 2.50e-03 1.48e+01 dihedral pdb=" CA LEU A 346 " pdb=" C LEU A 346 " pdb=" N THR A 347 " pdb=" CA THR A 347 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASP A 492 " pdb=" CB ASP A 492 " pdb=" CG ASP A 492 " pdb=" OD1 ASP A 492 " ideal model delta sinusoidal sigma weight residual -30.00 -87.59 57.59 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 3791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 683 0.032 - 0.064: 227 0.064 - 0.096: 64 0.096 - 0.128: 30 0.128 - 0.160: 4 Chirality restraints: 1008 Sorted by residual: chirality pdb=" CA GLU A 716 " pdb=" N GLU A 716 " pdb=" C GLU A 716 " pdb=" CB GLU A 716 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CB VAL A 332 " pdb=" CA VAL A 332 " pdb=" CG1 VAL A 332 " pdb=" CG2 VAL A 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CB ILE A 439 " pdb=" CA ILE A 439 " pdb=" CG1 ILE A 439 " pdb=" CG2 ILE A 439 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1005 not shown) Planarity restraints: 984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 716 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C GLU A 716 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU A 716 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 717 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 381 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.14e+00 pdb=" N PRO A 382 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 8 " -0.009 2.00e-02 2.50e+03 6.30e-03 8.92e-01 pdb=" N1 U B 8 " 0.016 2.00e-02 2.50e+03 pdb=" C2 U B 8 " -0.004 2.00e-02 2.50e+03 pdb=" O2 U B 8 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C5 U B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 8 " 0.000 2.00e-02 2.50e+03 ... (remaining 981 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 211 2.71 - 3.26: 5844 3.26 - 3.81: 10420 3.81 - 4.35: 13704 4.35 - 4.90: 21731 Nonbonded interactions: 51910 Sorted by model distance: nonbonded pdb="MG MG A1002 " pdb=" O2B ADP A1003 " model vdw 2.164 2.170 nonbonded pdb=" O CYS A 829 " pdb=" O2' G B 10 " model vdw 2.250 3.040 nonbonded pdb=" O SER A 378 " pdb=" ND2 ASN A 384 " model vdw 2.301 3.120 nonbonded pdb=" NZ LYS A 814 " pdb=" OE1 GLN A 902 " model vdw 2.308 3.120 nonbonded pdb=" NZ LYS A 458 " pdb=" OE2 GLU A 751 " model vdw 2.342 3.120 ... (remaining 51905 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.430 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:8.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 6368 Z= 0.130 Angle : 0.618 24.590 8766 Z= 0.297 Chirality : 0.038 0.160 1008 Planarity : 0.003 0.027 984 Dihedral : 13.391 83.078 2520 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.01 % Allowed : 10.55 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.23 (0.28), residues: 665 helix: -0.12 (0.27), residues: 316 sheet: -2.08 (0.47), residues: 92 loop : -2.99 (0.27), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 811 TYR 0.008 0.001 TYR A 390 PHE 0.008 0.001 PHE A 842 TRP 0.003 0.001 TRP A 908 HIS 0.002 0.000 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 ( 6364) covalent geometry : angle 0.51497 / 0.29 ( 8760) hydrogen bonds : bond 0.13589 / 8.81 ( 304) hydrogen bonds : angle 5.01460 / 3.40 ( 842) metal coordination : bond 0.07012 / 4.04 ( 4) metal coordination : angle 13.08373 / 9.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.311 Fit side-chains REVERT: A 369 MET cc_start: 0.9110 (mtm) cc_final: 0.8792 (mtm) REVERT: A 385 MET cc_start: 0.8671 (mmm) cc_final: 0.8470 (mmp) REVERT: A 492 ASP cc_start: 0.7216 (t70) cc_final: 0.6800 (t0) REVERT: A 498 GLN cc_start: 0.7766 (mm110) cc_final: 0.7544 (mp10) REVERT: A 560 MET cc_start: 0.8845 (mtt) cc_final: 0.8369 (mtt) REVERT: A 761 MET cc_start: 0.8748 (ttp) cc_final: 0.8516 (ttm) REVERT: A 786 HIS cc_start: 0.8184 (t70) cc_final: 0.7883 (t70) outliers start: 6 outliers final: 4 residues processed: 114 average time/residue: 0.5669 time to fit residues: 67.6641 Evaluate side-chains 84 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 800 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.0770 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 GLN A 393 GLN A 517 GLN A 588 GLN A 708 GLN A 769 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.129755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.109283 restraints weight = 6449.519| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.14 r_work: 0.3011 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6368 Z= 0.114 Angle : 0.508 6.494 8766 Z= 0.256 Chirality : 0.039 0.154 1008 Planarity : 0.003 0.030 984 Dihedral : 5.977 71.734 1160 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.35 % Allowed : 13.23 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.30), residues: 665 helix: 1.02 (0.28), residues: 320 sheet: -1.70 (0.48), residues: 93 loop : -2.50 (0.30), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 502 TYR 0.012 0.001 TYR A 390 PHE 0.008 0.001 PHE A 842 TRP 0.011 0.001 TRP A 771 HIS 0.003 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 6364) covalent geometry : angle 0.49850 / 0.26 ( 8760) hydrogen bonds : bond 0.03741 / 2.48 ( 304) hydrogen bonds : angle 3.64233 / 2.53 ( 842) metal coordination : bond 0.00851 / 0.47 ( 4) metal coordination : angle 3.80732 / 3.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.220 Fit side-chains REVERT: A 369 MET cc_start: 0.9240 (mtm) cc_final: 0.8959 (mtm) REVERT: A 385 MET cc_start: 0.8898 (mmm) cc_final: 0.8695 (mmp) REVERT: A 425 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7905 (m-30) REVERT: A 479 MET cc_start: 0.9250 (mtp) cc_final: 0.8876 (mtp) REVERT: A 492 ASP cc_start: 0.7253 (t70) cc_final: 0.6707 (t0) REVERT: A 498 GLN cc_start: 0.7978 (mm110) cc_final: 0.7502 (mp10) REVERT: A 560 MET cc_start: 0.8995 (mtt) cc_final: 0.8562 (mtt) REVERT: A 717 TYR cc_start: 0.8876 (t80) cc_final: 0.8664 (t80) REVERT: A 761 MET cc_start: 0.8730 (ttp) cc_final: 0.8417 (ttm) REVERT: A 786 HIS cc_start: 0.8331 (t70) cc_final: 0.8008 (t70) REVERT: A 883 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6325 (tm-30) REVERT: A 914 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7432 (tm-30) outliers start: 20 outliers final: 8 residues processed: 93 average time/residue: 0.5068 time to fit residues: 49.3998 Evaluate side-chains 88 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.128493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.108449 restraints weight = 6436.721| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.16 r_work: 0.2939 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6368 Z= 0.131 Angle : 0.526 6.039 8766 Z= 0.264 Chirality : 0.040 0.137 1008 Planarity : 0.003 0.031 984 Dihedral : 5.783 76.047 1154 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.18 % Allowed : 14.74 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 665 helix: 1.48 (0.29), residues: 321 sheet: -1.46 (0.48), residues: 89 loop : -2.36 (0.31), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 533 TYR 0.014 0.001 TYR A 390 PHE 0.009 0.001 PHE A 842 TRP 0.015 0.002 TRP A 771 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 6364) covalent geometry : angle 0.51863 / 0.26 ( 8760) hydrogen bonds : bond 0.03833 / 2.55 ( 304) hydrogen bonds : angle 3.58512 / 2.50 ( 842) metal coordination : bond 0.00613 / 0.31 ( 4) metal coordination : angle 3.34620 / 2.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.227 Fit side-chains REVERT: A 369 MET cc_start: 0.9204 (mtm) cc_final: 0.8917 (mtm) REVERT: A 425 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8039 (m-30) REVERT: A 479 MET cc_start: 0.9257 (mtp) cc_final: 0.8860 (mtp) REVERT: A 492 ASP cc_start: 0.7222 (t70) cc_final: 0.6625 (t0) REVERT: A 498 GLN cc_start: 0.8090 (mm110) cc_final: 0.7589 (mp10) REVERT: A 560 MET cc_start: 0.9061 (mtt) cc_final: 0.8578 (mtt) REVERT: A 679 LYS cc_start: 0.8599 (tttt) cc_final: 0.7606 (mttp) REVERT: A 708 GLN cc_start: 0.8431 (mt0) cc_final: 0.8163 (mt0) REVERT: A 761 MET cc_start: 0.8908 (ttp) cc_final: 0.8517 (ttm) REVERT: A 786 HIS cc_start: 0.8371 (t70) cc_final: 0.8057 (t70) REVERT: A 906 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8730 (p) REVERT: A 914 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7557 (tm-30) outliers start: 19 outliers final: 8 residues processed: 91 average time/residue: 0.5285 time to fit residues: 50.4228 Evaluate side-chains 86 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 36 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3286 r_free = 0.3286 target = 0.123464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.104337 restraints weight = 6409.383| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 0.94 r_work: 0.3015 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6368 Z= 0.188 Angle : 0.586 6.139 8766 Z= 0.294 Chirality : 0.043 0.160 1008 Planarity : 0.004 0.033 984 Dihedral : 6.194 86.735 1154 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.85 % Allowed : 14.07 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 665 helix: 1.48 (0.29), residues: 321 sheet: -1.14 (0.50), residues: 89 loop : -2.34 (0.31), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 533 TYR 0.016 0.002 TYR A 717 PHE 0.010 0.001 PHE A 842 TRP 0.006 0.002 TRP A 908 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 ( 6364) covalent geometry : angle 0.58027 / 0.29 ( 8760) hydrogen bonds : bond 0.04441 / 2.94 ( 304) hydrogen bonds : angle 3.68805 / 2.55 ( 842) metal coordination : bond 0.00690 / 0.34 ( 4) metal coordination : angle 3.24516 / 2.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.163 Fit side-chains REVERT: A 369 MET cc_start: 0.9197 (mtm) cc_final: 0.8923 (mtm) REVERT: A 425 ASP cc_start: 0.8354 (m-30) cc_final: 0.8084 (m-30) REVERT: A 492 ASP cc_start: 0.7370 (t70) cc_final: 0.6819 (t70) REVERT: A 498 GLN cc_start: 0.7986 (mm110) cc_final: 0.7562 (mp10) REVERT: A 560 MET cc_start: 0.9097 (mtt) cc_final: 0.8640 (mtt) REVERT: A 679 LYS cc_start: 0.8636 (tttt) cc_final: 0.7728 (mttp) REVERT: A 708 GLN cc_start: 0.8415 (mt0) cc_final: 0.8155 (mt0) REVERT: A 761 MET cc_start: 0.9056 (ttp) cc_final: 0.8664 (ttm) REVERT: A 786 HIS cc_start: 0.8443 (t70) cc_final: 0.8152 (t70) REVERT: A 906 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8829 (p) REVERT: A 914 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7377 (tm-30) outliers start: 23 outliers final: 10 residues processed: 89 average time/residue: 0.5301 time to fit residues: 49.5311 Evaluate side-chains 89 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 0.1980 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 588 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.128612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.107915 restraints weight = 6532.349| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.14 r_work: 0.2978 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6368 Z= 0.102 Angle : 0.494 6.622 8766 Z= 0.248 Chirality : 0.039 0.135 1008 Planarity : 0.003 0.036 984 Dihedral : 5.879 77.665 1154 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.35 % Allowed : 15.08 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.32), residues: 665 helix: 1.97 (0.29), residues: 321 sheet: -0.83 (0.53), residues: 93 loop : -2.17 (0.32), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 533 TYR 0.010 0.001 TYR A 717 PHE 0.009 0.001 PHE A 842 TRP 0.010 0.001 TRP A 771 HIS 0.002 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 6364) covalent geometry : angle 0.48923 / 0.25 ( 8760) hydrogen bonds : bond 0.03354 / 2.25 ( 304) hydrogen bonds : angle 3.46030 / 2.39 ( 842) metal coordination : bond 0.00463 / 0.24 ( 4) metal coordination : angle 2.77313 / 2.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.221 Fit side-chains REVERT: A 312 LYS cc_start: 0.7942 (mtmm) cc_final: 0.7538 (mtmm) REVERT: A 425 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: A 479 MET cc_start: 0.9212 (mtp) cc_final: 0.8781 (mtp) REVERT: A 492 ASP cc_start: 0.7021 (t70) cc_final: 0.6135 (t0) REVERT: A 498 GLN cc_start: 0.7944 (mm110) cc_final: 0.7495 (mp10) REVERT: A 560 MET cc_start: 0.9030 (mtt) cc_final: 0.8577 (mtt) REVERT: A 679 LYS cc_start: 0.8461 (tttt) cc_final: 0.7469 (mttp) REVERT: A 708 GLN cc_start: 0.8324 (mt0) cc_final: 0.8080 (mt0) REVERT: A 761 MET cc_start: 0.8812 (ttp) cc_final: 0.8390 (ttm) REVERT: A 786 HIS cc_start: 0.8290 (t70) cc_final: 0.7982 (t70) REVERT: A 906 SER cc_start: 0.9087 (OUTLIER) cc_final: 0.8769 (p) REVERT: A 914 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7206 (tt0) outliers start: 20 outliers final: 8 residues processed: 93 average time/residue: 0.6056 time to fit residues: 59.0230 Evaluate side-chains 89 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 867 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.126786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.108316 restraints weight = 6495.717| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.04 r_work: 0.2954 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6368 Z= 0.122 Angle : 0.516 7.172 8766 Z= 0.258 Chirality : 0.039 0.155 1008 Planarity : 0.003 0.034 984 Dihedral : 5.845 79.185 1153 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.69 % Allowed : 15.91 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.32), residues: 665 helix: 2.03 (0.29), residues: 321 sheet: -0.65 (0.52), residues: 96 loop : -2.05 (0.33), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 533 TYR 0.014 0.001 TYR A 717 PHE 0.009 0.001 PHE A 842 TRP 0.018 0.002 TRP A 771 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 6364) covalent geometry : angle 0.51069 / 0.26 ( 8760) hydrogen bonds : bond 0.03576 / 2.39 ( 304) hydrogen bonds : angle 3.45266 / 2.38 ( 842) metal coordination : bond 0.00541 / 0.28 ( 4) metal coordination : angle 2.95154 / 2.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.291 Fit side-chains REVERT: A 312 LYS cc_start: 0.8009 (mtmm) cc_final: 0.7553 (mtmm) REVERT: A 425 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: A 479 MET cc_start: 0.9240 (mtp) cc_final: 0.8872 (mtp) REVERT: A 492 ASP cc_start: 0.7059 (t70) cc_final: 0.6187 (t0) REVERT: A 498 GLN cc_start: 0.8007 (mm110) cc_final: 0.7564 (mp10) REVERT: A 560 MET cc_start: 0.9089 (mtt) cc_final: 0.8671 (mtt) REVERT: A 679 LYS cc_start: 0.8529 (tttt) cc_final: 0.7527 (mttp) REVERT: A 708 GLN cc_start: 0.8394 (mt0) cc_final: 0.8143 (mt0) REVERT: A 761 MET cc_start: 0.8932 (ttp) cc_final: 0.8542 (ttm) REVERT: A 786 HIS cc_start: 0.8362 (t70) cc_final: 0.8070 (t70) REVERT: A 906 SER cc_start: 0.9082 (OUTLIER) cc_final: 0.8785 (p) REVERT: A 914 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7445 (tm-30) outliers start: 22 outliers final: 10 residues processed: 89 average time/residue: 0.5238 time to fit residues: 49.0023 Evaluate side-chains 88 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN A 588 GLN A 867 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.122970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.103252 restraints weight = 6466.283| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.00 r_work: 0.2926 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6368 Z= 0.190 Angle : 0.592 7.593 8766 Z= 0.295 Chirality : 0.043 0.197 1008 Planarity : 0.004 0.033 984 Dihedral : 6.257 90.850 1153 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.35 % Allowed : 16.75 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.32), residues: 665 helix: 1.81 (0.29), residues: 321 sheet: -0.69 (0.54), residues: 84 loop : -2.05 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 533 TYR 0.021 0.002 TYR A 717 PHE 0.010 0.001 PHE A 842 TRP 0.006 0.001 TRP A 908 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 ( 6364) covalent geometry : angle 0.58619 / 0.29 ( 8760) hydrogen bonds : bond 0.04400 / 2.92 ( 304) hydrogen bonds : angle 3.63888 / 2.51 ( 842) metal coordination : bond 0.00712 / 0.37 ( 4) metal coordination : angle 3.14454 / 2.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.166 Fit side-chains REVERT: A 425 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: A 492 ASP cc_start: 0.7216 (t70) cc_final: 0.6291 (t0) REVERT: A 560 MET cc_start: 0.9089 (mtt) cc_final: 0.8629 (mtt) REVERT: A 708 GLN cc_start: 0.8426 (mt0) cc_final: 0.8164 (mt0) REVERT: A 761 MET cc_start: 0.8986 (ttp) cc_final: 0.8568 (ttm) REVERT: A 786 HIS cc_start: 0.8379 (t70) cc_final: 0.8083 (t70) REVERT: A 906 SER cc_start: 0.9157 (OUTLIER) cc_final: 0.8845 (p) REVERT: A 914 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7453 (tm-30) outliers start: 20 outliers final: 10 residues processed: 81 average time/residue: 0.5361 time to fit residues: 45.5000 Evaluate side-chains 82 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN A 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.124979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.106019 restraints weight = 6481.136| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 0.96 r_work: 0.2952 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6368 Z= 0.132 Angle : 0.538 7.601 8766 Z= 0.268 Chirality : 0.040 0.199 1008 Planarity : 0.003 0.035 984 Dihedral : 6.118 88.283 1153 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.02 % Allowed : 16.75 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.32), residues: 665 helix: 1.98 (0.29), residues: 321 sheet: -0.57 (0.53), residues: 96 loop : -1.95 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 533 TYR 0.017 0.002 TYR A 717 PHE 0.009 0.001 PHE A 842 TRP 0.004 0.001 TRP A 908 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 6364) covalent geometry : angle 0.53284 / 0.27 ( 8760) hydrogen bonds : bond 0.03784 / 2.53 ( 304) hydrogen bonds : angle 3.53513 / 2.43 ( 842) metal coordination : bond 0.00572 / 0.29 ( 4) metal coordination : angle 2.92373 / 2.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.245 Fit side-chains REVERT: A 425 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: A 492 ASP cc_start: 0.7128 (t70) cc_final: 0.6249 (t0) REVERT: A 560 MET cc_start: 0.9075 (mtt) cc_final: 0.8547 (mtt) REVERT: A 679 LYS cc_start: 0.8530 (tttt) cc_final: 0.7552 (mttp) REVERT: A 708 GLN cc_start: 0.8416 (mt0) cc_final: 0.8163 (mt0) REVERT: A 761 MET cc_start: 0.8947 (ttp) cc_final: 0.8543 (ttm) REVERT: A 786 HIS cc_start: 0.8337 (t70) cc_final: 0.7999 (t70) REVERT: A 906 SER cc_start: 0.9065 (OUTLIER) cc_final: 0.8771 (p) REVERT: A 914 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7143 (tt0) outliers start: 18 outliers final: 11 residues processed: 82 average time/residue: 0.5887 time to fit residues: 50.6080 Evaluate side-chains 83 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 0.0010 chunk 3 optimal weight: 0.6980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN A 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.126249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.105847 restraints weight = 6428.509| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.12 r_work: 0.2957 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6368 Z= 0.122 Angle : 0.527 8.106 8766 Z= 0.263 Chirality : 0.040 0.195 1008 Planarity : 0.003 0.035 984 Dihedral : 6.028 85.640 1153 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.18 % Allowed : 16.58 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.32), residues: 665 helix: 2.09 (0.29), residues: 321 sheet: -0.52 (0.53), residues: 96 loop : -1.89 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 533 TYR 0.015 0.001 TYR A 717 PHE 0.009 0.001 PHE A 842 TRP 0.004 0.001 TRP A 771 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 6364) covalent geometry : angle 0.52272 / 0.26 ( 8760) hydrogen bonds : bond 0.03609 / 2.42 ( 304) hydrogen bonds : angle 3.48710 / 2.40 ( 842) metal coordination : bond 0.00527 / 0.27 ( 4) metal coordination : angle 2.73780 / 2.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.237 Fit side-chains REVERT: A 312 LYS cc_start: 0.7880 (mtmm) cc_final: 0.7018 (mmtm) REVERT: A 425 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: A 492 ASP cc_start: 0.7054 (t70) cc_final: 0.6152 (t0) REVERT: A 560 MET cc_start: 0.9056 (mtt) cc_final: 0.8542 (mtt) REVERT: A 679 LYS cc_start: 0.8491 (tttt) cc_final: 0.7486 (mttp) REVERT: A 708 GLN cc_start: 0.8406 (mt0) cc_final: 0.8142 (mt0) REVERT: A 761 MET cc_start: 0.8894 (ttp) cc_final: 0.8475 (ttm) REVERT: A 786 HIS cc_start: 0.8311 (t70) cc_final: 0.8012 (t70) REVERT: A 906 SER cc_start: 0.9065 (OUTLIER) cc_final: 0.8748 (p) REVERT: A 914 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7119 (tt0) outliers start: 19 outliers final: 12 residues processed: 84 average time/residue: 0.5553 time to fit residues: 48.7985 Evaluate side-chains 89 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN A 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.126197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.106177 restraints weight = 6458.072| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.16 r_work: 0.2929 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6368 Z= 0.126 Angle : 0.536 7.982 8766 Z= 0.267 Chirality : 0.040 0.194 1008 Planarity : 0.003 0.035 984 Dihedral : 6.017 85.518 1153 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.51 % Allowed : 17.25 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.32), residues: 665 helix: 2.10 (0.29), residues: 321 sheet: -0.52 (0.53), residues: 96 loop : -1.87 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 533 TYR 0.019 0.002 TYR A 717 PHE 0.009 0.001 PHE A 842 TRP 0.004 0.001 TRP A 908 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 6364) covalent geometry : angle 0.53116 / 0.27 ( 8760) hydrogen bonds : bond 0.03661 / 2.46 ( 304) hydrogen bonds : angle 3.48194 / 2.39 ( 842) metal coordination : bond 0.00508 / 0.26 ( 4) metal coordination : angle 2.68644 / 2.17 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.222 Fit side-chains REVERT: A 312 LYS cc_start: 0.7933 (mtmm) cc_final: 0.7079 (mmtm) REVERT: A 425 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: A 479 MET cc_start: 0.9207 (mtp) cc_final: 0.8882 (mtp) REVERT: A 492 ASP cc_start: 0.7040 (t70) cc_final: 0.6127 (t0) REVERT: A 560 MET cc_start: 0.9085 (mtt) cc_final: 0.8579 (mtt) REVERT: A 679 LYS cc_start: 0.8547 (tttt) cc_final: 0.7560 (mttp) REVERT: A 708 GLN cc_start: 0.8420 (mt0) cc_final: 0.8155 (mt0) REVERT: A 761 MET cc_start: 0.8933 (ttp) cc_final: 0.8528 (ttm) REVERT: A 786 HIS cc_start: 0.8369 (t70) cc_final: 0.8074 (t70) REVERT: A 906 SER cc_start: 0.9080 (OUTLIER) cc_final: 0.8771 (p) REVERT: A 914 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7173 (tt0) outliers start: 15 outliers final: 11 residues processed: 78 average time/residue: 0.5463 time to fit residues: 44.6738 Evaluate side-chains 84 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 914 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 56 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 55 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.126079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.105981 restraints weight = 6440.277| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.17 r_work: 0.2934 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6368 Z= 0.129 Angle : 0.538 8.216 8766 Z= 0.268 Chirality : 0.040 0.189 1008 Planarity : 0.003 0.035 984 Dihedral : 6.024 85.536 1153 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.85 % Allowed : 16.92 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.32), residues: 665 helix: 2.12 (0.28), residues: 321 sheet: -0.54 (0.53), residues: 96 loop : -1.86 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 533 TYR 0.022 0.002 TYR A 717 PHE 0.009 0.001 PHE A 842 TRP 0.004 0.001 TRP A 908 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 6364) covalent geometry : angle 0.53379 / 0.27 ( 8760) hydrogen bonds : bond 0.03681 / 2.47 ( 304) hydrogen bonds : angle 3.48069 / 2.39 ( 842) metal coordination : bond 0.00498 / 0.26 ( 4) metal coordination : angle 2.68688 / 2.18 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1986.73 seconds wall clock time: 34 minutes 38.92 seconds (2078.92 seconds total)