Starting phenix.real_space_refine on Fri Sep 11 01:19:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dvu_27745/09_2026/8dvu_27745.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvu_27745/09_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_27745/09_2026/8dvu_27745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvu_27745/09_2026/8dvu_27745.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dvu_27745/09_2026/8dvu_27745.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dvu_27745/09_2026/8dvu_27745.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dvu_27745/09_2026/8dvu_27745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvu_27745/09_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-2.2.1-6174/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: {'RNAv2': 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: 1.42, 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: 0.50 Conformation dependent library (CDL) restraints added in 363.4 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: 1.13 Time building geometry restraints manager: 0.65 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: 8463 1.35 - 2.70: 223 2.70 - 4.06: 59 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: 3421 16.62 - 33.23: 240 33.23 - 49.85: 104 49.85 - 66.46: 18 66.46 - 83.08: 11 Dihedral angle restraints: 3794 sinusoidal: 1832 harmonic: 1962 Sorted by residual: dihedral pdb=" O5' U B 8 " pdb=" C5' U B 8 " pdb=" C4' U B 8 " pdb=" C3' U B 8 " ideal model delta sinusoidal sigma weight residual 180.00 157.25 22.75 3 6.40e+00 2.44e-02 1.64e+01 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 ... (remaining 3791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 802 0.048 - 0.097: 137 0.097 - 0.145: 32 0.145 - 0.193: 2 0.193 - 0.241: 35 Chirality restraints: 1008 Sorted by residual: chirality pdb=" P U B 58 " pdb=" OP1 U B 58 " pdb=" OP2 U B 58 " pdb=" O5' U B 58 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" P G B 6 " pdb=" OP1 G B 6 " pdb=" OP2 G B 6 " pdb=" O5' G B 6 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" P C B 23 " pdb=" OP1 C B 23 " pdb=" OP2 C B 23 " pdb=" O5' C B 23 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (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: 0.370 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.710 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.500 ------------------------------------------------------------------------------- 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= 0.133 Angle : 0.672 24.590 8766 Z= 0.308 Chirality : 0.057 0.241 1008 Planarity : 0.003 0.027 984 Dihedral : 14.357 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 0.00232 / 0.12 ( 6364) covalent geometry : angle 0.57802 / 0.30 ( 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 : 0.220 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: 0.5969 time to fit residues: 70.9896 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 : 0.138 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.129526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.108998 restraints weight = 6451.041| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.13 r_work: 0.2995 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1250 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= 0.116 Angle : 0.560 6.408 8766 Z= 0.264 Chirality : 0.045 0.154 1008 Planarity : 0.003 0.030 984 Dihedral : 9.186 71.679 1160 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.18 % Allowed : 13.40 % 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: -1.00 (0.30), residues: 665 helix: 1.01 (0.28), residues: 320 sheet: -1.69 (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 0.011 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 0.00264 / 0.12 ( 6364) covalent geometry : angle 0.55110 / 0.26 ( 8760) hydrogen bonds : bond 0.03799 / 2.53 ( 304) hydrogen bonds : angle 3.64265 / 2.53 ( 842) metal coordination : bond 0.00713 / 0.36 ( 4) metal coordination : angle 3.79575 / 2.98 ( 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 103 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.242 Fit side-chains REVERT: A 369 MET cc_start: 0.9240 (mtm) cc_final: 0.8962 (mtm) REVERT: A 385 MET cc_start: 0.8915 (mmm) cc_final: 0.8706 (mmp) REVERT: A 425 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: A 479 MET cc_start: 0.9257 (mtp) cc_final: 0.8882 (mtp) REVERT: A 492 ASP cc_start: 0.7257 (t70) cc_final: 0.6720 (t0) REVERT: A 498 GLN cc_start: 0.7989 (mm110) cc_final: 0.7517 (mp10) REVERT: A 560 MET cc_start: 0.9002 (mtt) cc_final: 0.8513 (mtt) REVERT: A 761 MET cc_start: 0.8743 (ttp) cc_final: 0.8432 (ttm) REVERT: A 786 HIS cc_start: 0.8348 (t70) cc_final: 0.8029 (t70) REVERT: A 883 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.6316 (tm-30) REVERT: A 914 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7463 (tm-30) outliers start: 19 outliers final: 7 residues processed: 91 average time/residue: 0.5507 time to fit residues: 52.5537 Evaluate side-chains 88 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 0.0010 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 chunk 30 optimal weight: 1.9990 overall best weight: 1.0090 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.127071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.107812 restraints weight = 6460.013| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 0.99 r_work: 0.2972 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1580 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= 0.136 Angle : 0.585 6.155 8766 Z= 0.274 Chirality : 0.046 0.166 1008 Planarity : 0.003 0.031 984 Dihedral : 8.988 76.414 1154 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % 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: -0.53 (0.31), residues: 665 helix: 1.45 (0.29), residues: 321 sheet: -1.47 (0.48), residues: 89 loop : -2.37 (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 0.005 0.001 TRP A 771 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 6364) covalent geometry : angle 0.57889 / 0.27 ( 8760) hydrogen bonds : bond 0.03858 / 2.57 ( 304) hydrogen bonds : angle 3.58710 / 2.50 ( 842) metal coordination : bond 0.00601 / 0.31 ( 4) metal coordination : angle 3.33230 / 2.59 ( 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 99 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.229 Fit side-chains REVERT: A 369 MET cc_start: 0.9178 (mtm) cc_final: 0.8886 (mtm) REVERT: A 425 ASP cc_start: 0.8279 (m-30) cc_final: 0.7977 (m-30) REVERT: A 479 MET cc_start: 0.9238 (mtp) cc_final: 0.8829 (mtp) REVERT: A 492 ASP cc_start: 0.7246 (t70) cc_final: 0.6671 (t0) REVERT: A 498 GLN cc_start: 0.7983 (mm110) cc_final: 0.7528 (mp10) REVERT: A 560 MET cc_start: 0.9048 (mtt) cc_final: 0.8565 (mtt) REVERT: A 679 LYS cc_start: 0.8580 (tttt) cc_final: 0.7609 (mttp) REVERT: A 708 GLN cc_start: 0.8438 (mt0) cc_final: 0.8169 (mt0) REVERT: A 761 MET cc_start: 0.8932 (ttp) cc_final: 0.8531 (ttm) REVERT: A 786 HIS cc_start: 0.8363 (t70) cc_final: 0.8049 (t70) REVERT: A 906 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8716 (p) REVERT: A 914 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7499 (tm-30) outliers start: 19 outliers final: 9 residues processed: 90 average time/residue: 0.5810 time to fit residues: 54.8109 Evaluate side-chains 87 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 491 LYS 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 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: 0.0470 chunk 41 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- 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 = 0.3294 r_free = 0.3294 target = 0.124069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.103021 restraints weight = 6407.771| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.15 r_work: 0.2919 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6368 Z= 0.203 Angle : 0.658 6.165 8766 Z= 0.309 Chirality : 0.050 0.190 1008 Planarity : 0.004 0.033 984 Dihedral : 9.253 88.441 1154 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.85 % Allowed : 13.74 % Favored : 82.41 % 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: -0.48 (0.31), residues: 665 helix: 1.42 (0.29), residues: 321 sheet: -1.18 (0.50), residues: 89 loop : -2.35 (0.31), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 533 TYR 0.018 0.002 TYR A 717 PHE 0.010 0.002 PHE A 842 TRP 0.014 0.002 TRP A 771 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.20 ( 6364) covalent geometry : angle 0.65307 / 0.31 ( 8760) hydrogen bonds : bond 0.04574 / 3.02 ( 304) hydrogen bonds : angle 3.71163 / 2.57 ( 842) metal coordination : bond 0.00652 / 0.33 ( 4) metal coordination : angle 3.26745 / 2.64 ( 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 : 0.226 Fit side-chains REVERT: A 369 MET cc_start: 0.9223 (mtm) cc_final: 0.8952 (mtm) REVERT: A 425 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8037 (m-30) REVERT: A 492 ASP cc_start: 0.7283 (t70) cc_final: 0.6715 (t70) REVERT: A 498 GLN cc_start: 0.7963 (mm110) cc_final: 0.7520 (mp10) REVERT: A 560 MET cc_start: 0.9082 (mtt) cc_final: 0.8630 (mtt) REVERT: A 708 GLN cc_start: 0.8414 (mt0) cc_final: 0.8152 (mt0) REVERT: A 761 MET cc_start: 0.9015 (ttp) cc_final: 0.8612 (ttm) REVERT: A 786 HIS cc_start: 0.8399 (t70) cc_final: 0.8103 (t70) REVERT: A 906 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8838 (p) REVERT: A 914 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7446 (tm-30) outliers start: 23 outliers final: 9 residues processed: 88 average time/residue: 0.5795 time to fit residues: 53.5085 Evaluate side-chains 87 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 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 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: 0.0040 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 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 = 0.3321 r_free = 0.3321 target = 0.126168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.106638 restraints weight = 6548.149| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 0.99 r_work: 0.2957 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1843 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= 0.120 Angle : 0.576 6.507 8766 Z= 0.269 Chirality : 0.046 0.174 1008 Planarity : 0.003 0.036 984 Dihedral : 9.083 82.864 1154 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.69 % Allowed : 15.08 % Favored : 81.24 % 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: -0.02 (0.32), residues: 665 helix: 1.83 (0.29), residues: 321 sheet: -0.98 (0.50), residues: 101 loop : -2.20 (0.33), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 533 TYR 0.012 0.001 TYR A 717 PHE 0.009 0.001 PHE A 842 TRP 0.003 0.001 TRP A 771 HIS 0.004 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 6364) covalent geometry : angle 0.57130 / 0.27 ( 8760) hydrogen bonds : bond 0.03631 / 2.42 ( 304) hydrogen bonds : angle 3.52724 / 2.43 ( 842) metal coordination : bond 0.00566 / 0.29 ( 4) metal coordination : angle 2.96799 / 2.40 ( 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 102 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.186 Fit side-chains REVERT: A 312 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7583 (mtmm) REVERT: A 425 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: A 492 ASP cc_start: 0.7192 (t70) cc_final: 0.6604 (t70) REVERT: A 560 MET cc_start: 0.9063 (mtt) cc_final: 0.8559 (mtt) REVERT: A 679 LYS cc_start: 0.8576 (tttt) cc_final: 0.7627 (mttp) REVERT: A 708 GLN cc_start: 0.8403 (mt0) cc_final: 0.8165 (mt0) REVERT: A 761 MET cc_start: 0.8935 (ttp) cc_final: 0.8523 (ttm) REVERT: A 786 HIS cc_start: 0.8360 (t70) cc_final: 0.8063 (t70) REVERT: A 906 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8802 (p) REVERT: A 914 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7240 (tt0) outliers start: 22 outliers final: 10 residues processed: 91 average time/residue: 0.6139 time to fit residues: 58.4856 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 : 0.182 ------------------------------------------------------------------------------- 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 467 ILE Chi-restraints excluded: chain A residue 525 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 GLN A 336 GLN A 588 GLN A 867 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.125873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.105190 restraints weight = 6491.099| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.14 r_work: 0.2972 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1878 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= 0.123 Angle : 0.578 7.076 8766 Z= 0.269 Chirality : 0.046 0.171 1008 Planarity : 0.003 0.036 984 Dihedral : 9.011 81.947 1154 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.52 % Allowed : 15.58 % Favored : 80.90 % 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: 0.24 (0.32), residues: 665 helix: 1.99 (0.29), residues: 321 sheet: -0.73 (0.52), residues: 96 loop : -2.02 (0.33), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 533 TYR 0.016 0.001 TYR A 717 PHE 0.009 0.001 PHE A 842 TRP 0.003 0.001 TRP A 512 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 6364) covalent geometry : angle 0.57293 / 0.27 ( 8760) hydrogen bonds : bond 0.03608 / 2.41 ( 304) hydrogen bonds : angle 3.46376 / 2.39 ( 842) metal coordination : bond 0.00545 / 0.29 ( 4) metal coordination : angle 2.94257 / 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 94 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.224 Fit side-chains REVERT: A 312 LYS cc_start: 0.7993 (mtmm) cc_final: 0.7547 (mtmm) REVERT: A 425 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: A 479 MET cc_start: 0.9231 (mtp) cc_final: 0.8863 (mtp) REVERT: A 492 ASP cc_start: 0.7085 (t70) cc_final: 0.6219 (t0) REVERT: A 560 MET cc_start: 0.9072 (mtt) cc_final: 0.8649 (mtt) REVERT: A 679 LYS cc_start: 0.8539 (tttt) cc_final: 0.7551 (mttp) REVERT: A 708 GLN cc_start: 0.8397 (mt0) cc_final: 0.8146 (mt0) REVERT: A 761 MET cc_start: 0.8933 (ttp) cc_final: 0.8553 (ttm) REVERT: A 786 HIS cc_start: 0.8352 (t70) cc_final: 0.8058 (t70) REVERT: A 906 SER cc_start: 0.9072 (OUTLIER) cc_final: 0.8769 (p) REVERT: A 914 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7419 (tm-30) outliers start: 21 outliers final: 10 residues processed: 84 average time/residue: 0.5784 time to fit residues: 50.9595 Evaluate side-chains 85 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 55 optimal weight: 0.0030 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 42 optimal weight: 0.0570 chunk 52 optimal weight: 0.9990 overall best weight: 1.0114 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.125530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.106723 restraints weight = 6456.537| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 0.94 r_work: 0.2959 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6368 Z= 0.135 Angle : 0.588 7.556 8766 Z= 0.274 Chirality : 0.046 0.175 1008 Planarity : 0.003 0.035 984 Dihedral : 9.028 83.731 1153 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.52 % Allowed : 15.75 % Favored : 80.74 % 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: 0.30 (0.32), residues: 665 helix: 2.01 (0.29), residues: 321 sheet: -0.65 (0.52), residues: 96 loop : -1.97 (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 0.00317 / 0.13 ( 6364) covalent geometry : angle 0.58346 / 0.27 ( 8760) hydrogen bonds : bond 0.03745 / 2.50 ( 304) hydrogen bonds : angle 3.47614 / 2.39 ( 842) metal coordination : bond 0.00569 / 0.29 ( 4) metal coordination : angle 2.89637 / 2.35 ( 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 92 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.206 Fit side-chains REVERT: A 312 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7671 (mtmm) REVERT: A 425 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7963 (m-30) REVERT: A 479 MET cc_start: 0.9223 (mtp) cc_final: 0.8848 (mtp) REVERT: A 491 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.6924 (tppt) REVERT: A 492 ASP cc_start: 0.7122 (t70) cc_final: 0.6244 (t0) REVERT: A 560 MET cc_start: 0.9075 (mtt) cc_final: 0.8578 (mtt) REVERT: A 679 LYS cc_start: 0.8531 (tttt) cc_final: 0.7540 (mttp) REVERT: A 708 GLN cc_start: 0.8415 (mt0) cc_final: 0.8157 (mt0) REVERT: A 761 MET cc_start: 0.8942 (ttp) cc_final: 0.8531 (ttm) REVERT: A 768 LEU cc_start: 0.8384 (tt) cc_final: 0.8182 (tp) REVERT: A 786 HIS cc_start: 0.8350 (t70) cc_final: 0.8014 (t70) REVERT: A 906 SER cc_start: 0.9076 (OUTLIER) cc_final: 0.8777 (p) REVERT: A 914 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7371 (tm-30) outliers start: 21 outliers final: 12 residues processed: 83 average time/residue: 0.5645 time to fit residues: 49.1447 Evaluate side-chains 87 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 491 LYS Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 599 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.126772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.106285 restraints weight = 6479.065| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.14 r_work: 0.2964 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6368 Z= 0.123 Angle : 0.587 7.850 8766 Z= 0.273 Chirality : 0.047 0.237 1008 Planarity : 0.003 0.035 984 Dihedral : 9.000 82.462 1153 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.35 % Allowed : 15.75 % Favored : 80.90 % 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: 0.41 (0.32), residues: 665 helix: 2.10 (0.29), residues: 321 sheet: -0.59 (0.53), residues: 96 loop : -1.92 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 533 TYR 0.016 0.001 TYR A 717 PHE 0.009 0.001 PHE A 842 TRP 0.003 0.001 TRP A 908 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 0.58277 / 0.27 ( 8760) hydrogen bonds : bond 0.03601 / 2.41 ( 304) hydrogen bonds : angle 3.45017 / 2.38 ( 842) metal coordination : bond 0.00538 / 0.28 ( 4) metal coordination : angle 2.88505 / 2.30 ( 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 94 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.177 Fit side-chains REVERT: A 312 LYS cc_start: 0.7969 (mtmm) cc_final: 0.7090 (mmtm) REVERT: A 425 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7959 (m-30) REVERT: A 479 MET cc_start: 0.9209 (mtp) cc_final: 0.8822 (mtp) REVERT: A 491 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.6917 (tppt) REVERT: A 492 ASP cc_start: 0.7078 (t70) cc_final: 0.6178 (t0) REVERT: A 560 MET cc_start: 0.9053 (mtt) cc_final: 0.8552 (mtt) REVERT: A 679 LYS cc_start: 0.8507 (tttt) cc_final: 0.7485 (mttp) REVERT: A 708 GLN cc_start: 0.8393 (mt0) cc_final: 0.8140 (mt0) REVERT: A 761 MET cc_start: 0.8898 (ttp) cc_final: 0.8485 (ttm) REVERT: A 786 HIS cc_start: 0.8327 (t70) cc_final: 0.7993 (t70) REVERT: A 906 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8771 (p) REVERT: A 914 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7152 (tt0) outliers start: 20 outliers final: 12 residues processed: 86 average time/residue: 0.5839 time to fit residues: 52.7742 Evaluate side-chains 86 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 491 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.122930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.102317 restraints weight = 6436.339| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.13 r_work: 0.2927 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6368 Z= 0.186 Angle : 0.648 7.799 8766 Z= 0.302 Chirality : 0.049 0.231 1008 Planarity : 0.004 0.033 984 Dihedral : 9.210 91.245 1153 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.02 % Allowed : 16.25 % Favored : 80.74 % 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: 0.16 (0.32), residues: 665 helix: 1.88 (0.29), residues: 321 sheet: -0.65 (0.54), residues: 84 loop : -1.99 (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 0.005 0.001 TRP A 908 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 ( 6364) covalent geometry : angle 0.64407 / 0.30 ( 8760) hydrogen bonds : bond 0.04298 / 2.85 ( 304) hydrogen bonds : angle 3.59578 / 2.48 ( 842) metal coordination : bond 0.00677 / 0.35 ( 4) metal coordination : angle 2.96359 / 2.36 ( 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 87 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.175 Fit side-chains REVERT: A 312 LYS cc_start: 0.7911 (mtmm) cc_final: 0.7061 (mmtm) REVERT: A 425 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8038 (m-30) REVERT: A 492 ASP cc_start: 0.7212 (t70) cc_final: 0.6264 (t0) REVERT: A 560 MET cc_start: 0.9086 (mtt) cc_final: 0.8603 (mtt) REVERT: A 708 GLN cc_start: 0.8412 (mt0) cc_final: 0.8148 (mt0) REVERT: A 761 MET cc_start: 0.8972 (ttp) cc_final: 0.8549 (ttm) REVERT: A 786 HIS cc_start: 0.8374 (t70) cc_final: 0.8046 (t70) REVERT: A 906 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8841 (p) REVERT: A 914 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7388 (tm-30) outliers start: 18 outliers final: 10 residues processed: 79 average time/residue: 0.5734 time to fit residues: 47.4702 Evaluate side-chains 80 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.125513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.105551 restraints weight = 6459.812| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.11 r_work: 0.2958 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6368 Z= 0.124 Angle : 0.598 8.047 8766 Z= 0.278 Chirality : 0.047 0.224 1008 Planarity : 0.003 0.035 984 Dihedral : 9.070 86.709 1153 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.68 % Allowed : 16.42 % Favored : 80.90 % 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: 0.42 (0.32), residues: 665 helix: 2.08 (0.29), residues: 321 sheet: -0.53 (0.53), residues: 96 loop : -1.90 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 533 TYR 0.018 0.001 TYR A 717 PHE 0.009 0.001 PHE A 842 TRP 0.003 0.001 TRP A 908 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 6364) covalent geometry : angle 0.59320 / 0.28 ( 8760) hydrogen bonds : bond 0.03647 / 2.44 ( 304) hydrogen bonds : angle 3.50053 / 2.41 ( 842) metal coordination : bond 0.00541 / 0.28 ( 4) metal coordination : angle 2.83087 / 2.26 ( 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 87 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.188 Fit side-chains REVERT: A 312 LYS cc_start: 0.7894 (mtmm) cc_final: 0.7050 (mmtm) REVERT: A 425 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7941 (m-30) REVERT: A 492 ASP cc_start: 0.7112 (t70) cc_final: 0.6220 (t0) REVERT: A 560 MET cc_start: 0.9057 (mtt) cc_final: 0.8532 (mtt) REVERT: A 679 LYS cc_start: 0.8512 (tttt) cc_final: 0.7510 (mttp) REVERT: A 708 GLN cc_start: 0.8412 (mt0) cc_final: 0.8155 (mt0) REVERT: A 761 MET cc_start: 0.8923 (ttp) cc_final: 0.8510 (ttm) REVERT: A 768 LEU cc_start: 0.8384 (tt) cc_final: 0.8177 (tp) REVERT: A 786 HIS cc_start: 0.8338 (t70) cc_final: 0.8005 (t70) REVERT: A 906 SER cc_start: 0.9086 (OUTLIER) cc_final: 0.8787 (p) REVERT: A 914 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7142 (tt0) outliers start: 16 outliers final: 10 residues processed: 80 average time/residue: 0.5865 time to fit residues: 49.2429 Evaluate side-chains 83 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.124476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.105731 restraints weight = 6436.783| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 0.95 r_work: 0.2954 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6368 Z= 0.145 Angle : 0.616 8.193 8766 Z= 0.286 Chirality : 0.047 0.226 1008 Planarity : 0.003 0.035 984 Dihedral : 9.091 88.788 1153 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.85 % Allowed : 16.58 % Favored : 80.57 % 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: 0.39 (0.32), residues: 665 helix: 2.05 (0.28), residues: 321 sheet: -0.58 (0.52), residues: 96 loop : -1.88 (0.34), residues: 248 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 0.009 0.001 PHE A 842 TRP 0.004 0.001 TRP A 908 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 6364) covalent geometry : angle 0.61185 / 0.29 ( 8760) hydrogen bonds : bond 0.03863 / 2.58 ( 304) hydrogen bonds : angle 3.52067 / 2.42 ( 842) metal coordination : bond 0.00552 / 0.29 ( 4) metal coordination : angle 2.75992 / 2.22 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2021.36 seconds wall clock time: 35 minutes 15.20 seconds (2115.20 seconds total)