Starting phenix.real_space_refine on Thu Jul 2 12:06:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lzt_63530/07_2026/9lzt_63530.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lzt_63530/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9lzt_63530/07_2026/9lzt_63530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lzt_63530/07_2026/9lzt_63530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lzt_63530/07_2026/9lzt_63530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lzt_63530/07_2026/9lzt_63530.map" } 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-dev-6108/lib/python3.11/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: 1.97, per 1000 atoms: 0.23 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: 0.87 Conformation dependent library (CDL) restraints added in 299.3 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: 1.04 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: 1.44 Time building geometry restraints manager: 1.12 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=" N9 A A 27 " pdb=" C4 A A 27 " ideal model delta sigma weight residual 1.374 1.380 -0.006 6.00e-03 2.78e+04 9.67e-01 bond pdb=" N1 C A 40 " pdb=" C2 C A 40 " ideal model delta sigma weight residual 1.397 1.407 -0.010 1.00e-02 1.00e+04 9.56e-01 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 ... (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=" C1' C A 40 " pdb=" N1 C A 40 " pdb=" C2 C A 40 " ideal model delta sigma weight residual 118.80 123.99 -5.19 1.10e+00 8.26e-01 2.23e+01 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=" N1 C A 40 " pdb=" C2 C A 40 " pdb=" O2 C A 40 " ideal model delta sigma weight residual 118.90 121.21 -2.31 6.00e-01 2.78e+00 1.48e+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=" O2 C A 40 " pdb=" C2 C A 40 " pdb=" N3 C A 40 " ideal model delta sigma weight residual 121.90 119.63 2.27 7.00e-01 2.04e+00 1.05e+01 ... (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: 1.390 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.050 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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= 0.099 Angle : 0.441 9.700 11903 Z= 0.289 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/Z covalent geometry : bond 0.00157 / 0.10 ( 8654) covalent geometry : angle 0.44109 / 0.29 (11903) hydrogen bonds : bond 0.13919 / 12.87 ( 399) hydrogen bonds : angle 5.01435 / 6.36 ( 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 : 0.335 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: 0.1452 time to fit residues: 36.1638 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 : 0.304 ------------------------------------------------------------------------------- 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... ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS B 263 ASN B 428 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.094615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.079839 restraints weight = 22329.139| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.23 r_work: 0.3224 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8654 Z= 0.143 Angle : 0.592 10.740 11903 Z= 0.309 Chirality : 0.038 0.199 1344 Planarity : 0.004 0.057 1347 Dihedral : 18.531 176.077 1778 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.80 % Allowed : 10.04 % Favored : 88.16 % 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: -0.74 (0.28), residues: 898 helix: 0.55 (0.22), residues: 538 sheet: -3.64 (1.47), residues: 10 loop : -2.07 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 648 TYR 0.020 0.001 TYR B 416 PHE 0.014 0.001 PHE B 314 TRP 0.005 0.001 TRP B 241 HIS 0.006 0.001 HIS B 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8654) covalent geometry : angle 0.59167 / 0.31 (11903) hydrogen bonds : bond 0.04595 / 4.50 ( 399) hydrogen bonds : angle 4.18702 / 5.07 ( 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 146 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7792 (mtpp) REVERT: B 312 GLN cc_start: 0.6272 (mm-40) cc_final: 0.5836 (mm-40) REVERT: B 545 ARG cc_start: 0.7641 (mtt180) cc_final: 0.6158 (mmm160) REVERT: B 656 LYS cc_start: 0.8130 (mtpp) cc_final: 0.7776 (mtpp) outliers start: 14 outliers final: 9 residues processed: 139 average time/residue: 0.1227 time to fit residues: 22.2758 Evaluate side-chains 136 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 402 LEU 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: 6.9990 chunk 75 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 0.0070 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 635 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 = 0.3607 r_free = 0.3607 target = 0.093022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.078143 restraints weight = 22029.878| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.21 r_work: 0.3182 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8654 Z= 0.131 Angle : 0.562 10.341 11903 Z= 0.295 Chirality : 0.038 0.197 1344 Planarity : 0.004 0.064 1347 Dihedral : 18.502 177.469 1778 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.80 % Allowed : 12.48 % Favored : 85.71 % 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: -0.40 (0.28), residues: 898 helix: 0.80 (0.22), residues: 546 sheet: -3.92 (0.94), residues: 16 loop : -1.86 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 923 TYR 0.022 0.001 TYR B 416 PHE 0.017 0.001 PHE B 314 TRP 0.005 0.001 TRP B 241 HIS 0.006 0.001 HIS B 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 8654) covalent geometry : angle 0.56220 / 0.30 (11903) hydrogen bonds : bond 0.04291 / 4.23 ( 399) hydrogen bonds : angle 4.06382 / 4.91 ( 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 144 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.352 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 23 LYS cc_start: 0.8182 (mtmt) cc_final: 0.7952 (mtpp) REVERT: B 77 LYS cc_start: 0.7050 (mptt) cc_final: 0.6815 (mptt) REVERT: B 312 GLN cc_start: 0.6338 (mm-40) cc_final: 0.5914 (mm-40) REVERT: B 313 TYR cc_start: 0.7499 (m-80) cc_final: 0.7206 (m-80) REVERT: B 545 ARG cc_start: 0.7837 (mtt180) cc_final: 0.6182 (mmm160) REVERT: B 656 LYS cc_start: 0.8160 (mtpp) cc_final: 0.7631 (mtpp) outliers start: 14 outliers final: 13 residues processed: 140 average time/residue: 0.1274 time to fit residues: 23.1076 Evaluate side-chains 134 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 359 VAL 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 793 LEU 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 898 GLU Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 909 GLU 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: 0.6980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.0050 chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 322 GLN B 620 ASN ** B 695 ASN ** 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 = 0.3584 r_free = 0.3584 target = 0.091903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.076843 restraints weight = 22356.074| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.23 r_work: 0.3155 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8654 Z= 0.126 Angle : 0.544 10.139 11903 Z= 0.288 Chirality : 0.038 0.194 1344 Planarity : 0.004 0.069 1347 Dihedral : 18.491 177.936 1778 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.80 % Allowed : 13.77 % Favored : 84.43 % 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: -0.19 (0.28), residues: 898 helix: 0.99 (0.22), residues: 542 sheet: -3.83 (0.92), residues: 16 loop : -1.80 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 923 TYR 0.023 0.001 TYR B 416 PHE 0.015 0.001 PHE B 314 TRP 0.005 0.001 TRP B 241 HIS 0.006 0.001 HIS B 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 8654) covalent geometry : angle 0.54427 / 0.29 (11903) hydrogen bonds : bond 0.04200 / 4.19 ( 399) hydrogen bonds : angle 4.00111 / 4.79 ( 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 136 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.357 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 23 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7992 (mtpp) REVERT: B 312 GLN cc_start: 0.6564 (mm-40) cc_final: 0.6144 (mm-40) REVERT: B 313 TYR cc_start: 0.7446 (m-80) cc_final: 0.7106 (m-80) REVERT: B 365 PHE cc_start: 0.7664 (t80) cc_final: 0.7276 (t80) REVERT: B 545 ARG cc_start: 0.7998 (mtt180) cc_final: 0.6268 (mmm160) outliers start: 14 outliers final: 12 residues processed: 132 average time/residue: 0.1221 time to fit residues: 21.0364 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 : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 ASP 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 422 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 898 GLU Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 909 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 36 optimal weight: 0.0020 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 0.0270 chunk 2 optimal weight: 5.9990 overall best weight: 0.9650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 HIS ** 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 = 0.3510 r_free = 0.3510 target = 0.087784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.072518 restraints weight = 22050.449| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.24 r_work: 0.3055 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8654 Z= 0.172 Angle : 0.622 10.663 11903 Z= 0.329 Chirality : 0.040 0.194 1344 Planarity : 0.004 0.074 1347 Dihedral : 18.506 178.800 1778 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.57 % Allowed : 12.74 % Favored : 84.68 % 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: -0.11 (0.28), residues: 898 helix: 0.96 (0.22), residues: 542 sheet: -3.60 (0.95), residues: 16 loop : -1.58 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 923 TYR 0.025 0.002 TYR B 416 PHE 0.018 0.002 PHE B 534 TRP 0.007 0.001 TRP B 241 HIS 0.007 0.001 HIS B 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 8654) covalent geometry : angle 0.62161 / 0.33 (11903) hydrogen bonds : bond 0.04822 / 4.84 ( 399) hydrogen bonds : angle 4.10748 / 4.95 ( 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 144 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 312 GLN cc_start: 0.6651 (mm-40) cc_final: 0.6173 (mm-40) REVERT: B 313 TYR cc_start: 0.7539 (m-80) cc_final: 0.7139 (m-80) REVERT: B 363 MET cc_start: 0.7673 (mtp) cc_final: 0.7353 (mmm) REVERT: B 365 PHE cc_start: 0.7716 (t80) cc_final: 0.7223 (t80) REVERT: B 397 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8137 (tp) REVERT: B 545 ARG cc_start: 0.8158 (mtt180) cc_final: 0.6406 (mmm160) REVERT: B 575 ASP cc_start: 0.8370 (p0) cc_final: 0.7848 (p0) outliers start: 20 outliers final: 13 residues processed: 138 average time/residue: 0.1171 time to fit residues: 21.1406 Evaluate side-chains 130 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 183 ASP 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 400 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 898 GLU Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 909 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 65 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 68 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 559 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 = 0.3513 r_free = 0.3513 target = 0.088033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.072785 restraints weight = 21994.688| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.24 r_work: 0.3062 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8654 Z= 0.141 Angle : 0.614 10.857 11903 Z= 0.325 Chirality : 0.040 0.194 1344 Planarity : 0.004 0.081 1347 Dihedral : 18.502 178.499 1778 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.67 % Allowed : 14.93 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.28), residues: 898 helix: 1.00 (0.22), residues: 542 sheet: -1.24 (2.22), residues: 5 loop : -1.57 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 648 TYR 0.024 0.001 TYR B 416 PHE 0.016 0.001 PHE B 314 TRP 0.004 0.001 TRP B 241 HIS 0.006 0.001 HIS B 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8654) covalent geometry : angle 0.61371 / 0.33 (11903) hydrogen bonds : bond 0.04585 / 4.59 ( 399) hydrogen bonds : angle 4.10564 / 4.95 ( 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 131 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.312 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 312 GLN cc_start: 0.6712 (mm-40) cc_final: 0.6215 (mm-40) REVERT: B 313 TYR cc_start: 0.7585 (m-80) cc_final: 0.7178 (m-80) REVERT: B 365 PHE cc_start: 0.7678 (t80) cc_final: 0.7314 (t80) REVERT: B 397 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8105 (tp) REVERT: B 545 ARG cc_start: 0.8194 (mtt180) cc_final: 0.6377 (mmm160) REVERT: B 575 ASP cc_start: 0.8154 (p0) cc_final: 0.7923 (p0) REVERT: B 869 TYR cc_start: 0.8821 (m-10) cc_final: 0.8610 (m-80) outliers start: 13 outliers final: 11 residues processed: 127 average time/residue: 0.1224 time to fit residues: 20.2965 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 : 0.312 ------------------------------------------------------------------------------- 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 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 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 898 GLU 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: 2.9990 chunk 51 optimal weight: 0.0980 chunk 77 optimal weight: 0.9980 chunk 90 optimal weight: 0.0670 chunk 47 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.0070 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3522 r_free = 0.3522 target = 0.088517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.073350 restraints weight = 22285.598| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.27 r_work: 0.3075 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8654 Z= 0.125 Angle : 0.606 11.707 11903 Z= 0.318 Chirality : 0.039 0.198 1344 Planarity : 0.004 0.080 1347 Dihedral : 18.522 178.546 1778 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.42 % Allowed : 15.06 % Favored : 83.53 % 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: 0.11 (0.28), residues: 898 helix: 1.11 (0.22), residues: 542 sheet: -1.32 (2.24), residues: 5 loop : -1.60 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 648 TYR 0.025 0.001 TYR B 416 PHE 0.015 0.001 PHE B 314 TRP 0.003 0.001 TRP B 423 HIS 0.005 0.001 HIS B 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8654) covalent geometry : angle 0.60620 / 0.32 (11903) hydrogen bonds : bond 0.04411 / 4.42 ( 399) hydrogen bonds : angle 4.11633 / 4.93 ( 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: 11 poor density : 121 time to evaluate : 0.297 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 312 GLN cc_start: 0.6716 (mm-40) cc_final: 0.6220 (mm-40) REVERT: B 313 TYR cc_start: 0.7575 (m-80) cc_final: 0.7136 (m-80) REVERT: B 365 PHE cc_start: 0.7663 (t80) cc_final: 0.7313 (t80) REVERT: B 397 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8101 (tp) REVERT: B 545 ARG cc_start: 0.8208 (mtt180) cc_final: 0.6382 (mmm160) outliers start: 11 outliers final: 9 residues processed: 129 average time/residue: 0.1219 time to fit residues: 20.6527 Evaluate side-chains 127 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 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 898 GLU 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: 3.9990 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.0170 chunk 30 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3504 r_free = 0.3504 target = 0.087475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.072347 restraints weight = 22037.461| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.24 r_work: 0.3052 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8654 Z= 0.136 Angle : 0.607 11.863 11903 Z= 0.318 Chirality : 0.039 0.192 1344 Planarity : 0.004 0.080 1347 Dihedral : 18.535 178.638 1778 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.67 % Allowed : 15.06 % Favored : 83.27 % 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: 0.15 (0.28), residues: 898 helix: 1.15 (0.22), residues: 542 sheet: -1.16 (2.21), residues: 5 loop : -1.58 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 868 TYR 0.026 0.001 TYR B 416 PHE 0.017 0.001 PHE B 314 TRP 0.005 0.001 TRP B 423 HIS 0.006 0.001 HIS B 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 8654) covalent geometry : angle 0.60719 / 0.32 (11903) hydrogen bonds : bond 0.04452 / 4.51 ( 399) hydrogen bonds : angle 4.13337 / 4.96 ( 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 126 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.307 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 26 MET cc_start: 0.8410 (tpp) cc_final: 0.8091 (mmm) REVERT: B 312 GLN cc_start: 0.6741 (mm-40) cc_final: 0.6242 (mm-40) REVERT: B 313 TYR cc_start: 0.7605 (m-80) cc_final: 0.7131 (m-80) REVERT: B 365 PHE cc_start: 0.7706 (t80) cc_final: 0.7348 (t80) REVERT: B 397 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8080 (tp) REVERT: B 545 ARG cc_start: 0.8302 (mtt180) cc_final: 0.6348 (mmm160) REVERT: B 775 ARG cc_start: 0.7653 (tpp80) cc_final: 0.7297 (tpp80) outliers start: 13 outliers final: 10 residues processed: 123 average time/residue: 0.1163 time to fit residues: 18.9041 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 : 0.305 ------------------------------------------------------------------------------- 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 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 898 GLU 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: 2.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 93 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 559 ASN ** B 695 ASN ** 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 = 0.3458 r_free = 0.3458 target = 0.085125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.069951 restraints weight = 22043.057| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.26 r_work: 0.2998 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8654 Z= 0.170 Angle : 0.649 12.605 11903 Z= 0.343 Chirality : 0.041 0.192 1344 Planarity : 0.004 0.081 1347 Dihedral : 18.586 178.738 1778 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.67 % Allowed : 15.06 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.28), residues: 898 helix: 1.10 (0.22), residues: 536 sheet: -1.12 (2.18), residues: 5 loop : -1.50 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 868 TYR 0.026 0.002 TYR B 416 PHE 0.020 0.002 PHE B 314 TRP 0.006 0.001 TRP B 241 HIS 0.007 0.001 HIS B 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 8654) covalent geometry : angle 0.64895 / 0.34 (11903) hydrogen bonds : bond 0.04814 / 4.94 ( 399) hydrogen bonds : angle 4.25231 / 5.09 ( 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 134 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 313 TYR cc_start: 0.7756 (m-80) cc_final: 0.7253 (m-80) REVERT: B 365 PHE cc_start: 0.7796 (t80) cc_final: 0.7307 (t80) REVERT: B 397 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8114 (tp) REVERT: B 545 ARG cc_start: 0.8458 (mtt180) cc_final: 0.6379 (mmm160) REVERT: B 575 ASP cc_start: 0.7937 (p0) cc_final: 0.7277 (p0) outliers start: 13 outliers final: 10 residues processed: 131 average time/residue: 0.1252 time to fit residues: 21.2949 Evaluate side-chains 125 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 283 LEU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 810 GLU 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 898 GLU 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: 2.9990 chunk 51 optimal weight: 0.6980 chunk 60 optimal weight: 0.0070 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3464 r_free = 0.3464 target = 0.085372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.070199 restraints weight = 22001.114| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.25 r_work: 0.3005 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8654 Z= 0.150 Angle : 0.663 12.615 11903 Z= 0.348 Chirality : 0.040 0.192 1344 Planarity : 0.004 0.081 1347 Dihedral : 18.634 178.556 1778 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.03 % Allowed : 16.09 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.28), residues: 898 helix: 1.09 (0.22), residues: 536 sheet: -1.45 (2.13), residues: 5 loop : -1.49 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 648 TYR 0.027 0.002 TYR B 88 PHE 0.022 0.002 PHE B 314 TRP 0.004 0.001 TRP B 241 HIS 0.006 0.001 HIS B 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 8654) covalent geometry : angle 0.66299 / 0.35 (11903) hydrogen bonds : bond 0.04690 / 4.74 ( 399) hydrogen bonds : angle 4.26441 / 5.05 ( 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 120 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 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: 0.6957 (mm-40) cc_final: 0.6468 (mm-40) REVERT: B 365 PHE cc_start: 0.7910 (t80) cc_final: 0.7691 (t80) REVERT: B 545 ARG cc_start: 0.8554 (mtt180) cc_final: 0.6356 (mmm160) REVERT: B 575 ASP cc_start: 0.8245 (p0) cc_final: 0.7529 (p0) outliers start: 8 outliers final: 7 residues processed: 118 average time/residue: 0.1097 time to fit residues: 17.0723 Evaluate side-chains 118 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 372 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 898 GLU 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: 0.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.0000 chunk 41 optimal weight: 0.1980 chunk 77 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3485 r_free = 0.3485 target = 0.086426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.071240 restraints weight = 22073.110| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.25 r_work: 0.3031 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8654 Z= 0.130 Angle : 0.655 12.888 11903 Z= 0.341 Chirality : 0.039 0.191 1344 Planarity : 0.004 0.081 1347 Dihedral : 18.630 178.551 1778 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.90 % Allowed : 16.34 % 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: 0.14 (0.29), residues: 898 helix: 1.13 (0.22), residues: 542 sheet: -1.26 (2.25), residues: 5 loop : -1.56 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 775 TYR 0.026 0.001 TYR B 416 PHE 0.017 0.001 PHE B 314 TRP 0.003 0.001 TRP B 423 HIS 0.005 0.001 HIS B 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 8654) covalent geometry : angle 0.65507 / 0.34 (11903) hydrogen bonds : bond 0.04426 / 4.43 ( 399) hydrogen bonds : angle 4.26305 / 5.02 ( 1117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1908.50 seconds wall clock time: 33 minutes 38.22 seconds (2018.22 seconds total)