Starting phenix.real_space_refine on Wed Feb 4 02:50:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lzt_63530/02_2026/9lzt_63530.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lzt_63530/02_2026/9lzt_63530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lzt_63530/02_2026/9lzt_63530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lzt_63530/02_2026/9lzt_63530.map" model { file = "/net/cci-nas-00/data/ceres_data/9lzt_63530/02_2026/9lzt_63530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lzt_63530/02_2026/9lzt_63530.cif" } resolution = 3.1 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= 0.003 sd= 0.458 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 51 5.49 5 Mg 1 5.21 5 S 27 5.16 5 C 5145 2.51 5 N 1438 2.21 5 O 1735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8397 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1083 Classifications: {'RNA': 51} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna2p': 14, 'rna3p': 36} Chain: "B" Number of atoms: 7313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7313 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 889} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" 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: 1.65, per 1000 atoms: 0.20 Number of scatterers: 8397 At special positions: 0 Unit cell: (87.248, 91.504, 118.104, 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 27 16.00 P 51 15.00 Mg 1 11.99 O 1735 8.00 N 1438 7.00 C 5145 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: 0.57 Conformation dependent library (CDL) restraints added in 233.0 milliseconds 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 3 sheets defined 66.3% alpha, 1.5% beta 7 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.778A pdb=" N TYR B 88 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 89 " --> pdb=" O PRO B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 118 through 149 Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 182 through 201 Processing helix chain 'B' and resid 202 through 207 removed outlier: 4.107A pdb=" N GLY B 206 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 207 " --> pdb=" O ARG B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 224 through 243 removed outlier: 3.618A pdb=" N CYS B 228 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 265 through 290 Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.737A pdb=" N ASN B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.634A pdb=" N PHE B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 305 through 310' Processing helix chain 'B' and resid 329 through 333 removed outlier: 3.634A pdb=" N ARG B 333 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 341 removed outlier: 3.794A pdb=" N ASP B 338 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B 341 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 373 removed outlier: 3.743A pdb=" N TYR B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 372 " --> pdb=" O TYR B 368 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 410 through 420 removed outlier: 3.589A pdb=" N LEU B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 removed outlier: 4.058A pdb=" N ARG B 424 " --> pdb=" O ARG B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 474 Processing helix chain 'B' and resid 477 through 502 Processing helix chain 'B' and resid 512 through 519 removed outlier: 3.698A pdb=" N ALA B 516 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N PHE B 517 " --> pdb=" O GLU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 535 removed outlier: 3.653A pdb=" N PHE B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 Processing helix chain 'B' and resid 561 through 571 Processing helix chain 'B' and resid 586 through 596 Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 610 through 619 Processing helix chain 'B' and resid 620 through 634 removed outlier: 3.685A pdb=" N ILE B 634 " --> pdb=" O ARG B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 661 through 675 Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.530A pdb=" N LYS B 684 " --> pdb=" O GLN B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 689 removed outlier: 3.621A pdb=" N ILE B 688 " --> pdb=" O ARG B 685 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 689 " --> pdb=" O SER B 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 685 through 689' Processing helix chain 'B' and resid 694 through 744 removed outlier: 3.572A pdb=" N ARG B 725 " --> pdb=" O ASN B 721 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR B 726 " --> pdb=" O ILE B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 766 removed outlier: 3.885A pdb=" N GLY B 766 " --> pdb=" O LYS B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 794 removed outlier: 4.481A pdb=" N LYS B 776 " --> pdb=" O PRO B 772 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP B 777 " --> pdb=" O ASP B 773 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU B 794 " --> pdb=" O ILE B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 803 removed outlier: 3.589A pdb=" N LEU B 800 " --> pdb=" O ASN B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 826 Processing helix chain 'B' and resid 835 through 847 removed outlier: 3.501A pdb=" N LEU B 847 " --> pdb=" O ARG B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 863 removed outlier: 3.538A pdb=" N VAL B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 863 " --> pdb=" O ASN B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 874 removed outlier: 5.778A pdb=" N HIS B 871 " --> pdb=" O ALA B 867 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA B 872 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR B 873 " --> pdb=" O TYR B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 877 No H-bonds generated for 'chain 'B' and resid 875 through 877' Processing helix chain 'B' and resid 882 through 900 Processing helix chain 'B' and resid 905 through 918 removed outlier: 3.706A pdb=" N GLU B 909 " --> pdb=" O GLY B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 929 Processing helix chain 'B' and resid 930 through 934 removed outlier: 4.415A pdb=" N TYR B 934 " --> pdb=" O PRO B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 944 Processing helix chain 'B' and resid 950 through 955 removed outlier: 3.701A pdb=" N ALA B 953 " --> pdb=" O ARG B 950 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA B 954 " --> pdb=" O ASN B 951 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60 Processing sheet with id=AA3, first strand: chain 'B' and resid 213 through 216 removed outlier: 3.637A pdb=" N GLU B 216 " --> pdb=" O ASN B 219 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN B 219 " --> pdb=" O GLU B 216 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2358 1.34 - 1.45: 1651 1.45 - 1.57: 4498 1.57 - 1.69: 101 1.69 - 1.81: 46 Bond restraints: 8654 Sorted by residual: bond pdb=" C3' A A 48 " pdb=" O3' A A 48 " ideal model delta sigma weight residual 1.427 1.447 -0.020 1.50e-02 4.44e+03 1.71e+00 bond pdb=" C3' A A 50 " pdb=" O3' A A 50 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.35e+00 bond pdb=" C GLU B 539 " pdb=" N PRO B 540 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.84e-01 bond pdb=" O3' A A 48 " pdb=" P C A 49 " ideal model delta sigma weight residual 1.607 1.619 -0.012 1.50e-02 4.44e+03 6.54e-01 bond pdb=" C ASN B 797 " pdb=" N PRO B 798 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 5.96e-01 ... (remaining 8649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 11810 1.94 - 3.88: 77 3.88 - 5.82: 14 5.82 - 7.76: 1 7.76 - 9.70: 1 Bond angle restraints: 11903 Sorted by residual: angle pdb=" N ARG B 315 " pdb=" CA ARG B 315 " pdb=" C ARG B 315 " ideal model delta sigma weight residual 114.56 109.63 4.93 1.27e+00 6.20e-01 1.51e+01 angle pdb=" C3' A A 48 " pdb=" O3' A A 48 " pdb=" P C A 49 " ideal model delta sigma weight residual 120.20 125.53 -5.33 1.50e+00 4.44e-01 1.26e+01 angle pdb=" C3' A A 50 " pdb=" O3' A A 50 " pdb=" P G A 51 " ideal model delta sigma weight residual 120.20 124.93 -4.73 1.50e+00 4.44e-01 9.95e+00 angle pdb=" C4' A A 48 " pdb=" C3' A A 48 " pdb=" O3' A A 48 " ideal model delta sigma weight residual 109.40 112.96 -3.56 1.50e+00 4.44e-01 5.62e+00 angle pdb=" O3' A A 50 " pdb=" C3' A A 50 " pdb=" C2' A A 50 " ideal model delta sigma weight residual 109.50 113.02 -3.52 1.50e+00 4.44e-01 5.50e+00 ... (remaining 11898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 5136 35.41 - 70.81: 135 70.81 - 106.22: 20 106.22 - 141.63: 0 141.63 - 177.03: 4 Dihedral angle restraints: 5295 sinusoidal: 2616 harmonic: 2679 Sorted by residual: dihedral pdb=" O4' C A 40 " pdb=" C1' C A 40 " pdb=" N1 C A 40 " pdb=" C2 C A 40 " ideal model delta sinusoidal sigma weight residual 200.00 58.21 141.79 1 1.50e+01 4.44e-03 7.62e+01 dihedral pdb=" O4' C A 37 " pdb=" C1' C A 37 " pdb=" N1 C A 37 " pdb=" C2 C A 37 " ideal model delta sinusoidal sigma weight residual -128.00 49.03 -177.03 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C4' A A 50 " pdb=" C3' A A 50 " pdb=" O3' A A 50 " pdb=" P G A 51 " ideal model delta sinusoidal sigma weight residual -110.00 61.44 -171.44 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 5292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1027 0.037 - 0.075: 261 0.075 - 0.112: 52 0.112 - 0.150: 2 0.150 - 0.187: 2 Chirality restraints: 1344 Sorted by residual: chirality pdb=" C3' A A 48 " pdb=" C4' A A 48 " pdb=" O3' A A 48 " pdb=" C2' A A 48 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" C3' A A 50 " pdb=" C4' A A 50 " pdb=" O3' A A 50 " pdb=" C2' A A 50 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" C1' C A 40 " pdb=" O4' C A 40 " pdb=" C2' C A 40 " pdb=" N1 C A 40 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 1341 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 797 " -0.041 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO B 798 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 798 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 798 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 936 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO B 937 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 937 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 937 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 930 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO B 931 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 931 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 931 " -0.016 5.00e-02 4.00e+02 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1201 2.76 - 3.29: 8503 3.29 - 3.83: 14202 3.83 - 4.36: 16828 4.36 - 4.90: 28132 Nonbonded interactions: 68866 Sorted by model distance: nonbonded pdb=" OP1 A A 32 " pdb=" OH TYR B 415 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR B 726 " pdb=" O LEU B 942 " model vdw 2.256 3.040 nonbonded pdb=" N2 G A 35 " pdb=" OD1 ASN B 951 " model vdw 2.284 3.120 nonbonded pdb=" O LYS B 15 " pdb=" OG1 THR B 27 " model vdw 2.290 3.040 nonbonded pdb=" OD2 ASP B 113 " pdb=" ND2 ASN B 115 " model vdw 2.301 3.120 ... (remaining 68861 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: 1.110 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.520 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 0.022 8654 Z= 0.092 Angle : 0.441 9.700 11903 Z= 0.256 Chirality : 0.034 0.187 1344 Planarity : 0.003 0.063 1347 Dihedral : 15.002 177.034 3571 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.32 % Allowed : 3.86 % Favored : 93.82 % 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: -1.94 (0.25), residues: 898 helix: -0.55 (0.20), residues: 551 sheet: -2.22 (2.00), residues: 10 loop : -2.43 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 899 TYR 0.012 0.001 TYR B 708 PHE 0.009 0.001 PHE B 884 TRP 0.004 0.001 TRP B 256 HIS 0.003 0.001 HIS B 888 Details of bonding type rmsd covalent geometry : bond 0.00157 ( 8654) covalent geometry : angle 0.44101 (11903) hydrogen bonds : bond 0.13919 ( 399) hydrogen bonds : angle 5.01435 ( 1117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 ASN cc_start: 0.7438 (m-40) cc_final: 0.7158 (m110) REVERT: B 312 GLN cc_start: 0.5784 (mm-40) cc_final: 0.5429 (mm-40) REVERT: B 372 ILE cc_start: 0.4446 (OUTLIER) cc_final: 0.4121 (tp) REVERT: B 545 ARG cc_start: 0.7214 (mtt180) cc_final: 0.6078 (mmm160) REVERT: B 651 GLU cc_start: 0.7324 (tt0) cc_final: 0.6707 (tt0) outliers start: 18 outliers final: 2 residues processed: 200 average time/residue: 0.1300 time to fit residues: 32.2798 Evaluate side-chains 132 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 880 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.0570 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS B 322 GLN B 428 ASN B 559 ASN B 620 ASN ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.092422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.077419 restraints weight = 22072.455| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.24 r_work: 0.3165 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8654 Z= 0.130 Angle : 0.563 9.426 11903 Z= 0.292 Chirality : 0.037 0.187 1344 Planarity : 0.004 0.044 1347 Dihedral : 18.450 177.332 1778 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.80 % Allowed : 11.58 % Favored : 86.62 % 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: -0.68 (0.28), residues: 898 helix: 0.53 (0.22), residues: 547 sheet: -2.34 (1.75), residues: 10 loop : -2.02 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 923 TYR 0.022 0.001 TYR B 416 PHE 0.014 0.001 PHE B 534 TRP 0.005 0.001 TRP B 241 HIS 0.005 0.001 HIS B 888 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8654) covalent geometry : angle 0.56308 (11903) hydrogen bonds : bond 0.04345 ( 399) hydrogen bonds : angle 4.08156 ( 1117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7380 (ttt) REVERT: B 312 GLN cc_start: 0.6465 (mm-40) cc_final: 0.6010 (mm-40) REVERT: B 313 TYR cc_start: 0.7530 (m-80) cc_final: 0.7306 (m-80) REVERT: B 365 PHE cc_start: 0.7472 (t80) cc_final: 0.7163 (t80) REVERT: B 545 ARG cc_start: 0.7912 (mtt180) cc_final: 0.6174 (mmm160) REVERT: B 575 ASP cc_start: 0.8091 (p0) cc_final: 0.7879 (p0) REVERT: B 579 ASN cc_start: 0.8343 (m-40) cc_final: 0.8079 (m-40) outliers start: 14 outliers final: 8 residues processed: 142 average time/residue: 0.1047 time to fit residues: 19.3193 Evaluate side-chains 125 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 897 ASN Chi-restraints excluded: chain B residue 909 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 0.0170 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 0.0470 chunk 68 optimal weight: 0.0670 chunk 72 optimal weight: 0.7980 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.091311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.076207 restraints weight = 21924.301| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.23 r_work: 0.3140 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8654 Z= 0.115 Angle : 0.545 10.285 11903 Z= 0.282 Chirality : 0.037 0.187 1344 Planarity : 0.004 0.067 1347 Dihedral : 18.454 178.040 1778 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.54 % Allowed : 14.16 % Favored : 84.30 % 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: -0.29 (0.28), residues: 898 helix: 0.89 (0.22), residues: 544 sheet: -3.70 (0.98), residues: 16 loop : -1.82 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 923 TYR 0.024 0.001 TYR B 416 PHE 0.013 0.001 PHE B 534 TRP 0.004 0.001 TRP B 241 HIS 0.005 0.001 HIS B 888 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8654) covalent geometry : angle 0.54473 (11903) hydrogen bonds : bond 0.04097 ( 399) hydrogen bonds : angle 4.04886 ( 1117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ILE cc_start: 0.8317 (tt) cc_final: 0.8093 (tt) REVERT: B 312 GLN cc_start: 0.6599 (mm-40) cc_final: 0.6087 (mm-40) REVERT: B 313 TYR cc_start: 0.7415 (m-80) cc_final: 0.7062 (m-80) REVERT: B 365 PHE cc_start: 0.7529 (t80) cc_final: 0.7236 (t80) REVERT: B 545 ARG cc_start: 0.7991 (mtt180) cc_final: 0.6151 (mmm160) REVERT: B 656 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7708 (mtpp) outliers start: 12 outliers final: 9 residues processed: 127 average time/residue: 0.1108 time to fit residues: 18.2595 Evaluate side-chains 124 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 897 ASN Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 21 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 HIS ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.086752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.071384 restraints weight = 22350.386| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.27 r_work: 0.3029 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8654 Z= 0.140 Angle : 0.579 10.501 11903 Z= 0.300 Chirality : 0.039 0.184 1344 Planarity : 0.004 0.076 1347 Dihedral : 18.473 178.717 1778 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.93 % Allowed : 13.51 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.28), residues: 898 helix: 1.06 (0.22), residues: 536 sheet: -1.82 (1.86), residues: 5 loop : -1.60 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 923 TYR 0.024 0.002 TYR B 416 PHE 0.016 0.001 PHE B 534 TRP 0.006 0.001 TRP B 241 HIS 0.006 0.001 HIS B 888 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8654) covalent geometry : angle 0.57865 (11903) hydrogen bonds : bond 0.04612 ( 399) hydrogen bonds : angle 4.08827 ( 1117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 312 GLN cc_start: 0.6694 (mm-40) cc_final: 0.6152 (mm-40) REVERT: B 397 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8001 (tp) REVERT: B 545 ARG cc_start: 0.8362 (mtt180) cc_final: 0.6321 (mmm160) REVERT: B 575 ASP cc_start: 0.8157 (p0) cc_final: 0.7893 (p0) REVERT: B 651 GLU cc_start: 0.8178 (tt0) cc_final: 0.7932 (tp30) outliers start: 15 outliers final: 8 residues processed: 135 average time/residue: 0.1116 time to fit residues: 19.6479 Evaluate side-chains 126 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 897 ASN Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 36 optimal weight: 0.0060 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 87 optimal weight: 0.0050 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** 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 = 0.3453 r_free = 0.3453 target = 0.084952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.069704 restraints weight = 22017.077| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.25 r_work: 0.2990 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8654 Z= 0.150 Angle : 0.604 10.448 11903 Z= 0.313 Chirality : 0.039 0.185 1344 Planarity : 0.004 0.085 1347 Dihedral : 18.620 178.536 1778 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.42 % Allowed : 14.54 % Favored : 84.04 % 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: 0.09 (0.28), residues: 898 helix: 1.11 (0.22), residues: 534 sheet: -1.78 (1.61), residues: 5 loop : -1.54 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 176 TYR 0.026 0.002 TYR B 88 PHE 0.018 0.002 PHE B 365 TRP 0.005 0.001 TRP B 241 HIS 0.007 0.001 HIS B 888 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8654) covalent geometry : angle 0.60428 (11903) hydrogen bonds : bond 0.04684 ( 399) hydrogen bonds : angle 4.13916 ( 1117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 312 GLN cc_start: 0.7002 (mm-40) cc_final: 0.6510 (mm-40) REVERT: B 397 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8180 (tp) REVERT: B 420 ASN cc_start: 0.9004 (m-40) cc_final: 0.8308 (m-40) REVERT: B 545 ARG cc_start: 0.8662 (mtt180) cc_final: 0.6329 (mmm160) REVERT: B 575 ASP cc_start: 0.8425 (p0) cc_final: 0.8140 (p0) outliers start: 11 outliers final: 8 residues processed: 126 average time/residue: 0.1064 time to fit residues: 17.4716 Evaluate side-chains 128 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 897 ASN Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 65 optimal weight: 0.0970 chunk 67 optimal weight: 3.9990 chunk 22 optimal weight: 0.0030 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 0.0010 chunk 76 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.086506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.071203 restraints weight = 22080.658| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.26 r_work: 0.3034 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8654 Z= 0.120 Angle : 0.585 11.006 11903 Z= 0.302 Chirality : 0.038 0.186 1344 Planarity : 0.004 0.086 1347 Dihedral : 18.621 178.363 1778 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.42 % Allowed : 15.44 % Favored : 83.14 % 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: 0.28 (0.28), residues: 898 helix: 1.28 (0.23), residues: 534 sheet: -1.44 (1.69), residues: 5 loop : -1.51 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 176 TYR 0.021 0.001 TYR B 416 PHE 0.013 0.001 PHE B 534 TRP 0.004 0.001 TRP B 423 HIS 0.005 0.001 HIS B 888 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8654) covalent geometry : angle 0.58507 (11903) hydrogen bonds : bond 0.04311 ( 399) hydrogen bonds : angle 4.03818 ( 1117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.7475 (mptt) cc_final: 0.7241 (mttt) REVERT: B 312 GLN cc_start: 0.6778 (mm-40) cc_final: 0.6268 (mm-40) REVERT: B 397 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8076 (tp) REVERT: B 420 ASN cc_start: 0.8872 (m-40) cc_final: 0.8248 (m110) REVERT: B 545 ARG cc_start: 0.8455 (mtt180) cc_final: 0.6260 (mmm160) REVERT: B 575 ASP cc_start: 0.8063 (p0) cc_final: 0.7699 (p0) REVERT: B 651 GLU cc_start: 0.8255 (tp30) cc_final: 0.7858 (tp30) REVERT: B 775 ARG cc_start: 0.7608 (tpp80) cc_final: 0.7329 (tpp80) outliers start: 11 outliers final: 7 residues processed: 124 average time/residue: 0.1005 time to fit residues: 16.1186 Evaluate side-chains 123 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 897 ASN Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 82 optimal weight: 0.8980 chunk 51 optimal weight: 0.0060 chunk 77 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN ** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.087054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.071686 restraints weight = 22483.706| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.27 r_work: 0.3040 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8654 Z= 0.121 Angle : 0.599 11.633 11903 Z= 0.308 Chirality : 0.038 0.188 1344 Planarity : 0.004 0.087 1347 Dihedral : 18.629 177.992 1778 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.54 % Allowed : 15.70 % Favored : 82.75 % 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: 0.20 (0.28), residues: 898 helix: 1.23 (0.23), residues: 538 sheet: -3.37 (0.91), residues: 16 loop : -1.48 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 868 TYR 0.033 0.001 TYR B 807 PHE 0.013 0.001 PHE B 534 TRP 0.004 0.001 TRP B 423 HIS 0.005 0.001 HIS B 888 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8654) covalent geometry : angle 0.59907 (11903) hydrogen bonds : bond 0.04251 ( 399) hydrogen bonds : angle 4.01042 ( 1117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 312 GLN cc_start: 0.6854 (mm-40) cc_final: 0.6378 (mm-40) REVERT: B 397 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8105 (tp) REVERT: B 420 ASN cc_start: 0.8861 (m-40) cc_final: 0.8267 (m110) REVERT: B 545 ARG cc_start: 0.8492 (mtt180) cc_final: 0.6262 (mmm160) REVERT: B 575 ASP cc_start: 0.7969 (p0) cc_final: 0.7293 (p0) REVERT: B 651 GLU cc_start: 0.8550 (tp30) cc_final: 0.8284 (mm-30) outliers start: 12 outliers final: 8 residues processed: 129 average time/residue: 0.1145 time to fit residues: 19.0871 Evaluate side-chains 124 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 897 ASN Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.0270 chunk 30 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.085406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.069964 restraints weight = 22144.938| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.26 r_work: 0.3001 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8654 Z= 0.141 Angle : 0.637 12.374 11903 Z= 0.327 Chirality : 0.039 0.193 1344 Planarity : 0.004 0.089 1347 Dihedral : 18.694 178.059 1778 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.42 % Allowed : 15.96 % Favored : 82.63 % 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: 0.26 (0.28), residues: 898 helix: 1.38 (0.23), residues: 521 sheet: -3.19 (1.01), residues: 16 loop : -1.50 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 648 TYR 0.019 0.002 TYR B 416 PHE 0.015 0.001 PHE B 534 TRP 0.004 0.001 TRP B 423 HIS 0.006 0.001 HIS B 888 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8654) covalent geometry : angle 0.63651 (11903) hydrogen bonds : bond 0.04493 ( 399) hydrogen bonds : angle 4.12213 ( 1117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 312 GLN cc_start: 0.6975 (mm-40) cc_final: 0.6494 (mm-40) REVERT: B 397 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8079 (tp) REVERT: B 420 ASN cc_start: 0.8817 (m-40) cc_final: 0.8216 (m110) REVERT: B 545 ARG cc_start: 0.8594 (mtt180) cc_final: 0.6389 (mmm160) REVERT: B 575 ASP cc_start: 0.7972 (p0) cc_final: 0.7698 (p0) outliers start: 11 outliers final: 8 residues processed: 126 average time/residue: 0.1213 time to fit residues: 19.7747 Evaluate side-chains 125 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 897 ASN Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 87 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 83 optimal weight: 0.0060 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** 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 = 0.3443 r_free = 0.3443 target = 0.084064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.068641 restraints weight = 22076.265| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.26 r_work: 0.2974 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8654 Z= 0.154 Angle : 0.662 12.362 11903 Z= 0.343 Chirality : 0.040 0.194 1344 Planarity : 0.005 0.088 1347 Dihedral : 18.786 178.011 1778 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.54 % Allowed : 16.73 % Favored : 81.72 % 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: 0.26 (0.28), residues: 898 helix: 1.27 (0.23), residues: 529 sheet: -3.04 (1.12), residues: 16 loop : -1.39 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 251 TYR 0.020 0.002 TYR B 416 PHE 0.017 0.001 PHE B 534 TRP 0.004 0.001 TRP B 241 HIS 0.006 0.001 HIS B 888 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8654) covalent geometry : angle 0.66206 (11903) hydrogen bonds : bond 0.04764 ( 399) hydrogen bonds : angle 4.27094 ( 1117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 312 GLN cc_start: 0.7063 (mm-40) cc_final: 0.6563 (mm-40) REVERT: B 397 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8216 (tp) REVERT: B 420 ASN cc_start: 0.8936 (m-40) cc_final: 0.8338 (m110) REVERT: B 545 ARG cc_start: 0.8782 (mtt180) cc_final: 0.6424 (mmm160) REVERT: B 575 ASP cc_start: 0.8264 (p0) cc_final: 0.7929 (p0) outliers start: 12 outliers final: 8 residues processed: 127 average time/residue: 0.1321 time to fit residues: 21.6825 Evaluate side-chains 125 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 897 ASN Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.082331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.067036 restraints weight = 22153.643| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.28 r_work: 0.2933 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8654 Z= 0.181 Angle : 0.695 12.148 11903 Z= 0.360 Chirality : 0.041 0.196 1344 Planarity : 0.005 0.090 1347 Dihedral : 18.959 177.677 1778 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.54 % Allowed : 16.34 % Favored : 82.11 % 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: 0.09 (0.28), residues: 898 helix: 1.00 (0.22), residues: 544 sheet: 0.42 (2.43), residues: 5 loop : -1.45 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 176 TYR 0.025 0.002 TYR B 88 PHE 0.032 0.002 PHE B 314 TRP 0.005 0.001 TRP B 241 HIS 0.007 0.001 HIS B 888 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8654) covalent geometry : angle 0.69474 (11903) hydrogen bonds : bond 0.05092 ( 399) hydrogen bonds : angle 4.39713 ( 1117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 312 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6769 (mm-40) REVERT: B 313 TYR cc_start: 0.8057 (m-80) cc_final: 0.7667 (m-80) REVERT: B 397 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8281 (tp) REVERT: B 420 ASN cc_start: 0.8939 (m-40) cc_final: 0.8340 (m110) REVERT: B 545 ARG cc_start: 0.8841 (mtt180) cc_final: 0.6473 (mmm160) REVERT: B 575 ASP cc_start: 0.8291 (p0) cc_final: 0.7957 (p0) outliers start: 12 outliers final: 9 residues processed: 127 average time/residue: 0.1136 time to fit residues: 18.8926 Evaluate side-chains 125 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 897 ASN Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 59 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 chunk 67 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** 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 = 0.3451 r_free = 0.3451 target = 0.084349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.069106 restraints weight = 22227.795| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.25 r_work: 0.2986 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8654 Z= 0.138 Angle : 0.686 16.279 11903 Z= 0.348 Chirality : 0.039 0.182 1344 Planarity : 0.005 0.089 1347 Dihedral : 18.938 177.489 1778 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.42 % Allowed : 16.73 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.29), residues: 898 helix: 1.23 (0.23), residues: 540 sheet: -3.04 (1.15), residues: 16 loop : -1.28 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 648 TYR 0.019 0.001 TYR B 416 PHE 0.017 0.001 PHE B 534 TRP 0.002 0.001 TRP B 241 HIS 0.005 0.001 HIS B 888 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8654) covalent geometry : angle 0.68609 (11903) hydrogen bonds : bond 0.04548 ( 399) hydrogen bonds : angle 4.29073 ( 1117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1926.42 seconds wall clock time: 33 minutes 47.71 seconds (2027.71 seconds total)