Starting phenix.real_space_refine on Thu Jul 2 03:24:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ktw_62568/07_2026/9ktw_62568.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ktw_62568/07_2026/9ktw_62568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ktw_62568/07_2026/9ktw_62568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ktw_62568/07_2026/9ktw_62568.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ktw_62568/07_2026/9ktw_62568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ktw_62568/07_2026/9ktw_62568.map" } resolution = 2.6 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= 0.039 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 39 5.49 5 S 34 5.16 5 C 3833 2.51 5 N 1073 2.21 5 O 1274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 6254 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 5424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5424 Classifications: {'peptide': 675} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 648} Chain breaks: 1 Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 829 Classifications: {'RNA': 39} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 19} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4570 SG CYS B 810 38.659 48.489 20.427 1.00 22.86 S ATOM 4596 SG CYS B 813 39.138 48.347 16.649 1.00 40.77 S ATOM 4915 SG CYS B 864 36.312 50.502 18.076 1.00 39.31 S ATOM 4954 SG CYS B 869 36.283 46.616 18.304 1.00 37.50 S Time building chain proxies: 1.64, per 1000 atoms: 0.26 Number of scatterers: 6254 At special positions: 0 Unit cell: (74.186, 84.784, 98.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 34 16.00 P 39 15.00 O 1274 8.00 N 1073 7.00 C 3833 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: 0.61 Conformation dependent library (CDL) restraints added in 241.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 869 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 813 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 810 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 864 " Number of angles added : 6 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1286 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 5 sheets defined 51.7% alpha, 12.3% beta 19 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 269 through 283 Processing helix chain 'B' and resid 299 through 314 Processing helix chain 'B' and resid 325 through 329 removed outlier: 3.991A pdb=" N ALA B 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 340 Processing helix chain 'B' and resid 347 through 358 removed outlier: 3.740A pdb=" N LEU B 351 " --> pdb=" O THR B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 removed outlier: 4.140A pdb=" N ILE B 365 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 377 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 419 through 434 Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.540A pdb=" N LEU B 449 " --> pdb=" O ASN B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 490 removed outlier: 3.547A pdb=" N ILE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 506 through 521 Processing helix chain 'B' and resid 527 through 558 Processing helix chain 'B' and resid 559 through 576 removed outlier: 3.741A pdb=" N ALA B 563 " --> pdb=" O ARG B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 602 removed outlier: 3.891A pdb=" N LYS B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLU B 596 " --> pdb=" O GLU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 625 removed outlier: 3.740A pdb=" N LEU B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 650 removed outlier: 3.581A pdb=" N ASP B 641 " --> pdb=" O ARG B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 685 Processing helix chain 'B' and resid 698 through 701 Processing helix chain 'B' and resid 720 through 728 Processing helix chain 'B' and resid 744 through 769 removed outlier: 3.875A pdb=" N ILE B 748 " --> pdb=" O ASN B 744 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B 759 " --> pdb=" O MET B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 794 Processing helix chain 'B' and resid 835 through 841 removed outlier: 4.009A pdb=" N LYS B 839 " --> pdb=" O GLY B 835 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 835 through 841' Processing sheet with id=AA1, first strand: chain 'B' and resid 321 through 324 removed outlier: 6.681A pdb=" N VAL B 293 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU B 346 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE B 295 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 372 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 261 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 457 through 462 removed outlier: 6.101A pdb=" N GLY B 659 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 816 through 819 removed outlier: 6.922A pdb=" N LEU B 808 " --> pdb=" O ALA B 817 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR B 819 " --> pdb=" O LYS B 806 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS B 806 " --> pdb=" O TYR B 819 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 830 through 833 removed outlier: 4.403A pdb=" N ILE B 916 " --> pdb=" O VAL B 823 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 842 through 845 removed outlier: 6.643A pdb=" N ILE B 862 " --> pdb=" O TRP B 873 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.75 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: 1534 1.33 - 1.45: 1367 1.45 - 1.57: 3431 1.57 - 1.69: 76 1.69 - 1.81: 48 Bond restraints: 6456 Sorted by residual: bond pdb=" CB GLU B 591 " pdb=" CG GLU B 591 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 bond pdb=" N1 U C 8 " pdb=" C2 U C 8 " ideal model delta sigma weight residual 1.381 1.390 -0.009 9.00e-03 1.23e+04 9.68e-01 bond pdb=" N3 C C 55 " pdb=" C4 C C 55 " ideal model delta sigma weight residual 1.335 1.329 0.006 7.00e-03 2.04e+04 8.09e-01 bond pdb=" N3 C C 12 " pdb=" C4 C C 12 " ideal model delta sigma weight residual 1.335 1.329 0.006 7.00e-03 2.04e+04 7.43e-01 bond pdb=" N3 C C 21 " pdb=" C4 C C 21 " ideal model delta sigma weight residual 1.335 1.329 0.006 7.00e-03 2.04e+04 6.99e-01 ... (remaining 6451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 8483 1.00 - 2.00: 335 2.00 - 2.99: 54 2.99 - 3.99: 11 3.99 - 4.99: 8 Bond angle restraints: 8891 Sorted by residual: angle pdb=" C1' U C 8 " pdb=" N1 U C 8 " pdb=" C2 U C 8 " ideal model delta sigma weight residual 117.70 121.64 -3.94 1.20e+00 6.94e-01 1.08e+01 angle pdb=" C1' C C 24 " pdb=" N1 C C 24 " pdb=" C2 C C 24 " ideal model delta sigma weight residual 118.80 122.21 -3.41 1.10e+00 8.26e-01 9.63e+00 angle pdb=" CA ILE B 406 " pdb=" CB ILE B 406 " pdb=" CG1 ILE B 406 " ideal model delta sigma weight residual 110.40 114.69 -4.29 1.70e+00 3.46e-01 6.37e+00 angle pdb=" C1' C C 24 " pdb=" N1 C C 24 " pdb=" C6 C C 24 " ideal model delta sigma weight residual 120.80 117.90 2.90 1.20e+00 6.94e-01 5.83e+00 angle pdb=" CB ILE B 406 " pdb=" CG1 ILE B 406 " pdb=" CD1 ILE B 406 " ideal model delta sigma weight residual 113.80 118.79 -4.99 2.10e+00 2.27e-01 5.65e+00 ... (remaining 8886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 3300 17.41 - 34.82: 425 34.82 - 52.23: 167 52.23 - 69.64: 75 69.64 - 87.05: 19 Dihedral angle restraints: 3986 sinusoidal: 2006 harmonic: 1980 Sorted by residual: dihedral pdb=" CA LEU B 346 " pdb=" C LEU B 346 " pdb=" N THR B 347 " pdb=" CA THR B 347 " ideal model delta harmonic sigma weight residual 180.00 157.75 22.25 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA GLU B 716 " pdb=" C GLU B 716 " pdb=" N TYR B 717 " pdb=" CA TYR B 717 " ideal model delta harmonic sigma weight residual 180.00 -162.87 -17.13 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASP B 896 " pdb=" CB ASP B 896 " pdb=" CG ASP B 896 " pdb=" OD1 ASP B 896 " ideal model delta sinusoidal sigma weight residual -30.00 -88.64 58.64 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 3983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 614 0.028 - 0.057: 255 0.057 - 0.085: 98 0.085 - 0.114: 42 0.114 - 0.142: 16 Chirality restraints: 1025 Sorted by residual: chirality pdb=" CA VAL B 332 " pdb=" N VAL B 332 " pdb=" C VAL B 332 " pdb=" CB VAL B 332 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE B 360 " pdb=" N ILE B 360 " pdb=" C ILE B 360 " pdb=" CB ILE B 360 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CB ILE B 406 " pdb=" CA ILE B 406 " pdb=" CG1 ILE B 406 " pdb=" CG2 ILE B 406 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1022 not shown) Planarity restraints: 995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 525 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO B 526 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 526 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 526 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 381 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.16e+00 pdb=" N PRO B 382 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 382 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 382 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 332 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO B 333 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 333 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 333 " -0.020 5.00e-02 4.00e+02 ... (remaining 992 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 974 2.77 - 3.30: 5436 3.30 - 3.83: 10765 3.83 - 4.37: 12802 4.37 - 4.90: 20785 Nonbonded interactions: 50762 Sorted by model distance: nonbonded pdb=" N GLU B 447 " pdb=" OE1 GLU B 447 " model vdw 2.234 3.120 nonbonded pdb=" O ASN B 625 " pdb=" OG1 THR B 628 " model vdw 2.354 3.040 nonbonded pdb=" OG1 THR B 832 " pdb=" O PRO B 885 " model vdw 2.363 3.040 nonbonded pdb=" NH2 ARG B 728 " pdb=" OE2 GLU B 758 " model vdw 2.365 3.120 nonbonded pdb=" NZ LYS B 635 " pdb=" O TYR B 715 " model vdw 2.395 3.120 ... (remaining 50757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.410 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6460 Z= 0.143 Angle : 0.488 4.991 8897 Z= 0.318 Chirality : 0.040 0.142 1025 Planarity : 0.004 0.055 995 Dihedral : 19.711 87.048 2700 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.49 % Allowed : 25.54 % Favored : 71.97 % 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: 1.14 (0.31), residues: 671 helix: 1.95 (0.29), residues: 319 sheet: 0.73 (0.45), residues: 118 loop : -0.91 (0.33), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 730 TYR 0.019 0.001 TYR B 454 PHE 0.011 0.001 PHE B 918 TRP 0.005 0.001 TRP B 908 HIS 0.004 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 ( 6456) covalent geometry : angle 0.48204 / 0.32 ( 8891) hydrogen bonds : bond 0.14494 / 10.72 ( 334) hydrogen bonds : angle 4.91352 / 3.57 ( 919) metal coordination : bond 0.00635 / 0.31 ( 4) metal coordination : angle 2.92778 / 1.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.250 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 104 average time/residue: 0.6709 time to fit residues: 72.4196 Evaluate side-chains 102 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 909 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 317 HIS B 645 ASN B 708 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124637 restraints weight = 5532.363| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.41 r_work: 0.3199 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6460 Z= 0.200 Angle : 0.597 8.538 8897 Z= 0.322 Chirality : 0.046 0.161 1025 Planarity : 0.005 0.052 995 Dihedral : 15.683 74.568 1343 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.31 % Allowed : 23.22 % Favored : 72.47 % 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: 0.93 (0.30), residues: 671 helix: 1.70 (0.29), residues: 321 sheet: 0.82 (0.46), residues: 118 loop : -1.04 (0.32), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 730 TYR 0.015 0.002 TYR B 566 PHE 0.017 0.002 PHE B 295 TRP 0.007 0.001 TRP B 908 HIS 0.006 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 ( 6456) covalent geometry : angle 0.58773 / 0.32 ( 8891) hydrogen bonds : bond 0.07003 / 4.64 ( 334) hydrogen bonds : angle 4.25075 / 3.09 ( 919) metal coordination : bond 0.01200 / 0.60 ( 4) metal coordination : angle 3.97269 / 2.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.231 Fit side-chains REVERT: B 533 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7364 (ptt90) REVERT: B 575 ARG cc_start: 0.5297 (OUTLIER) cc_final: 0.4719 (ttm110) REVERT: B 610 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8565 (ttmt) REVERT: B 730 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7410 (mtt-85) REVERT: B 834 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7601 (mp) REVERT: B 866 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7007 (ttt180) REVERT: B 923 MET cc_start: 0.4913 (OUTLIER) cc_final: 0.4620 (mtm) outliers start: 26 outliers final: 8 residues processed: 106 average time/residue: 0.6917 time to fit residues: 76.1687 Evaluate side-chains 102 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 730 ARG Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 836 ASP Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 923 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 4 optimal weight: 0.0040 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 645 ASN B 708 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.156234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.125128 restraints weight = 5523.976| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.24 r_work: 0.3326 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6460 Z= 0.105 Angle : 0.454 4.735 8897 Z= 0.252 Chirality : 0.039 0.137 1025 Planarity : 0.004 0.045 995 Dihedral : 15.165 74.948 1326 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.98 % Allowed : 23.05 % Favored : 72.97 % 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: 1.36 (0.31), residues: 671 helix: 2.10 (0.29), residues: 322 sheet: 1.00 (0.46), residues: 118 loop : -0.91 (0.33), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 730 TYR 0.012 0.001 TYR B 566 PHE 0.011 0.001 PHE B 918 TRP 0.005 0.001 TRP B 908 HIS 0.004 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 ( 6456) covalent geometry : angle 0.44654 / 0.25 ( 8891) hydrogen bonds : bond 0.04945 / 3.23 ( 334) hydrogen bonds : angle 3.89088 / 2.83 ( 919) metal coordination : bond 0.00603 / 0.29 ( 4) metal coordination : angle 3.19518 / 1.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.227 Fit side-chains REVERT: B 312 LYS cc_start: 0.8381 (tttm) cc_final: 0.7868 (tppt) REVERT: B 575 ARG cc_start: 0.5215 (OUTLIER) cc_final: 0.4704 (ttm110) REVERT: B 778 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6547 (tm-30) REVERT: B 834 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7566 (mp) REVERT: B 866 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6824 (ttp-170) REVERT: B 923 MET cc_start: 0.4720 (OUTLIER) cc_final: 0.4485 (mtm) outliers start: 24 outliers final: 5 residues processed: 110 average time/residue: 0.6690 time to fit residues: 76.4023 Evaluate side-chains 96 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 923 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 26 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 0.0870 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.157746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122933 restraints weight = 5546.146| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.39 r_work: 0.3338 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6460 Z= 0.096 Angle : 0.429 4.658 8897 Z= 0.237 Chirality : 0.039 0.136 1025 Planarity : 0.004 0.044 995 Dihedral : 15.067 74.185 1324 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.99 % Allowed : 25.21 % Favored : 71.81 % 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: 1.59 (0.31), residues: 671 helix: 2.31 (0.29), residues: 322 sheet: 1.05 (0.46), residues: 118 loop : -0.79 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 730 TYR 0.011 0.001 TYR B 566 PHE 0.019 0.001 PHE B 579 TRP 0.003 0.001 TRP B 646 HIS 0.003 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.10 ( 6456) covalent geometry : angle 0.42214 / 0.24 ( 8891) hydrogen bonds : bond 0.04306 / 2.79 ( 334) hydrogen bonds : angle 3.66881 / 2.67 ( 919) metal coordination : bond 0.00567 / 0.28 ( 4) metal coordination : angle 2.90522 / 1.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.241 Fit side-chains REVERT: B 312 LYS cc_start: 0.8361 (tttm) cc_final: 0.7845 (tppt) REVERT: B 575 ARG cc_start: 0.5190 (OUTLIER) cc_final: 0.4697 (ttm110) REVERT: B 749 GLU cc_start: 0.7983 (tt0) cc_final: 0.7771 (mm-30) REVERT: B 778 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6523 (tm-30) REVERT: B 834 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7512 (mp) REVERT: B 866 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.6736 (ttp-170) REVERT: B 867 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.5864 (pp30) outliers start: 18 outliers final: 5 residues processed: 103 average time/residue: 0.7154 time to fit residues: 76.5346 Evaluate side-chains 94 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 867 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 55 optimal weight: 0.0470 chunk 4 optimal weight: 0.0050 chunk 49 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.4892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.158075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.128726 restraints weight = 5620.009| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.61 r_work: 0.3292 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6460 Z= 0.092 Angle : 0.416 4.733 8897 Z= 0.229 Chirality : 0.039 0.137 1025 Planarity : 0.004 0.044 995 Dihedral : 14.908 73.825 1321 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.15 % Allowed : 24.71 % Favored : 72.14 % 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: 1.70 (0.32), residues: 671 helix: 2.39 (0.29), residues: 322 sheet: 1.10 (0.47), residues: 118 loop : -0.72 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 730 TYR 0.011 0.001 TYR B 566 PHE 0.009 0.001 PHE B 579 TRP 0.003 0.001 TRP B 646 HIS 0.003 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00175 / 0.09 ( 6456) covalent geometry : angle 0.40975 / 0.23 ( 8891) hydrogen bonds : bond 0.04032 / 2.62 ( 334) hydrogen bonds : angle 3.58430 / 2.62 ( 919) metal coordination : bond 0.00532 / 0.26 ( 4) metal coordination : angle 2.73990 / 1.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.236 Fit side-chains REVERT: B 312 LYS cc_start: 0.8430 (tttm) cc_final: 0.7874 (tppt) REVERT: B 533 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7063 (ptt90) REVERT: B 575 ARG cc_start: 0.5162 (OUTLIER) cc_final: 0.4646 (ttm110) REVERT: B 610 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8072 (ttmt) REVERT: B 749 GLU cc_start: 0.8097 (tt0) cc_final: 0.7803 (mm-30) REVERT: B 778 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6573 (tm-30) REVERT: B 834 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7616 (mp) REVERT: B 866 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6763 (ttp-170) REVERT: B 867 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.5930 (pp30) outliers start: 19 outliers final: 5 residues processed: 102 average time/residue: 0.6916 time to fit residues: 73.3570 Evaluate side-chains 95 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 867 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 0.0020 chunk 9 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.158659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127071 restraints weight = 5576.786| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.31 r_work: 0.3366 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6460 Z= 0.091 Angle : 0.411 4.738 8897 Z= 0.226 Chirality : 0.038 0.137 1025 Planarity : 0.004 0.045 995 Dihedral : 14.882 73.835 1321 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.15 % Allowed : 24.88 % Favored : 71.97 % 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: 1.74 (0.32), residues: 671 helix: 2.43 (0.29), residues: 322 sheet: 1.07 (0.47), residues: 118 loop : -0.67 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 730 TYR 0.014 0.001 TYR B 454 PHE 0.013 0.001 PHE B 579 TRP 0.003 0.001 TRP B 646 HIS 0.002 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00174 / 0.09 ( 6456) covalent geometry : angle 0.40503 / 0.23 ( 8891) hydrogen bonds : bond 0.03949 / 2.55 ( 334) hydrogen bonds : angle 3.53399 / 2.58 ( 919) metal coordination : bond 0.00541 / 0.27 ( 4) metal coordination : angle 2.60514 / 1.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.215 Fit side-chains REVERT: B 312 LYS cc_start: 0.8381 (tttm) cc_final: 0.7879 (tppt) REVERT: B 533 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6977 (ptt90) REVERT: B 575 ARG cc_start: 0.5023 (OUTLIER) cc_final: 0.4684 (ttm110) REVERT: B 778 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6513 (tm-30) REVERT: B 834 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7545 (mp) REVERT: B 866 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6692 (ttp-170) REVERT: B 867 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.5930 (pp30) outliers start: 19 outliers final: 7 residues processed: 101 average time/residue: 0.6477 time to fit residues: 68.0008 Evaluate side-chains 98 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 867 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.158385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127434 restraints weight = 5536.290| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.27 r_work: 0.3355 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6460 Z= 0.096 Angle : 0.425 4.749 8897 Z= 0.233 Chirality : 0.039 0.139 1025 Planarity : 0.004 0.046 995 Dihedral : 14.868 73.916 1321 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.15 % Allowed : 24.21 % Favored : 72.64 % 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: 1.75 (0.32), residues: 671 helix: 2.44 (0.29), residues: 322 sheet: 1.06 (0.47), residues: 118 loop : -0.68 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 730 TYR 0.015 0.001 TYR B 454 PHE 0.015 0.001 PHE B 579 TRP 0.003 0.001 TRP B 646 HIS 0.002 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.10 ( 6456) covalent geometry : angle 0.42012 / 0.23 ( 8891) hydrogen bonds : bond 0.04068 / 2.63 ( 334) hydrogen bonds : angle 3.53349 / 2.58 ( 919) metal coordination : bond 0.00576 / 0.28 ( 4) metal coordination : angle 2.61025 / 1.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.222 Fit side-chains REVERT: B 312 LYS cc_start: 0.8392 (tttm) cc_final: 0.7888 (tppt) REVERT: B 533 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6993 (ptt90) REVERT: B 575 ARG cc_start: 0.5065 (OUTLIER) cc_final: 0.4742 (ttm110) REVERT: B 778 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: B 834 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7564 (mp) REVERT: B 866 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6740 (ttp-170) REVERT: B 867 GLN cc_start: 0.6780 (OUTLIER) cc_final: 0.5937 (pp30) outliers start: 19 outliers final: 8 residues processed: 102 average time/residue: 0.6102 time to fit residues: 64.7971 Evaluate side-chains 99 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 867 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 0.0570 chunk 67 optimal weight: 10.0000 overall best weight: 1.3100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.155427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.123609 restraints weight = 5629.098| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.32 r_work: 0.3315 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6460 Z= 0.122 Angle : 0.471 5.188 8897 Z= 0.256 Chirality : 0.041 0.140 1025 Planarity : 0.004 0.045 995 Dihedral : 14.894 74.172 1321 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.99 % Allowed : 24.54 % Favored : 72.47 % 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: 1.60 (0.32), residues: 671 helix: 2.34 (0.29), residues: 322 sheet: 0.99 (0.47), residues: 118 loop : -0.78 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 730 TYR 0.015 0.002 TYR B 454 PHE 0.012 0.001 PHE B 579 TRP 0.004 0.001 TRP B 908 HIS 0.004 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 6456) covalent geometry : angle 0.46525 / 0.26 ( 8891) hydrogen bonds : bond 0.04828 / 3.12 ( 334) hydrogen bonds : angle 3.65708 / 2.67 ( 919) metal coordination : bond 0.00794 / 0.40 ( 4) metal coordination : angle 2.81190 / 1.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.190 Fit side-chains REVERT: B 312 LYS cc_start: 0.8403 (tttm) cc_final: 0.7894 (tppt) REVERT: B 533 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7067 (ptt90) REVERT: B 575 ARG cc_start: 0.5066 (OUTLIER) cc_final: 0.4714 (ttm110) REVERT: B 778 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6558 (tm-30) REVERT: B 834 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7528 (mp) REVERT: B 866 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6821 (ttp-170) REVERT: B 867 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.5933 (pp30) outliers start: 18 outliers final: 8 residues processed: 99 average time/residue: 0.6614 time to fit residues: 68.0045 Evaluate side-chains 98 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 867 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.156020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120803 restraints weight = 5591.160| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.40 r_work: 0.3329 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6460 Z= 0.112 Angle : 0.456 5.244 8897 Z= 0.250 Chirality : 0.040 0.141 1025 Planarity : 0.004 0.045 995 Dihedral : 14.862 74.110 1321 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.99 % Allowed : 24.21 % Favored : 72.80 % 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: 1.61 (0.32), residues: 671 helix: 2.35 (0.29), residues: 322 sheet: 0.98 (0.47), residues: 118 loop : -0.76 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 730 TYR 0.017 0.001 TYR B 454 PHE 0.016 0.001 PHE B 579 TRP 0.004 0.001 TRP B 646 HIS 0.003 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 6456) covalent geometry : angle 0.45063 / 0.25 ( 8891) hydrogen bonds : bond 0.04647 / 3.00 ( 334) hydrogen bonds : angle 3.64626 / 2.66 ( 919) metal coordination : bond 0.00717 / 0.36 ( 4) metal coordination : angle 2.81681 / 1.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: B 312 LYS cc_start: 0.8375 (tttm) cc_final: 0.7865 (tppt) REVERT: B 533 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.7016 (ptt90) REVERT: B 778 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6547 (tm-30) REVERT: B 834 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7539 (mp) REVERT: B 866 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6753 (ttp-170) REVERT: B 867 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.5891 (pp30) outliers start: 18 outliers final: 8 residues processed: 99 average time/residue: 0.6517 time to fit residues: 67.2049 Evaluate side-chains 97 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 867 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.156287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121222 restraints weight = 5579.851| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.39 r_work: 0.3334 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6460 Z= 0.109 Angle : 0.453 5.468 8897 Z= 0.248 Chirality : 0.040 0.140 1025 Planarity : 0.004 0.045 995 Dihedral : 14.833 74.073 1321 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.49 % Allowed : 24.88 % Favored : 72.64 % 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: 1.63 (0.32), residues: 671 helix: 2.37 (0.29), residues: 322 sheet: 0.98 (0.47), residues: 118 loop : -0.75 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 730 TYR 0.018 0.001 TYR B 454 PHE 0.012 0.001 PHE B 579 TRP 0.004 0.001 TRP B 646 HIS 0.003 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 6456) covalent geometry : angle 0.44775 / 0.25 ( 8891) hydrogen bonds : bond 0.04523 / 2.92 ( 334) hydrogen bonds : angle 3.62493 / 2.64 ( 919) metal coordination : bond 0.00687 / 0.34 ( 4) metal coordination : angle 2.70880 / 1.62 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: B 312 LYS cc_start: 0.8377 (tttm) cc_final: 0.7863 (tppt) REVERT: B 533 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6916 (ptt90) REVERT: B 778 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: B 834 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7552 (mp) REVERT: B 866 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6754 (ttp-170) REVERT: B 867 GLN cc_start: 0.6676 (OUTLIER) cc_final: 0.5828 (pp30) outliers start: 15 outliers final: 8 residues processed: 96 average time/residue: 0.6311 time to fit residues: 63.0446 Evaluate side-chains 97 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 867 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 38 optimal weight: 0.0470 chunk 36 optimal weight: 4.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.157674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126718 restraints weight = 5610.838| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.27 r_work: 0.3349 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6460 Z= 0.099 Angle : 0.438 5.891 8897 Z= 0.240 Chirality : 0.039 0.140 1025 Planarity : 0.004 0.045 995 Dihedral : 14.797 73.923 1321 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.49 % Allowed : 24.88 % Favored : 72.64 % 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: 1.72 (0.32), residues: 671 helix: 2.44 (0.29), residues: 322 sheet: 1.01 (0.47), residues: 118 loop : -0.70 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 730 TYR 0.018 0.001 TYR B 454 PHE 0.015 0.001 PHE B 579 TRP 0.004 0.001 TRP B 646 HIS 0.002 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.10 ( 6456) covalent geometry : angle 0.43265 / 0.24 ( 8891) hydrogen bonds : bond 0.04173 / 2.70 ( 334) hydrogen bonds : angle 3.56410 / 2.60 ( 919) metal coordination : bond 0.00568 / 0.28 ( 4) metal coordination : angle 2.60788 / 1.56 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2490.54 seconds wall clock time: 43 minutes 9.35 seconds (2589.35 seconds total)