Starting phenix.real_space_refine on Tue Feb 3 22:22:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qwz_53431/02_2026/9qwz_53431.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qwz_53431/02_2026/9qwz_53431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qwz_53431/02_2026/9qwz_53431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qwz_53431/02_2026/9qwz_53431.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qwz_53431/02_2026/9qwz_53431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qwz_53431/02_2026/9qwz_53431.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 3 Type Number sf(0) Gaussians C 4249 2.51 5 N 1433 2.21 5 O 1433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 7115 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 7075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1425, 7075 Classifications: {'peptide': 1425} Incomplete info: {'truncation_to_alanine': 1270} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1370} Chain breaks: 21 Unresolved chain link angles: 54 Unresolved non-hydrogen bonds: 4356 Unresolved non-hydrogen angles: 5561 Unresolved non-hydrogen dihedrals: 3597 Unresolved non-hydrogen chiralities: 450 Planarities with less than four sites: {'ASP:plan': 57, 'ASN:plan1': 51, 'PHE:plan': 54, 'GLN:plan1': 86, 'ARG:plan': 63, 'GLU:plan': 74, 'HIS:plan': 36, 'TYR:plan': 45, 'TRP:plan': 11} Unresolved non-hydrogen planarities: 2197 Time building chain proxies: 1.68, per 1000 atoms: 0.24 Number of scatterers: 7115 At special positions: 0 Unit cell: (139.48, 103.976, 149.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1433 8.00 N 1433 7.00 C 4249 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: 0.83 Conformation dependent library (CDL) restraints added in 313.4 milliseconds 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 55.5% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'D' and resid 291 through 296 removed outlier: 3.794A pdb=" N ARG D 295 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 1809 through 1829 removed outlier: 3.952A pdb=" N PHE B1817 " --> pdb=" O ASP B1813 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP B1820 " --> pdb=" O ASN B1816 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA B1821 " --> pdb=" O PHE B1817 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B1824 " --> pdb=" O ASP B1820 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1848 Processing helix chain 'B' and resid 1882 through 1891 Processing helix chain 'B' and resid 1926 through 1931 Processing helix chain 'B' and resid 2473 through 2492 Processing helix chain 'B' and resid 2494 through 2515 removed outlier: 4.376A pdb=" N ASN B2503 " --> pdb=" O GLU B2499 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ALA B2504 " --> pdb=" O ARG B2500 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B2515 " --> pdb=" O LEU B2511 " (cutoff:3.500A) Processing helix chain 'B' and resid 2518 through 2533 Processing helix chain 'B' and resid 2535 through 2562 Processing helix chain 'B' and resid 2566 through 2584 Processing helix chain 'B' and resid 2584 through 2594 Processing helix chain 'B' and resid 2619 through 2635 removed outlier: 3.701A pdb=" N THR B2623 " --> pdb=" O CYS B2619 " (cutoff:3.500A) Processing helix chain 'B' and resid 2652 through 2671 Processing helix chain 'B' and resid 2674 through 2686 removed outlier: 4.292A pdb=" N LYS B2680 " --> pdb=" O ASN B2676 " (cutoff:3.500A) Processing helix chain 'B' and resid 2690 through 2706 removed outlier: 3.735A pdb=" N SER B2694 " --> pdb=" O ASP B2690 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER B2696 " --> pdb=" O ALA B2692 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B2706 " --> pdb=" O ILE B2702 " (cutoff:3.500A) Processing helix chain 'B' and resid 2968 through 2985 removed outlier: 3.504A pdb=" N THR B2984 " --> pdb=" O ARG B2980 " (cutoff:3.500A) Processing helix chain 'B' and resid 2986 through 2991 removed outlier: 4.154A pdb=" N ASN B2990 " --> pdb=" O GLN B2987 " (cutoff:3.500A) Processing helix chain 'B' and resid 2996 through 3007 removed outlier: 3.908A pdb=" N MET B3000 " --> pdb=" O ALA B2996 " (cutoff:3.500A) Processing helix chain 'B' and resid 3008 through 3010 No H-bonds generated for 'chain 'B' and resid 3008 through 3010' Processing helix chain 'B' and resid 3014 through 3033 Processing helix chain 'B' and resid 3038 through 3043 removed outlier: 3.906A pdb=" N LYS B3041 " --> pdb=" O ASP B3038 " (cutoff:3.500A) Processing helix chain 'B' and resid 3046 through 3064 Processing helix chain 'B' and resid 3079 through 3093 Processing helix chain 'B' and resid 3093 through 3112 removed outlier: 4.114A pdb=" N GLU B3107 " --> pdb=" O LYS B3103 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR B3108 " --> pdb=" O SER B3104 " (cutoff:3.500A) Processing helix chain 'B' and resid 3141 through 3148 Processing helix chain 'B' and resid 3155 through 3178 Proline residue: B3168 - end of helix Processing helix chain 'B' and resid 3188 through 3200 Processing helix chain 'B' and resid 3203 through 3219 Processing helix chain 'B' and resid 3220 through 3246 Processing helix chain 'B' and resid 3265 through 3286 removed outlier: 3.581A pdb=" N HIS B3275 " --> pdb=" O SER B3271 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG B3286 " --> pdb=" O ILE B3282 " (cutoff:3.500A) Processing helix chain 'B' and resid 3287 through 3297 Processing helix chain 'B' and resid 3300 through 3311 Processing helix chain 'B' and resid 3312 through 3314 No H-bonds generated for 'chain 'B' and resid 3312 through 3314' Processing helix chain 'B' and resid 3315 through 3328 removed outlier: 3.524A pdb=" N LEU B3319 " --> pdb=" O VAL B3315 " (cutoff:3.500A) Processing helix chain 'B' and resid 3329 through 3336 Processing helix chain 'B' and resid 3387 through 3403 Processing helix chain 'B' and resid 3404 through 3417 Processing helix chain 'B' and resid 3421 through 3439 removed outlier: 3.804A pdb=" N ARG B3425 " --> pdb=" O SER B3421 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B3438 " --> pdb=" O HIS B3434 " (cutoff:3.500A) Processing helix chain 'B' and resid 3440 through 3455 Processing helix chain 'B' and resid 3457 through 3462 removed outlier: 4.188A pdb=" N TYR B3461 " --> pdb=" O GLU B3457 " (cutoff:3.500A) Processing helix chain 'B' and resid 3465 through 3479 Processing helix chain 'B' and resid 3482 through 3506 Processing helix chain 'B' and resid 3509 through 3518 removed outlier: 3.694A pdb=" N TYR B3513 " --> pdb=" O ASN B3509 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY B3518 " --> pdb=" O ASN B3514 " (cutoff:3.500A) Processing helix chain 'B' and resid 3603 through 3607 removed outlier: 4.037A pdb=" N ASN B3607 " --> pdb=" O GLU B3604 " (cutoff:3.500A) Processing helix chain 'B' and resid 3728 through 3766 removed outlier: 4.216A pdb=" N ARG B3757 " --> pdb=" O LEU B3753 " (cutoff:3.500A) Proline residue: B3758 - end of helix removed outlier: 3.584A pdb=" N LYS B3766 " --> pdb=" O ASN B3762 " (cutoff:3.500A) Processing helix chain 'B' and resid 3799 through 3803 Processing helix chain 'B' and resid 3805 through 3843 removed outlier: 3.794A pdb=" N ASN B3809 " --> pdb=" O GLY B3805 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER B3842 " --> pdb=" O ALA B3838 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER B3843 " --> pdb=" O ALA B3839 " (cutoff:3.500A) Processing helix chain 'B' and resid 3852 through 3860 Processing helix chain 'B' and resid 3872 through 3891 Processing helix chain 'B' and resid 3893 through 3904 Processing helix chain 'B' and resid 3905 through 3913 Processing helix chain 'B' and resid 3918 through 3933 removed outlier: 4.032A pdb=" N THR B3933 " --> pdb=" O MET B3929 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 1851 through 1855 removed outlier: 6.223A pdb=" N ALA B1851 " --> pdb=" O PHE B2197 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B2199 " --> pdb=" O ALA B1851 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU B1853 " --> pdb=" O ILE B2199 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLU B2201 " --> pdb=" O GLU B1853 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR B1855 " --> pdb=" O GLU B2201 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR B2196 " --> pdb=" O LYS B2193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1911 through 1912 Processing sheet with id=AA3, first strand: chain 'B' and resid 1956 through 1959 removed outlier: 4.378A pdb=" N CYS B1975 " --> pdb=" O LEU B1992 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2004 through 2006 Processing sheet with id=AA5, first strand: chain 'B' and resid 2046 through 2052 removed outlier: 3.933A pdb=" N ASN B2090 " --> pdb=" O THR B2072 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2110 through 2114 removed outlier: 3.669A pdb=" N SER B2112 " --> pdb=" O SER B2125 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER B2125 " --> pdb=" O SER B2112 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR B2114 " --> pdb=" O PHE B2123 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2213 through 2220 Processing sheet with id=AA8, first strand: chain 'B' and resid 3250 through 3251 Processing sheet with id=AA9, first strand: chain 'B' and resid 3543 through 3546 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 3543 through 3546 current: chain 'B' and resid 3560 through 3571 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 3560 through 3571 current: chain 'B' and resid 3613 through 3614 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 3586 through 3587 632 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 1433 1.28 - 1.35: 1410 1.35 - 1.42: 0 1.42 - 1.48: 1433 1.48 - 1.55: 2816 Bond restraints: 7092 Sorted by residual: bond pdb=" C GLN B3848 " pdb=" N PRO B3849 " ideal model delta sigma weight residual 1.332 1.315 0.017 1.12e-02 7.97e+03 2.40e+00 bond pdb=" CA LEU B3472 " pdb=" C LEU B3472 " ideal model delta sigma weight residual 1.523 1.505 0.018 1.30e-02 5.92e+03 1.98e+00 bond pdb=" C LYS B2193 " pdb=" N PRO B2194 " ideal model delta sigma weight residual 1.335 1.317 0.018 1.36e-02 5.41e+03 1.85e+00 bond pdb=" CA VAL B3307 " pdb=" C VAL B3307 " ideal model delta sigma weight residual 1.524 1.508 0.016 1.22e-02 6.72e+03 1.75e+00 bond pdb=" C ILE B3566 " pdb=" N GLY B3567 " ideal model delta sigma weight residual 1.330 1.315 0.015 1.22e-02 6.72e+03 1.59e+00 ... (remaining 7087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 9092 1.18 - 2.35: 682 2.35 - 3.53: 76 3.53 - 4.71: 9 4.71 - 5.88: 3 Bond angle restraints: 9862 Sorted by residual: angle pdb=" N VAL B2492 " pdb=" CA VAL B2492 " pdb=" C VAL B2492 " ideal model delta sigma weight residual 113.71 107.83 5.88 9.50e-01 1.11e+00 3.83e+01 angle pdb=" N VAL B2991 " pdb=" CA VAL B2991 " pdb=" C VAL B2991 " ideal model delta sigma weight residual 110.62 113.90 -3.28 1.02e+00 9.61e-01 1.03e+01 angle pdb=" C VAL B2991 " pdb=" CA VAL B2991 " pdb=" CB VAL B2991 " ideal model delta sigma weight residual 112.14 108.39 3.75 1.35e+00 5.49e-01 7.71e+00 angle pdb=" N THR B2089 " pdb=" CA THR B2089 " pdb=" C THR B2089 " ideal model delta sigma weight residual 112.12 115.78 -3.66 1.34e+00 5.57e-01 7.44e+00 angle pdb=" C LYS B3036 " pdb=" N LYS B3037 " pdb=" CA LYS B3037 " ideal model delta sigma weight residual 121.54 126.61 -5.07 1.91e+00 2.74e-01 7.06e+00 ... (remaining 9857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.38: 3779 5.38 - 10.76: 321 10.76 - 16.14: 60 16.14 - 21.51: 13 21.51 - 26.89: 3 Dihedral angle restraints: 4176 sinusoidal: 0 harmonic: 4176 Sorted by residual: dihedral pdb=" CA TYR B3461 " pdb=" C TYR B3461 " pdb=" N GLY B3462 " pdb=" CA GLY B3462 " ideal model delta harmonic sigma weight residual 180.00 153.11 26.89 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA VAL B2192 " pdb=" C VAL B2192 " pdb=" N LYS B2193 " pdb=" CA LYS B2193 " ideal model delta harmonic sigma weight residual 180.00 156.20 23.80 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA CYS B2127 " pdb=" C CYS B2127 " pdb=" N GLN B2128 " pdb=" CA GLN B2128 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 4173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 724 0.025 - 0.050: 391 0.050 - 0.074: 158 0.074 - 0.099: 55 0.099 - 0.124: 55 Chirality restraints: 1383 Sorted by residual: chirality pdb=" CA VAL B1950 " pdb=" N VAL B1950 " pdb=" C VAL B1950 " pdb=" CB VAL B1950 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA PRO B2998 " pdb=" N PRO B2998 " pdb=" C PRO B2998 " pdb=" CB PRO B2998 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE B2231 " pdb=" N ILE B2231 " pdb=" C ILE B2231 " pdb=" CB ILE B2231 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 1380 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B3800 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C ALA B3800 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA B3800 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN B3801 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B2679 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.86e+00 pdb=" C SER B2679 " 0.024 2.00e-02 2.50e+03 pdb=" O SER B2679 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS B2680 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B2681 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C ILE B2681 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE B2681 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR B2682 " 0.008 2.00e-02 2.50e+03 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 4785 3.01 - 3.48: 7682 3.48 - 3.95: 9146 3.95 - 4.43: 10477 4.43 - 4.90: 15276 Nonbonded interactions: 47366 Sorted by model distance: nonbonded pdb=" O ALA B3800 " pdb=" CB CYS B3804 " model vdw 2.536 3.440 nonbonded pdb=" O THR B2135 " pdb=" N LEU B2144 " model vdw 2.566 3.120 nonbonded pdb=" O VAL B2589 " pdb=" CB GLU B2593 " model vdw 2.577 2.752 nonbonded pdb=" N LYS B2193 " pdb=" O LYS B2193 " model vdw 2.586 2.496 nonbonded pdb=" N VAL B3152 " pdb=" N PHE B3153 " model vdw 2.591 2.560 ... (remaining 47361 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 group one per residue 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: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.120 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.004 0.018 7092 Z= 0.296 Angle : 0.671 5.882 9862 Z= 0.467 Chirality : 0.041 0.124 1383 Planarity : 0.003 0.015 1410 Dihedral : 5.454 26.892 1410 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.50 (0.22), residues: 1387 helix: 0.75 (0.19), residues: 755 sheet: -1.00 (0.41), residues: 162 loop : -1.81 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B1966 PHE 0.000 0.000 PHE D 291 TRP 0.000 0.000 TRP B2007 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 7092) covalent geometry : angle 0.67085 ( 9862) hydrogen bonds : bond 0.11233 ( 632) hydrogen bonds : angle 6.36226 ( 1842) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.258 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0321 time to fit residues: 2.3334 Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.055131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.046189 restraints weight = 79707.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.045493 restraints weight = 90257.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.044742 restraints weight = 111168.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.044828 restraints weight = 92828.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.044932 restraints weight = 79103.006| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 7092 Z= 0.119 Angle : 0.373 4.418 9862 Z= 0.240 Chirality : 0.039 0.129 1383 Planarity : 0.002 0.014 1410 Dihedral : 4.197 19.976 1410 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.82 (0.23), residues: 1387 helix: 2.01 (0.19), residues: 758 sheet: -0.53 (0.42), residues: 154 loop : -1.58 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B1966 PHE 0.000 0.000 PHE D 291 TRP 0.000 0.000 TRP B2007 Details of bonding type rmsd covalent geometry : bond 0.00160 ( 7092) covalent geometry : angle 0.37330 ( 9862) hydrogen bonds : bond 0.03468 ( 632) hydrogen bonds : angle 4.26543 ( 1842) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.297 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0307 time to fit residues: 2.3813 Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 92 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 chunk 24 optimal weight: 40.0000 chunk 112 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 58 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 chunk 121 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.053176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.043411 restraints weight = 80633.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.042749 restraints weight = 102769.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.042764 restraints weight = 103596.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.042726 restraints weight = 83383.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.042735 restraints weight = 81275.721| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7092 Z= 0.309 Angle : 0.568 6.478 9862 Z= 0.378 Chirality : 0.041 0.131 1383 Planarity : 0.004 0.017 1410 Dihedral : 5.635 26.905 1410 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.86 (0.22), residues: 1387 helix: 0.55 (0.18), residues: 762 sheet: -1.32 (0.45), residues: 133 loop : -2.10 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B1966 PHE 0.000 0.000 PHE D 291 TRP 0.000 0.000 TRP B2007 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 7092) covalent geometry : angle 0.56776 ( 9862) hydrogen bonds : bond 0.05528 ( 632) hydrogen bonds : angle 5.89465 ( 1842) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.314 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0301 time to fit residues: 2.2362 Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 40.0000 chunk 97 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 39 optimal weight: 0.0030 chunk 41 optimal weight: 20.0000 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.055177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.045266 restraints weight = 79387.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.044688 restraints weight = 105132.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.044877 restraints weight = 99121.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.044839 restraints weight = 78605.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.044855 restraints weight = 76984.118| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.007 7092 Z= 0.088 Angle : 0.342 4.156 9862 Z= 0.218 Chirality : 0.038 0.134 1383 Planarity : 0.002 0.010 1410 Dihedral : 3.854 19.509 1410 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.11 (0.24), residues: 1387 helix: 2.39 (0.19), residues: 755 sheet: -0.69 (0.45), residues: 142 loop : -1.56 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B1966 PHE 0.000 0.000 PHE D 291 TRP 0.000 0.000 TRP B2007 Details of bonding type rmsd covalent geometry : bond 0.00117 ( 7092) covalent geometry : angle 0.34215 ( 9862) hydrogen bonds : bond 0.02944 ( 632) hydrogen bonds : angle 3.92393 ( 1842) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.179 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0328 time to fit residues: 2.4290 Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 102 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 24 optimal weight: 40.0000 chunk 42 optimal weight: 1.9990 chunk 18 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.052865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.043190 restraints weight = 81546.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.042572 restraints weight = 97383.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.042723 restraints weight = 104215.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.042793 restraints weight = 83277.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.042828 restraints weight = 82249.503| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7092 Z= 0.329 Angle : 0.574 5.232 9862 Z= 0.387 Chirality : 0.041 0.135 1383 Planarity : 0.004 0.015 1410 Dihedral : 5.540 26.978 1410 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.59 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.75 (0.22), residues: 1387 helix: 0.74 (0.18), residues: 754 sheet: -1.46 (0.46), residues: 126 loop : -2.14 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B1966 PHE 0.000 0.000 PHE D 291 TRP 0.000 0.000 TRP B2007 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 7092) covalent geometry : angle 0.57416 ( 9862) hydrogen bonds : bond 0.05466 ( 632) hydrogen bonds : angle 5.80351 ( 1842) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0314 time to fit residues: 2.3876 Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 23 optimal weight: 30.0000 chunk 132 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 0.0670 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 40.0000 chunk 33 optimal weight: 9.9990 overall best weight: 1.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.054606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.044829 restraints weight = 80028.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.044049 restraints weight = 104559.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.044191 restraints weight = 111308.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.044234 restraints weight = 86503.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.044306 restraints weight = 81105.596| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 7092 Z= 0.106 Angle : 0.360 4.048 9862 Z= 0.230 Chirality : 0.039 0.135 1383 Planarity : 0.002 0.010 1410 Dihedral : 4.149 18.570 1410 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.79 (0.24), residues: 1387 helix: 2.23 (0.19), residues: 755 sheet: -1.04 (0.46), residues: 132 loop : -1.80 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B1966 PHE 0.000 0.000 PHE D 291 TRP 0.000 0.000 TRP B2007 Details of bonding type rmsd covalent geometry : bond 0.00143 ( 7092) covalent geometry : angle 0.35977 ( 9862) hydrogen bonds : bond 0.03219 ( 632) hydrogen bonds : angle 4.21932 ( 1842) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.245 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0270 time to fit residues: 2.0065 Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 117 optimal weight: 40.0000 chunk 131 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.055803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.046301 restraints weight = 79471.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.045724 restraints weight = 100012.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.045745 restraints weight = 89749.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.045555 restraints weight = 73081.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.045599 restraints weight = 74510.292| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.006 7092 Z= 0.068 Angle : 0.300 4.160 9862 Z= 0.190 Chirality : 0.038 0.129 1383 Planarity : 0.001 0.009 1410 Dihedral : 3.126 13.830 1410 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.85 (0.25), residues: 1387 helix: 3.19 (0.19), residues: 755 sheet: -0.83 (0.42), residues: 157 loop : -1.44 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B1966 PHE 0.000 0.000 PHE D 291 TRP 0.000 0.000 TRP B2007 Details of bonding type rmsd covalent geometry : bond 0.00090 ( 7092) covalent geometry : angle 0.29957 ( 9862) hydrogen bonds : bond 0.02354 ( 632) hydrogen bonds : angle 3.33083 ( 1842) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.275 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0312 time to fit residues: 2.3613 Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 13 optimal weight: 0.0040 chunk 17 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.054238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.044285 restraints weight = 80031.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.043655 restraints weight = 108295.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.044004 restraints weight = 105896.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.043909 restraints weight = 81700.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.044009 restraints weight = 81365.102| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7092 Z= 0.176 Angle : 0.393 3.832 9862 Z= 0.258 Chirality : 0.039 0.128 1383 Planarity : 0.002 0.009 1410 Dihedral : 3.919 18.448 1410 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.26 (0.24), residues: 1387 helix: 2.61 (0.19), residues: 759 sheet: -1.05 (0.45), residues: 140 loop : -1.57 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B1966 PHE 0.000 0.000 PHE D 291 TRP 0.000 0.000 TRP B2007 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7092) covalent geometry : angle 0.39306 ( 9862) hydrogen bonds : bond 0.03534 ( 632) hydrogen bonds : angle 4.17712 ( 1842) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.161 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0302 time to fit residues: 2.1738 Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 126 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 117 optimal weight: 40.0000 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.051720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.041828 restraints weight = 81579.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.041693 restraints weight = 96887.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.041759 restraints weight = 89733.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.041646 restraints weight = 80085.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.041673 restraints weight = 79656.463| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7092 Z= 0.443 Angle : 0.720 5.611 9862 Z= 0.488 Chirality : 0.043 0.149 1383 Planarity : 0.005 0.022 1410 Dihedral : 6.497 30.910 1410 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.92 (0.21), residues: 1387 helix: -0.29 (0.17), residues: 751 sheet: -1.52 (0.50), residues: 110 loop : -2.64 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B1966 PHE 0.000 0.000 PHE D 291 TRP 0.000 0.000 TRP B2007 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 7092) covalent geometry : angle 0.71964 ( 9862) hydrogen bonds : bond 0.06762 ( 632) hydrogen bonds : angle 6.87881 ( 1842) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.269 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0253 time to fit residues: 1.9613 Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 131 optimal weight: 2.9990 chunk 18 optimal weight: 40.0000 chunk 66 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 55 optimal weight: 0.0980 chunk 35 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.053165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.043175 restraints weight = 80337.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.042692 restraints weight = 94935.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.042919 restraints weight = 87770.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.042915 restraints weight = 75272.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.042945 restraints weight = 71884.180| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 7092 Z= 0.180 Angle : 0.433 4.220 9862 Z= 0.284 Chirality : 0.039 0.139 1383 Planarity : 0.002 0.011 1410 Dihedral : 4.956 22.144 1410 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.55 (0.23), residues: 1387 helix: 1.12 (0.19), residues: 758 sheet: -1.75 (0.46), residues: 124 loop : -2.37 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B1966 PHE 0.000 0.000 PHE D 291 TRP 0.000 0.000 TRP B2007 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7092) covalent geometry : angle 0.43292 ( 9862) hydrogen bonds : bond 0.04041 ( 632) hydrogen bonds : angle 5.04877 ( 1842) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0314 time to fit residues: 2.3122 Evaluate side-chains 34 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.6980 chunk 138 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 125 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 overall best weight: 6.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.051764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.042030 restraints weight = 81276.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.041145 restraints weight = 119515.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.041386 restraints weight = 109469.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.041399 restraints weight = 91354.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.041472 restraints weight = 87321.985| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7092 Z= 0.366 Angle : 0.628 4.914 9862 Z= 0.424 Chirality : 0.042 0.139 1383 Planarity : 0.004 0.018 1410 Dihedral : 6.297 28.485 1410 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.98 % Favored : 87.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.21), residues: 1387 helix: -0.17 (0.18), residues: 751 sheet: -1.96 (0.50), residues: 103 loop : -2.92 (0.24), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B1966 PHE 0.000 0.000 PHE D 291 TRP 0.000 0.000 TRP B2007 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 7092) covalent geometry : angle 0.62762 ( 9862) hydrogen bonds : bond 0.06131 ( 632) hydrogen bonds : angle 6.50897 ( 1842) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1041.15 seconds wall clock time: 18 minutes 27.10 seconds (1107.10 seconds total)