Starting phenix.real_space_refine on Tue Aug 4 18:34:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s0z_54428/08_2026/9s0z_54428.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s0z_54428/08_2026/9s0z_54428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s0z_54428/08_2026/9s0z_54428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s0z_54428/08_2026/9s0z_54428.map" model { file = "/net/cci-nas-00/data/ceres_data/9s0z_54428/08_2026/9s0z_54428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s0z_54428/08_2026/9s0z_54428.cif" } resolution = 3.0 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= 0.019 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 P 5 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 3680 2.51 5 N 1014 2.21 5 O 1063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5795 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 5691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5691 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 671} Chain breaks: 5 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Classifications: {'RNA': 5} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.52, per 1000 atoms: 0.26 Number of scatterers: 5795 At special positions: 0 Unit cell: (79.056, 92.232, 111.264, 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) S 32 16.00 P 5 15.00 Mg 1 11.99 O 1063 8.00 N 1014 7.00 C 3680 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: 0.53 Conformation dependent library (CDL) restraints added in 366.7 milliseconds 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1336 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 34.9% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 143 through 153 Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'B' and resid 279 through 289 Processing helix chain 'B' and resid 299 through 306 removed outlier: 4.039A pdb=" N GLY B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 414 through 432 removed outlier: 4.021A pdb=" N LEU B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 443 Processing helix chain 'B' and resid 505 through 524 removed outlier: 3.509A pdb=" N ILE B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 538 through 550 removed outlier: 3.529A pdb=" N GLN B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 579 removed outlier: 3.683A pdb=" N TYR B 569 " --> pdb=" O ARG B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.713A pdb=" N GLY B 614 " --> pdb=" O ASN B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 691 removed outlier: 3.666A pdb=" N GLN B 681 " --> pdb=" O LYS B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 716 removed outlier: 3.795A pdb=" N LEU B 713 " --> pdb=" O GLN B 709 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 714 " --> pdb=" O LEU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 727 removed outlier: 3.532A pdb=" N ASP B 723 " --> pdb=" O PRO B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 816 Processing helix chain 'B' and resid 817 through 819 No H-bonds generated for 'chain 'B' and resid 817 through 819' Processing helix chain 'B' and resid 830 through 846 Processing helix chain 'B' and resid 852 through 856 removed outlier: 3.691A pdb=" N LEU B 855 " --> pdb=" O ASN B 852 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 659 through 664 removed outlier: 3.669A pdb=" N ASP B 633 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE B 629 " --> pdb=" O SER B 651 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N CYS B 634 " --> pdb=" O ASP B 703 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 698 " --> pdb=" O THR B 737 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE B 739 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL B 700 " --> pdb=" O ILE B 739 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL B 741 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARG B 702 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU B 736 " --> pdb=" O ASP B 800 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASP B 800 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 738 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS B 114 " --> pdb=" O GLN B 752 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN B 752 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 257 through 259 removed outlier: 5.224A pdb=" N ILE B 264 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 137 through 138 removed outlier: 5.524A pdb=" N LEU B 198 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N HIS B 134 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 200 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 137 through 138 Processing sheet with id=AA5, first strand: chain 'B' and resid 227 through 229 Processing sheet with id=AA6, first strand: chain 'B' and resid 240 through 242 Processing sheet with id=AA7, first strand: chain 'B' and resid 317 through 319 removed outlier: 3.596A pdb=" N VAL B 309 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE B 308 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 463 through 464 removed outlier: 3.628A pdb=" N ILE B 463 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 531 through 535 removed outlier: 6.283A pdb=" N LEU B 499 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL B 535 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR B 501 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR B 502 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL B 557 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL B 587 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N CYS B 559 " --> pdb=" O VAL B 587 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.68 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: 1672 1.33 - 1.45: 926 1.45 - 1.57: 3273 1.57 - 1.69: 9 1.69 - 1.81: 48 Bond restraints: 5928 Sorted by residual: bond pdb=" P A C 3 " pdb=" O5' A C 3 " ideal model delta sigma weight residual 1.593 1.615 -0.022 1.00e-02 1.00e+04 4.86e+00 bond pdb=" O5' A C 3 " pdb=" C5' A C 3 " ideal model delta sigma weight residual 1.424 1.453 -0.029 1.60e-02 3.91e+03 3.37e+00 bond pdb=" C1' A C 3 " pdb=" N9 A C 3 " ideal model delta sigma weight residual 1.483 1.457 0.026 1.50e-02 4.44e+03 2.91e+00 bond pdb=" P A C 3 " pdb=" OP2 A C 3 " ideal model delta sigma weight residual 1.485 1.517 -0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" C4' A C 3 " pdb=" C3' A C 3 " ideal model delta sigma weight residual 1.521 1.533 -0.012 1.00e-02 1.00e+04 1.45e+00 ... (remaining 5923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 7836 1.59 - 3.19: 185 3.19 - 4.78: 27 4.78 - 6.38: 5 6.38 - 7.97: 5 Bond angle restraints: 8058 Sorted by residual: angle pdb=" O5' C C 4 " pdb=" C5' C C 4 " pdb=" C4' C C 4 " ideal model delta sigma weight residual 109.40 112.86 -3.46 8.00e-01 1.56e+00 1.87e+01 angle pdb=" O5' U C 2 " pdb=" C5' U C 2 " pdb=" C4' U C 2 " ideal model delta sigma weight residual 109.40 111.71 -2.31 8.00e-01 1.56e+00 8.32e+00 angle pdb=" O5' U C 1 " pdb=" C5' U C 1 " pdb=" C4' U C 1 " ideal model delta sigma weight residual 109.40 111.67 -2.27 8.00e-01 1.56e+00 8.07e+00 angle pdb=" C SER B 237 " pdb=" N ASP B 238 " pdb=" CA ASP B 238 " ideal model delta sigma weight residual 123.46 119.93 3.53 1.35e+00 5.49e-01 6.82e+00 angle pdb=" O5' C C 5 " pdb=" C5' C C 5 " pdb=" C4' C C 5 " ideal model delta sigma weight residual 109.40 111.43 -2.03 8.00e-01 1.56e+00 6.43e+00 ... (remaining 8053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.42: 3227 18.42 - 36.83: 282 36.83 - 55.25: 49 55.25 - 73.67: 9 73.67 - 92.08: 12 Dihedral angle restraints: 3579 sinusoidal: 1510 harmonic: 2069 Sorted by residual: dihedral pdb=" CA ASP B 433 " pdb=" CB ASP B 433 " pdb=" CG ASP B 433 " pdb=" OD1 ASP B 433 " ideal model delta sinusoidal sigma weight residual -30.00 -86.05 56.05 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CA GLU B 654 " pdb=" C GLU B 654 " pdb=" N GLY B 655 " pdb=" CA GLY B 655 " ideal model delta harmonic sigma weight residual -180.00 -164.30 -15.70 0 5.00e+00 4.00e-02 9.86e+00 dihedral pdb=" CA GLN B 720 " pdb=" C GLN B 720 " pdb=" N PHE B 721 " pdb=" CA PHE B 721 " ideal model delta harmonic sigma weight residual 180.00 164.68 15.32 0 5.00e+00 4.00e-02 9.39e+00 ... (remaining 3576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 818 0.080 - 0.161: 89 0.161 - 0.241: 0 0.241 - 0.322: 1 0.322 - 0.402: 1 Chirality restraints: 909 Sorted by residual: chirality pdb=" P A C 3 " pdb=" OP1 A C 3 " pdb=" OP2 A C 3 " pdb=" O5' A C 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.81 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CB ILE B 457 " pdb=" CA ILE B 457 " pdb=" CG1 ILE B 457 " pdb=" CG2 ILE B 457 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ILE B 645 " pdb=" N ILE B 645 " pdb=" C ILE B 645 " pdb=" CB ILE B 645 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 906 not shown) Planarity restraints: 1009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 497 " -0.007 2.00e-02 2.50e+03 9.19e-03 2.11e+00 pdb=" CG TRP B 497 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 497 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 497 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B 497 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 497 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 497 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 497 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 497 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 497 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 705 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C VAL B 705 " -0.023 2.00e-02 2.50e+03 pdb=" O VAL B 705 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY B 706 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 829 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.72e+00 pdb=" N PRO B 830 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 830 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 830 " -0.018 5.00e-02 4.00e+02 ... (remaining 1006 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 35 2.50 - 3.10: 4070 3.10 - 3.70: 8806 3.70 - 4.30: 12655 4.30 - 4.90: 21229 Nonbonded interactions: 46795 Sorted by model distance: nonbonded pdb=" NE2 GLN B 608 " pdb="MG MG B 901 " model vdw 1.895 2.250 nonbonded pdb=" OP1 U C 1 " pdb="MG MG B 901 " model vdw 2.111 2.170 nonbonded pdb=" OE1 GLN B 608 " pdb="MG MG B 901 " model vdw 2.173 2.170 nonbonded pdb=" OXT LEU B 862 " pdb="MG MG B 901 " model vdw 2.219 2.170 nonbonded pdb=" NZ LYS B 566 " pdb=" O GLN B 845 " model vdw 2.222 3.120 ... (remaining 46790 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: 1.060 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.660 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 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 : 0.005 0.046 5928 Z= 0.211 Angle : 0.623 7.969 8058 Z= 0.331 Chirality : 0.049 0.402 909 Planarity : 0.004 0.033 1009 Dihedral : 15.051 92.082 2243 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.46 (0.31), residues: 692 helix: -0.72 (0.33), residues: 228 sheet: -0.81 (0.40), residues: 173 loop : -1.09 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 772 TYR 0.016 0.002 TYR B 313 PHE 0.019 0.002 PHE B 470 TRP 0.024 0.002 TRP B 497 HIS 0.006 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 ( 5928) covalent geometry : angle 0.62310 / 0.33 ( 8058) hydrogen bonds : bond 0.25702 / 17.81 ( 238) hydrogen bonds : angle 9.21969 / 6.36 ( 678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.265 Fit side-chains REVERT: B 113 VAL cc_start: 0.7389 (p) cc_final: 0.7020 (t) REVERT: B 265 MET cc_start: 0.7071 (mtt) cc_final: 0.6779 (mtm) REVERT: B 476 PHE cc_start: 0.7092 (m-10) cc_final: 0.6768 (m-80) REVERT: B 494 LEU cc_start: 0.5102 (tp) cc_final: 0.4770 (tp) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.6650 time to fit residues: 89.2137 Evaluate side-chains 52 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 132 GLN B 225 ASN B 475 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.116529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.097065 restraints weight = 14654.167| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.05 r_work: 0.3598 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 5928 Z= 0.214 Angle : 0.754 10.478 8058 Z= 0.390 Chirality : 0.051 0.187 909 Planarity : 0.005 0.047 1009 Dihedral : 9.228 93.344 854 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.17 % Allowed : 14.10 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.20 (0.30), residues: 692 helix: -0.03 (0.32), residues: 233 sheet: -0.65 (0.43), residues: 148 loop : -1.38 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 160 TYR 0.015 0.002 TYR B 776 PHE 0.017 0.002 PHE B 470 TRP 0.020 0.002 TRP B 497 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 ( 5928) covalent geometry : angle 0.75442 / 0.39 ( 8058) hydrogen bonds : bond 0.05578 / 3.95 ( 238) hydrogen bonds : angle 6.72694 / 4.67 ( 678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.232 Fit side-chains REVERT: B 111 ILE cc_start: 0.7241 (mt) cc_final: 0.7036 (mm) REVERT: B 176 GLN cc_start: 0.7356 (pm20) cc_final: 0.7137 (pm20) REVERT: B 224 MET cc_start: 0.8010 (mtp) cc_final: 0.7735 (ptp) REVERT: B 231 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.6416 (mtt-85) REVERT: B 284 MET cc_start: 0.8225 (mtt) cc_final: 0.7795 (tmm) REVERT: B 397 MET cc_start: 0.3065 (ptp) cc_final: 0.2615 (ptp) REVERT: B 476 PHE cc_start: 0.7558 (m-10) cc_final: 0.7257 (m-80) REVERT: B 551 THR cc_start: 0.5796 (p) cc_final: 0.5503 (t) outliers start: 20 outliers final: 6 residues processed: 74 average time/residue: 0.4193 time to fit residues: 33.1489 Evaluate side-chains 57 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 ARG Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 628 MET Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.0970 chunk 63 optimal weight: 0.0980 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.114429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.095022 restraints weight = 14374.576| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.01 r_work: 0.3564 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5928 Z= 0.153 Angle : 0.635 11.779 8058 Z= 0.328 Chirality : 0.046 0.178 909 Planarity : 0.004 0.047 1009 Dihedral : 9.091 92.589 854 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.17 % Allowed : 15.53 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.97 (0.30), residues: 692 helix: 0.47 (0.33), residues: 228 sheet: -0.96 (0.41), residues: 152 loop : -1.24 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 160 TYR 0.012 0.001 TYR B 313 PHE 0.020 0.002 PHE B 285 TRP 0.008 0.001 TRP B 325 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 5928) covalent geometry : angle 0.63486 / 0.33 ( 8058) hydrogen bonds : bond 0.04457 / 3.15 ( 238) hydrogen bonds : angle 6.08074 / 4.21 ( 678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.263 Fit side-chains REVERT: B 111 ILE cc_start: 0.7407 (mt) cc_final: 0.7202 (mm) REVERT: B 265 MET cc_start: 0.7719 (mtm) cc_final: 0.7488 (mtm) REVERT: B 323 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.7741 (tp) REVERT: B 397 MET cc_start: 0.2928 (ptp) cc_final: 0.2396 (ptp) REVERT: B 476 PHE cc_start: 0.7545 (m-10) cc_final: 0.7283 (m-80) REVERT: B 551 THR cc_start: 0.6173 (p) cc_final: 0.5838 (t) REVERT: B 622 MET cc_start: 0.7146 (mmm) cc_final: 0.6633 (mmm) outliers start: 20 outliers final: 8 residues processed: 64 average time/residue: 0.3915 time to fit residues: 26.9792 Evaluate side-chains 53 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 0.0040 chunk 42 optimal weight: 0.4980 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN B 510 ASN B 845 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.109701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.089922 restraints weight = 14460.518| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.04 r_work: 0.3477 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5928 Z= 0.182 Angle : 0.644 13.829 8058 Z= 0.328 Chirality : 0.048 0.236 909 Planarity : 0.004 0.046 1009 Dihedral : 9.088 90.110 854 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.17 % Allowed : 18.38 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.08 (0.30), residues: 692 helix: 0.43 (0.32), residues: 230 sheet: -1.10 (0.40), residues: 156 loop : -1.31 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 565 TYR 0.029 0.002 TYR B 542 PHE 0.026 0.002 PHE B 665 TRP 0.009 0.001 TRP B 687 HIS 0.009 0.002 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 5928) covalent geometry : angle 0.64365 / 0.33 ( 8058) hydrogen bonds : bond 0.04080 / 2.86 ( 238) hydrogen bonds : angle 5.65192 / 3.87 ( 678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.229 Fit side-chains REVERT: B 111 ILE cc_start: 0.7702 (mt) cc_final: 0.7436 (mm) REVERT: B 141 MET cc_start: 0.4738 (mpt) cc_final: 0.4208 (mpm) REVERT: B 266 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7803 (tm) REVERT: B 284 MET cc_start: 0.8234 (mtt) cc_final: 0.7717 (tmm) REVERT: B 397 MET cc_start: 0.3757 (ptp) cc_final: 0.3432 (ptp) REVERT: B 476 PHE cc_start: 0.7705 (m-10) cc_final: 0.7445 (m-80) REVERT: B 551 THR cc_start: 0.6794 (p) cc_final: 0.6549 (t) REVERT: B 622 MET cc_start: 0.7145 (mmm) cc_final: 0.6668 (mmm) REVERT: B 845 GLN cc_start: 0.7932 (tp40) cc_final: 0.7641 (tp-100) outliers start: 20 outliers final: 9 residues processed: 56 average time/residue: 0.3797 time to fit residues: 23.0007 Evaluate side-chains 50 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 805 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN B 315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.107163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.087152 restraints weight = 14498.794| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.11 r_work: 0.3422 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5928 Z= 0.170 Angle : 0.618 13.192 8058 Z= 0.316 Chirality : 0.046 0.179 909 Planarity : 0.004 0.043 1009 Dihedral : 8.954 89.266 854 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.65 % Allowed : 19.18 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.07 (0.31), residues: 692 helix: 0.54 (0.33), residues: 235 sheet: -1.24 (0.40), residues: 153 loop : -1.34 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 643 TYR 0.015 0.001 TYR B 693 PHE 0.026 0.002 PHE B 285 TRP 0.024 0.002 TRP B 325 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 5928) covalent geometry : angle 0.61778 / 0.32 ( 8058) hydrogen bonds : bond 0.03715 / 2.60 ( 238) hydrogen bonds : angle 5.49449 / 3.76 ( 678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.225 Fit side-chains REVERT: B 111 ILE cc_start: 0.7552 (mt) cc_final: 0.7291 (mm) REVERT: B 141 MET cc_start: 0.4696 (mpt) cc_final: 0.4243 (mpm) REVERT: B 266 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7861 (tp) REVERT: B 323 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8261 (tp) REVERT: B 476 PHE cc_start: 0.7856 (m-10) cc_final: 0.7620 (m-80) REVERT: B 622 MET cc_start: 0.7771 (mmm) cc_final: 0.7263 (mmm) REVERT: B 684 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8511 (mt) REVERT: B 845 GLN cc_start: 0.7970 (tp40) cc_final: 0.7685 (tp-100) outliers start: 23 outliers final: 7 residues processed: 62 average time/residue: 0.3607 time to fit residues: 24.1366 Evaluate side-chains 44 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.105264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.085202 restraints weight = 14435.409| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.12 r_work: 0.3387 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5928 Z= 0.171 Angle : 0.620 12.257 8058 Z= 0.313 Chirality : 0.046 0.167 909 Planarity : 0.005 0.059 1009 Dihedral : 8.873 88.062 854 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.01 % Allowed : 21.71 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.07 (0.31), residues: 692 helix: 0.58 (0.32), residues: 235 sheet: -1.19 (0.40), residues: 153 loop : -1.41 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 643 TYR 0.016 0.001 TYR B 776 PHE 0.011 0.002 PHE B 470 TRP 0.009 0.001 TRP B 687 HIS 0.008 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 5928) covalent geometry : angle 0.61999 / 0.31 ( 8058) hydrogen bonds : bond 0.03701 / 2.61 ( 238) hydrogen bonds : angle 5.40203 / 3.70 ( 678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.235 Fit side-chains REVERT: B 111 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7365 (mm) REVERT: B 141 MET cc_start: 0.4665 (mpt) cc_final: 0.4242 (mpm) REVERT: B 266 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7937 (tp) REVERT: B 284 MET cc_start: 0.8394 (mtt) cc_final: 0.7690 (tmm) REVERT: B 476 PHE cc_start: 0.7927 (m-10) cc_final: 0.7695 (m-80) REVERT: B 622 MET cc_start: 0.7833 (mmm) cc_final: 0.7436 (mmm) REVERT: B 845 GLN cc_start: 0.8049 (tp40) cc_final: 0.7776 (tp-100) outliers start: 19 outliers final: 9 residues processed: 55 average time/residue: 0.3611 time to fit residues: 21.5587 Evaluate side-chains 46 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 0.0770 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.0670 chunk 46 optimal weight: 0.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.105252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.085310 restraints weight = 14374.188| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.11 r_work: 0.3373 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5928 Z= 0.133 Angle : 0.590 12.326 8058 Z= 0.296 Chirality : 0.045 0.171 909 Planarity : 0.004 0.046 1009 Dihedral : 8.804 87.940 854 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.38 % Allowed : 22.82 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.92 (0.31), residues: 692 helix: 0.81 (0.33), residues: 235 sheet: -1.15 (0.40), residues: 153 loop : -1.40 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 565 TYR 0.011 0.001 TYR B 313 PHE 0.028 0.002 PHE B 285 TRP 0.010 0.001 TRP B 325 HIS 0.002 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 5928) covalent geometry : angle 0.58974 / 0.30 ( 8058) hydrogen bonds : bond 0.03455 / 2.46 ( 238) hydrogen bonds : angle 5.24229 / 3.56 ( 678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: B 141 MET cc_start: 0.5035 (mpt) cc_final: 0.4624 (mpm) REVERT: B 266 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7898 (tp) REVERT: B 397 MET cc_start: 0.3160 (ptp) cc_final: 0.2923 (ptm) REVERT: B 622 MET cc_start: 0.7802 (mmm) cc_final: 0.7509 (mmm) REVERT: B 845 GLN cc_start: 0.8058 (tp40) cc_final: 0.7771 (tp-100) outliers start: 15 outliers final: 9 residues processed: 50 average time/residue: 0.3539 time to fit residues: 19.2251 Evaluate side-chains 46 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 0.0570 chunk 65 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN B 399 ASN ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.107871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.088878 restraints weight = 14241.862| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.80 r_work: 0.3505 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5928 Z= 0.140 Angle : 0.590 12.269 8058 Z= 0.293 Chirality : 0.045 0.168 909 Planarity : 0.004 0.042 1009 Dihedral : 8.769 87.074 854 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.85 % Allowed : 22.98 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.81 (0.31), residues: 692 helix: 1.01 (0.34), residues: 229 sheet: -1.22 (0.39), residues: 153 loop : -1.31 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 125 TYR 0.012 0.001 TYR B 776 PHE 0.009 0.001 PHE B 470 TRP 0.009 0.001 TRP B 687 HIS 0.003 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 5928) covalent geometry : angle 0.58973 / 0.29 ( 8058) hydrogen bonds : bond 0.03409 / 2.41 ( 238) hydrogen bonds : angle 5.14277 / 3.50 ( 678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: B 141 MET cc_start: 0.4947 (mpt) cc_final: 0.4588 (mpm) REVERT: B 266 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7937 (tt) REVERT: B 284 MET cc_start: 0.7872 (mtt) cc_final: 0.7303 (tmm) REVERT: B 622 MET cc_start: 0.7484 (mmm) cc_final: 0.7062 (mmm) REVERT: B 845 GLN cc_start: 0.7954 (tp40) cc_final: 0.7726 (tp-100) outliers start: 18 outliers final: 9 residues processed: 52 average time/residue: 0.3510 time to fit residues: 19.9181 Evaluate side-chains 46 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.108265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.089302 restraints weight = 14481.188| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.84 r_work: 0.3499 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5928 Z= 0.126 Angle : 0.587 12.230 8058 Z= 0.289 Chirality : 0.045 0.162 909 Planarity : 0.004 0.040 1009 Dihedral : 8.709 86.472 854 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.90 % Allowed : 24.25 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.71 (0.32), residues: 692 helix: 1.11 (0.34), residues: 229 sheet: -1.18 (0.40), residues: 158 loop : -1.26 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 643 TYR 0.012 0.001 TYR B 313 PHE 0.031 0.001 PHE B 285 TRP 0.009 0.001 TRP B 687 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 5928) covalent geometry : angle 0.58708 / 0.29 ( 8058) hydrogen bonds : bond 0.03307 / 2.35 ( 238) hydrogen bonds : angle 5.09929 / 3.47 ( 678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 141 MET cc_start: 0.5056 (mpt) cc_final: 0.4547 (mpm) REVERT: B 194 ILE cc_start: 0.4723 (mm) cc_final: 0.4515 (mm) REVERT: B 284 MET cc_start: 0.7818 (mtt) cc_final: 0.7301 (tmm) REVERT: B 622 MET cc_start: 0.7488 (mmm) cc_final: 0.6953 (mmm) outliers start: 12 outliers final: 9 residues processed: 45 average time/residue: 0.3768 time to fit residues: 18.3936 Evaluate side-chains 44 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 40 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.0370 chunk 51 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.108516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.089537 restraints weight = 14444.150| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.81 r_work: 0.3511 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5928 Z= 0.109 Angle : 0.600 12.283 8058 Z= 0.293 Chirality : 0.045 0.159 909 Planarity : 0.004 0.040 1009 Dihedral : 8.687 86.581 854 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.43 % Allowed : 24.56 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.67 (0.32), residues: 692 helix: 1.24 (0.34), residues: 229 sheet: -1.21 (0.39), residues: 158 loop : -1.27 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 484 TYR 0.014 0.001 TYR B 693 PHE 0.036 0.001 PHE B 285 TRP 0.009 0.001 TRP B 687 HIS 0.002 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 5928) covalent geometry : angle 0.59983 / 0.29 ( 8058) hydrogen bonds : bond 0.03182 / 2.27 ( 238) hydrogen bonds : angle 5.01743 / 3.41 ( 678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 141 MET cc_start: 0.5006 (mpt) cc_final: 0.4475 (mpm) REVERT: B 194 ILE cc_start: 0.4693 (mm) cc_final: 0.4469 (mm) REVERT: B 284 MET cc_start: 0.7859 (mtt) cc_final: 0.7336 (tmm) REVERT: B 320 VAL cc_start: 0.8263 (t) cc_final: 0.7937 (t) outliers start: 9 outliers final: 8 residues processed: 42 average time/residue: 0.3888 time to fit residues: 17.6836 Evaluate side-chains 42 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.106865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.087827 restraints weight = 14292.875| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.78 r_work: 0.3484 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.6695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5928 Z= 0.160 Angle : 0.641 12.160 8058 Z= 0.313 Chirality : 0.046 0.164 909 Planarity : 0.004 0.040 1009 Dihedral : 8.722 85.273 854 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.74 % Allowed : 24.56 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.76 (0.32), residues: 692 helix: 1.10 (0.33), residues: 229 sheet: -1.20 (0.39), residues: 158 loop : -1.31 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 424 TYR 0.011 0.001 TYR B 542 PHE 0.010 0.001 PHE B 470 TRP 0.010 0.001 TRP B 687 HIS 0.004 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 5928) covalent geometry : angle 0.64098 / 0.31 ( 8058) hydrogen bonds : bond 0.03427 / 2.43 ( 238) hydrogen bonds : angle 5.11490 / 3.48 ( 678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.30 seconds wall clock time: 32 minutes 0.34 seconds (1920.34 seconds total)