Starting phenix.real_space_refine on Wed Jun 3 21:25:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9px7_71960/06_2026/9px7_71960.cif Found real_map, /net/cci-nas-00/data/ceres_data/9px7_71960/06_2026/9px7_71960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9px7_71960/06_2026/9px7_71960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9px7_71960/06_2026/9px7_71960.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9px7_71960/06_2026/9px7_71960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9px7_71960/06_2026/9px7_71960.map" } resolution = 3.4 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= 0.016 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2778 2.51 5 N 702 2.21 5 O 798 1.98 5 H 4296 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8580 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1430 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 1.01, per 1000 atoms: 0.12 Number of scatterers: 8580 At special positions: 0 Unit cell: (74.26, 94, 46.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 798 8.00 N 702 7.00 C 2778 6.00 H 4296 1.00 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: 0.74 Conformation dependent library (CDL) restraints added in 134.6 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 34 removed outlier: 6.384A pdb=" N HIS A 31 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ARG B 34 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE A 33 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N HIS B 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ARG C 34 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE B 33 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS C 31 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ARG D 34 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE C 33 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N HIS D 31 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ARG E 34 " --> pdb=" O HIS D 31 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE D 33 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N HIS E 31 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ARG F 34 " --> pdb=" O HIS E 31 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE E 33 " --> pdb=" O ARG F 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 66 removed outlier: 6.965A pdb=" N PHE A 64 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 65 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU A 66 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE B 64 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 65 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU B 66 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N PHE C 64 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL D 65 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU C 66 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE D 64 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL E 65 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU D 66 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N PHE E 64 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL F 65 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLU E 66 " --> pdb=" O VAL F 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 72 removed outlier: 6.283A pdb=" N VAL A 71 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL B 71 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL C 71 " --> pdb=" O GLU D 72 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL D 71 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL E 71 " --> pdb=" O GLU F 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 79 removed outlier: 7.063A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER B 77 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR C 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER C 77 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR D 78 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER D 77 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR E 78 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER E 77 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR F 78 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 89 through 97 removed outlier: 6.989A pdb=" N HIS B 90 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N HIS C 90 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N HIS D 90 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N HIS E 90 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N HIS F 90 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 104 through 110 removed outlier: 6.894A pdb=" N ALA A 109 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU B 110 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ALA B 109 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU C 110 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA C 109 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU D 110 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA D 109 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU E 110 " --> pdb=" O ALA D 109 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 357 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: 1.75 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4296 1.03 - 1.22: 0 1.22 - 1.42: 1833 1.42 - 1.61: 2541 1.61 - 1.80: 12 Bond restraints: 8682 Sorted by residual: bond pdb=" CA ASP C 99 " pdb=" CB ASP C 99 " ideal model delta sigma weight residual 1.529 1.540 -0.010 1.69e-02 3.50e+03 3.70e-01 bond pdb=" CA ALA F 81 " pdb=" C ALA F 81 " ideal model delta sigma weight residual 1.530 1.524 0.007 1.08e-02 8.57e+03 3.64e-01 bond pdb=" C PRO B 86 " pdb=" O PRO B 86 " ideal model delta sigma weight residual 1.238 1.230 0.008 1.36e-02 5.41e+03 3.54e-01 bond pdb=" CA ASP D 99 " pdb=" CB ASP D 99 " ideal model delta sigma weight residual 1.529 1.539 -0.010 1.69e-02 3.50e+03 3.53e-01 bond pdb=" CA ALA B 81 " pdb=" C ALA B 81 " ideal model delta sigma weight residual 1.530 1.524 0.006 1.08e-02 8.57e+03 3.48e-01 ... (remaining 8677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.61: 13363 0.61 - 1.21: 1822 1.21 - 1.82: 437 1.82 - 2.42: 62 2.42 - 3.03: 18 Bond angle restraints: 15702 Sorted by residual: angle pdb=" CA GLU A 89 " pdb=" CB GLU A 89 " pdb=" CG GLU A 89 " ideal model delta sigma weight residual 114.10 116.79 -2.69 2.00e+00 2.50e-01 1.80e+00 angle pdb=" CA GLU E 89 " pdb=" CB GLU E 89 " pdb=" CG GLU E 89 " ideal model delta sigma weight residual 114.10 116.78 -2.68 2.00e+00 2.50e-01 1.80e+00 angle pdb=" C SER D 85 " pdb=" N PRO D 86 " pdb=" CA PRO D 86 " ideal model delta sigma weight residual 118.97 120.36 -1.39 1.04e+00 9.25e-01 1.78e+00 angle pdb=" CA GLU F 89 " pdb=" CB GLU F 89 " pdb=" CG GLU F 89 " ideal model delta sigma weight residual 114.10 116.76 -2.66 2.00e+00 2.50e-01 1.77e+00 angle pdb=" CA GLU D 89 " pdb=" CB GLU D 89 " pdb=" CG GLU D 89 " ideal model delta sigma weight residual 114.10 116.75 -2.65 2.00e+00 2.50e-01 1.76e+00 ... (remaining 15697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 3738 17.36 - 34.72: 264 34.72 - 52.08: 78 52.08 - 69.45: 36 69.45 - 86.81: 6 Dihedral angle restraints: 4122 sinusoidal: 2184 harmonic: 1938 Sorted by residual: dihedral pdb=" CB GLU D 63 " pdb=" CG GLU D 63 " pdb=" CD GLU D 63 " pdb=" OE1 GLU D 63 " ideal model delta sinusoidal sigma weight residual 0.00 86.81 -86.81 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU A 63 " pdb=" CG GLU A 63 " pdb=" CD GLU A 63 " pdb=" OE1 GLU A 63 " ideal model delta sinusoidal sigma weight residual 0.00 86.79 -86.79 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU C 63 " pdb=" CG GLU C 63 " pdb=" CD GLU C 63 " pdb=" OE1 GLU C 63 " ideal model delta sinusoidal sigma weight residual 0.00 86.76 -86.76 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 4119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 340 0.027 - 0.053: 232 0.053 - 0.079: 39 0.079 - 0.106: 53 0.106 - 0.132: 44 Chirality restraints: 708 Sorted by residual: chirality pdb=" CA PRO D 86 " pdb=" N PRO D 86 " pdb=" C PRO D 86 " pdb=" CB PRO D 86 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA PRO F 86 " pdb=" N PRO F 86 " pdb=" C PRO F 86 " pdb=" CB PRO F 86 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA PRO C 86 " pdb=" N PRO C 86 " pdb=" C PRO C 86 " pdb=" CB PRO C 86 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 705 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 85 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 86 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 86 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 86 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 85 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.49e+00 pdb=" N PRO E 86 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 86 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 86 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 85 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO B 86 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 86 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 86 " -0.017 5.00e-02 4.00e+02 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.47: 5907 2.47 - 3.00: 19221 3.00 - 3.54: 21858 3.54 - 4.07: 31658 4.07 - 4.60: 42531 Nonbonded interactions: 121175 Sorted by model distance: nonbonded pdb=" HB2 SER C 112 " pdb=" H SER D 112 " model vdw 1.941 2.270 nonbonded pdb=" HB2 SER D 112 " pdb=" H SER E 112 " model vdw 1.969 2.270 nonbonded pdb=" HG SER C 117 " pdb=" HD2 TYR D 114 " model vdw 1.980 2.100 nonbonded pdb=" HG SER D 117 " pdb=" HD2 TYR E 114 " model vdw 1.983 2.100 nonbonded pdb=" HG SER B 117 " pdb=" HD2 TYR C 114 " model vdw 1.985 2.100 ... (remaining 121170 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.660 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: 0.050 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.060 Find NCS groups from input model: 0.070 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 0.019 4386 Z= 0.114 Angle : 0.449 3.029 5970 Z= 0.250 Chirality : 0.049 0.132 708 Planarity : 0.004 0.031 732 Dihedral : 14.713 86.807 1548 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.28 % Allowed : 5.13 % Favored : 93.59 % 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: -2.98 (0.31), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 34 TYR 0.003 0.001 TYR D 105 PHE 0.014 0.002 PHE D 33 TRP 0.001 0.000 TRP D 79 HIS 0.001 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 4386) covalent geometry : angle 0.44865 / 0.25 ( 5970) hydrogen bonds : bond 0.20601 / 14.61 ( 119) hydrogen bonds : angle 6.99476 / 4.90 ( 357) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8143 (pt0) cc_final: 0.7419 (mm-30) REVERT: A 69 TYR cc_start: 0.8917 (m-80) cc_final: 0.8699 (m-80) REVERT: A 80 LYS cc_start: 0.8725 (tptm) cc_final: 0.8086 (pttm) REVERT: B 63 GLU cc_start: 0.8676 (tt0) cc_final: 0.8471 (tt0) REVERT: C 80 LYS cc_start: 0.8981 (tptm) cc_final: 0.8744 (tptp) REVERT: D 72 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7282 (mt-10) REVERT: E 75 THR cc_start: 0.9113 (p) cc_final: 0.8908 (p) REVERT: F 33 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7978 (t80) REVERT: F 66 GLU cc_start: 0.8032 (pt0) cc_final: 0.7812 (tp30) outliers start: 6 outliers final: 5 residues processed: 90 average time/residue: 0.1393 time to fit residues: 15.9644 Evaluate side-chains 68 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain E residue 33 PHE Chi-restraints excluded: chain F residue 33 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.124785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.113058 restraints weight = 28963.744| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 3.18 r_work: 0.4018 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4386 Z= 0.179 Angle : 0.528 3.807 5970 Z= 0.298 Chirality : 0.049 0.135 708 Planarity : 0.004 0.037 732 Dihedral : 6.314 38.582 600 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 1.92 % Allowed : 7.91 % Favored : 90.17 % 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: -2.68 (0.33), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 103 TYR 0.011 0.001 TYR C 69 PHE 0.009 0.002 PHE F 95 TRP 0.003 0.001 TRP A 79 HIS 0.005 0.001 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 4386) covalent geometry : angle 0.52840 / 0.30 ( 5970) hydrogen bonds : bond 0.04610 / 3.32 ( 119) hydrogen bonds : angle 5.90840 / 4.12 ( 357) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7727 (pt0) cc_final: 0.7162 (mm-30) REVERT: A 80 LYS cc_start: 0.8768 (tptm) cc_final: 0.7633 (pttm) REVERT: D 18 ASP cc_start: 0.8762 (t0) cc_final: 0.8482 (t0) REVERT: E 72 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8040 (mt-10) REVERT: F 66 GLU cc_start: 0.8370 (pt0) cc_final: 0.7161 (tp30) outliers start: 9 outliers final: 6 residues processed: 79 average time/residue: 0.1180 time to fit residues: 12.4378 Evaluate side-chains 76 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.105702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.098274 restraints weight = 32237.716| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.37 r_work: 0.3986 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4386 Z= 0.178 Angle : 0.498 3.399 5970 Z= 0.282 Chirality : 0.048 0.130 708 Planarity : 0.004 0.042 732 Dihedral : 4.763 15.337 588 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 1.92 % Allowed : 10.47 % Favored : 87.61 % 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: -2.68 (0.33), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 103 TYR 0.011 0.001 TYR C 69 PHE 0.010 0.002 PHE E 33 TRP 0.003 0.001 TRP F 79 HIS 0.002 0.001 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 ( 4386) covalent geometry : angle 0.49841 / 0.28 ( 5970) hydrogen bonds : bond 0.04449 / 3.21 ( 119) hydrogen bonds : angle 5.80309 / 4.02 ( 357) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7546 (pt0) cc_final: 0.7118 (mm-30) REVERT: A 80 LYS cc_start: 0.8744 (tptm) cc_final: 0.7730 (pttm) REVERT: E 63 GLU cc_start: 0.8773 (tt0) cc_final: 0.8380 (tt0) REVERT: E 70 LYS cc_start: 0.8376 (tttp) cc_final: 0.8164 (ttpt) REVERT: F 66 GLU cc_start: 0.8375 (pt0) cc_final: 0.7096 (tp30) outliers start: 9 outliers final: 8 residues processed: 75 average time/residue: 0.1286 time to fit residues: 12.9424 Evaluate side-chains 75 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.127002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.115445 restraints weight = 28696.008| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 3.00 r_work: 0.4011 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4386 Z= 0.152 Angle : 0.492 3.603 5970 Z= 0.277 Chirality : 0.048 0.133 708 Planarity : 0.004 0.040 732 Dihedral : 4.781 15.135 588 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 2.14 % Allowed : 10.90 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.33), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 103 TYR 0.013 0.001 TYR D 69 PHE 0.009 0.001 PHE C 33 TRP 0.002 0.001 TRP F 79 HIS 0.002 0.001 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 4386) covalent geometry : angle 0.49163 / 0.28 ( 5970) hydrogen bonds : bond 0.03732 / 2.68 ( 119) hydrogen bonds : angle 5.68931 / 3.93 ( 357) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7585 (pt0) cc_final: 0.7140 (mm-30) REVERT: A 80 LYS cc_start: 0.8821 (tptm) cc_final: 0.7769 (pttm) REVERT: C 65 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8357 (p) REVERT: D 65 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8418 (p) REVERT: E 70 LYS cc_start: 0.8459 (tttp) cc_final: 0.8214 (ttpt) REVERT: F 66 GLU cc_start: 0.8443 (pt0) cc_final: 0.7010 (tp30) outliers start: 10 outliers final: 6 residues processed: 76 average time/residue: 0.1219 time to fit residues: 12.3668 Evaluate side-chains 77 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 HIS C 31 HIS D 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.118589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.108629 restraints weight = 31074.130| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 3.09 r_work: 0.3958 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4386 Z= 0.260 Angle : 0.539 3.812 5970 Z= 0.308 Chirality : 0.049 0.138 708 Planarity : 0.005 0.045 732 Dihedral : 5.081 15.846 588 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 3.63 % Allowed : 9.83 % Favored : 86.54 % 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: -2.87 (0.32), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 103 TYR 0.010 0.001 TYR B 69 PHE 0.011 0.002 PHE E 33 TRP 0.005 0.002 TRP F 79 HIS 0.003 0.001 HIS D 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.26 ( 4386) covalent geometry : angle 0.53929 / 0.31 ( 5970) hydrogen bonds : bond 0.04358 / 3.09 ( 119) hydrogen bonds : angle 6.02657 / 4.16 ( 357) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7615 (pt0) cc_final: 0.7192 (mm-30) REVERT: A 80 LYS cc_start: 0.8734 (tptm) cc_final: 0.7765 (pttm) REVERT: B 65 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8604 (p) REVERT: C 65 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8359 (p) REVERT: D 65 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8417 (p) REVERT: E 65 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8497 (p) REVERT: E 70 LYS cc_start: 0.8506 (tttp) cc_final: 0.8269 (ttpt) REVERT: F 66 GLU cc_start: 0.8524 (pt0) cc_final: 0.7134 (tp30) outliers start: 17 outliers final: 12 residues processed: 80 average time/residue: 0.1230 time to fit residues: 13.3023 Evaluate side-chains 86 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.121839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.111716 restraints weight = 29402.557| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.94 r_work: 0.3921 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4386 Z= 0.220 Angle : 0.516 3.790 5970 Z= 0.295 Chirality : 0.049 0.137 708 Planarity : 0.004 0.046 732 Dihedral : 5.147 16.048 588 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 3.42 % Allowed : 11.32 % Favored : 85.26 % 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: -2.92 (0.32), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 103 TYR 0.013 0.001 TYR D 69 PHE 0.011 0.002 PHE E 33 TRP 0.004 0.001 TRP F 79 HIS 0.003 0.001 HIS D 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 ( 4386) covalent geometry : angle 0.51621 / 0.30 ( 5970) hydrogen bonds : bond 0.04088 / 2.91 ( 119) hydrogen bonds : angle 5.97020 / 4.12 ( 357) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7349 (pt0) cc_final: 0.7054 (mm-30) REVERT: B 65 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8397 (p) REVERT: C 65 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8158 (p) REVERT: D 65 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8254 (p) REVERT: D 99 ASP cc_start: 0.9170 (p0) cc_final: 0.8883 (p0) REVERT: E 65 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8257 (p) REVERT: E 70 LYS cc_start: 0.8376 (tttp) cc_final: 0.8175 (ttpt) REVERT: F 65 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8531 (p) REVERT: F 66 GLU cc_start: 0.8400 (pt0) cc_final: 0.7038 (tp30) outliers start: 16 outliers final: 11 residues processed: 79 average time/residue: 0.1175 time to fit residues: 12.8065 Evaluate side-chains 84 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4380 r_free = 0.4380 target = 0.127063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.116474 restraints weight = 29005.924| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.92 r_work: 0.4103 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4386 Z= 0.093 Angle : 0.470 3.688 5970 Z= 0.262 Chirality : 0.050 0.130 708 Planarity : 0.004 0.041 732 Dihedral : 4.810 15.532 588 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.92 % Allowed : 12.82 % Favored : 85.26 % 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: -2.69 (0.33), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 103 TYR 0.010 0.001 TYR E 78 PHE 0.008 0.001 PHE C 33 TRP 0.002 0.001 TRP E 79 HIS 0.002 0.001 HIS D 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 ( 4386) covalent geometry : angle 0.47027 / 0.26 ( 5970) hydrogen bonds : bond 0.03070 / 2.19 ( 119) hydrogen bonds : angle 5.45119 / 3.75 ( 357) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8036 (m-80) cc_final: 0.7611 (m-80) REVERT: A 80 LYS cc_start: 0.8510 (tptm) cc_final: 0.7534 (pttm) REVERT: B 65 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8137 (p) REVERT: C 65 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7887 (p) REVERT: D 99 ASP cc_start: 0.9200 (p0) cc_final: 0.8845 (p0) REVERT: F 66 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.6652 (tp30) outliers start: 9 outliers final: 4 residues processed: 73 average time/residue: 0.1306 time to fit residues: 12.6075 Evaluate side-chains 74 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.119667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 18)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.109362 restraints weight = 29937.386| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 3.01 r_work: 0.3942 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4386 Z= 0.239 Angle : 0.517 4.578 5970 Z= 0.296 Chirality : 0.048 0.138 708 Planarity : 0.005 0.046 732 Dihedral : 5.006 15.831 588 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 2.78 % Allowed : 11.97 % Favored : 85.26 % 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: -2.88 (0.33), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 103 TYR 0.022 0.001 TYR D 69 PHE 0.010 0.002 PHE E 33 TRP 0.005 0.001 TRP F 79 HIS 0.003 0.001 HIS D 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.24 ( 4386) covalent geometry : angle 0.51746 / 0.30 ( 5970) hydrogen bonds : bond 0.03994 / 2.81 ( 119) hydrogen bonds : angle 5.86536 / 4.06 ( 357) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: B 65 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8323 (p) REVERT: C 65 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8195 (p) REVERT: D 65 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8304 (p) REVERT: D 99 ASP cc_start: 0.9201 (p0) cc_final: 0.8905 (p0) REVERT: E 65 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8234 (p) REVERT: F 65 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8693 (p) REVERT: F 66 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.6930 (tp30) outliers start: 13 outliers final: 7 residues processed: 74 average time/residue: 0.1213 time to fit residues: 12.1468 Evaluate side-chains 79 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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 = 0.4355 r_free = 0.4355 target = 0.124640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.113717 restraints weight = 29031.356| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 3.02 r_work: 0.3962 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4386 Z= 0.158 Angle : 0.486 4.690 5970 Z= 0.275 Chirality : 0.048 0.130 708 Planarity : 0.004 0.043 732 Dihedral : 4.956 15.716 588 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 2.99 % Allowed : 11.54 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.33), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 103 TYR 0.020 0.001 TYR D 69 PHE 0.009 0.002 PHE E 33 TRP 0.002 0.001 TRP F 79 HIS 0.003 0.001 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 4386) covalent geometry : angle 0.48576 / 0.28 ( 5970) hydrogen bonds : bond 0.03526 / 2.49 ( 119) hydrogen bonds : angle 5.66394 / 3.91 ( 357) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: B 65 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8356 (p) REVERT: C 65 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8158 (p) REVERT: D 65 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8217 (p) REVERT: D 99 ASP cc_start: 0.9254 (p0) cc_final: 0.8984 (p0) REVERT: E 65 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8269 (p) REVERT: F 65 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8689 (p) REVERT: F 66 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.6918 (tp30) outliers start: 14 outliers final: 7 residues processed: 73 average time/residue: 0.1267 time to fit residues: 12.4368 Evaluate side-chains 79 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4408 r_free = 0.4408 target = 0.128048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.117348 restraints weight = 28651.296| |-----------------------------------------------------------------------------| r_work (start): 0.4454 rms_B_bonded: 2.94 r_work: 0.4334 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4228 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4386 Z= 0.086 Angle : 0.456 5.064 5970 Z= 0.252 Chirality : 0.049 0.127 708 Planarity : 0.004 0.038 732 Dihedral : 4.578 15.021 588 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 1.92 % Allowed : 12.82 % Favored : 85.26 % 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: -2.64 (0.33), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 34 TYR 0.011 0.001 TYR B 69 PHE 0.008 0.001 PHE C 33 TRP 0.002 0.001 TRP F 79 HIS 0.002 0.001 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 ( 4386) covalent geometry : angle 0.45649 / 0.25 ( 5970) hydrogen bonds : bond 0.02636 / 1.87 ( 119) hydrogen bonds : angle 5.09134 / 3.49 ( 357) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8408 (tptm) cc_final: 0.7432 (pttm) REVERT: B 65 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8127 (p) REVERT: C 65 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7838 (p) REVERT: D 65 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7876 (p) REVERT: D 99 ASP cc_start: 0.9245 (p0) cc_final: 0.8985 (p0) REVERT: F 16 VAL cc_start: 0.9100 (t) cc_final: 0.8825 (p) REVERT: F 65 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8518 (p) REVERT: F 66 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.6523 (tp30) outliers start: 9 outliers final: 4 residues processed: 73 average time/residue: 0.1384 time to fit residues: 13.3360 Evaluate side-chains 77 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.125140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.114479 restraints weight = 29097.338| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 2.98 r_work: 0.4045 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4386 Z= 0.114 Angle : 0.471 4.969 5970 Z= 0.259 Chirality : 0.049 0.137 708 Planarity : 0.004 0.038 732 Dihedral : 4.535 14.859 588 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 2.56 % Allowed : 12.39 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.33), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 103 TYR 0.010 0.001 TYR B 69 PHE 0.009 0.001 PHE C 95 TRP 0.002 0.001 TRP F 79 HIS 0.002 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 4386) covalent geometry : angle 0.47142 / 0.26 ( 5970) hydrogen bonds : bond 0.02889 / 2.04 ( 119) hydrogen bonds : angle 5.16767 / 3.55 ( 357) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.15 seconds wall clock time: 36 minutes 55.11 seconds (2215.11 seconds total)