Starting phenix.real_space_refine on Tue Aug 4 15:11:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9p_65784/08_2026/9w9p_65784.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9p_65784/08_2026/9w9p_65784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w9p_65784/08_2026/9w9p_65784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9p_65784/08_2026/9w9p_65784.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w9p_65784/08_2026/9w9p_65784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9p_65784/08_2026/9w9p_65784.map" } resolution = 2.8 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= 0.003 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2742 2.51 5 N 702 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4254 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 709 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: 0.51, per 1000 atoms: 0.12 Number of scatterers: 4254 At special positions: 0 Unit cell: (119.97, 146.01, 31.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 804 8.00 N 702 7.00 C 2742 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: 0.18 Conformation dependent library (CDL) restraints added in 94.4 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 20 sheets defined 0.0% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.516A pdb=" N LYS A 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 21 removed outlier: 6.946A pdb=" N VAL A 20 " --> pdb=" O ARG E 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 31 through 34 removed outlier: 6.552A pdb=" N HIS A 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ARG C 34 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE A 33 " --> pdb=" O ARG C 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.217A pdb=" N THR A 59 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 65 through 66 removed outlier: 6.558A pdb=" N VAL A 65 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 71 through 73 removed outlier: 6.439A pdb=" N VAL A 71 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 76 through 80 removed outlier: 6.798A pdb=" N SER A 77 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR C 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N LYS A 76 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N TRP E 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TYR A 78 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 89 through 99 removed outlier: 6.901A pdb=" N HIS C 90 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS A 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL E 93 " --> pdb=" O HIS A 90 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU A 92 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE E 95 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL A 94 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA E 97 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR A 96 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ASP E 99 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASN A 98 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 104 through 106 removed outlier: 6.471A pdb=" N ARG A 104 " --> pdb=" O TYR E 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 109 through 110 removed outlier: 6.459A pdb=" N ALA A 109 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 14 through 16 removed outlier: 6.515A pdb=" N LYS B 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 20 through 21 removed outlier: 6.943A pdb=" N VAL B 20 " --> pdb=" O ARG F 21 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 31 through 34 removed outlier: 6.552A pdb=" N HIS B 31 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ARG D 34 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE B 33 " --> pdb=" O ARG D 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.216A pdb=" N THR B 59 " --> pdb=" O THR F 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.557A pdb=" N VAL B 65 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 71 through 73 removed outlier: 6.440A pdb=" N VAL B 71 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 76 through 80 removed outlier: 6.799A pdb=" N SER B 77 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR D 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N LYS B 76 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N TRP F 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR B 78 " --> pdb=" O TRP F 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 89 through 99 removed outlier: 6.900A pdb=" N HIS D 90 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N HIS B 90 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL F 93 " --> pdb=" O HIS B 90 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU B 92 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N PHE F 95 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL B 94 " --> pdb=" O PHE F 95 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA F 97 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR B 96 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ASP F 99 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASN B 98 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 104 through 106 removed outlier: 6.470A pdb=" N ARG B 104 " --> pdb=" O TYR F 105 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 109 through 110 removed outlier: 6.464A pdb=" N ALA B 109 " --> pdb=" O LEU F 110 " (cutoff:3.500A) 48 hydrogen bonds defined for protein. 144 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: 0.38 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1332 1.34 - 1.46: 776 1.46 - 1.57: 2230 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 4350 Sorted by residual: bond pdb=" C SER D 23 " pdb=" N PRO D 24 " ideal model delta sigma weight residual 1.326 1.339 -0.013 1.44e-02 4.82e+03 8.53e-01 bond pdb=" N PRO F 102 " pdb=" CA PRO F 102 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 8.07e-01 bond pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 7.58e-01 bond pdb=" N PRO D 102 " pdb=" CA PRO D 102 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 7.32e-01 bond pdb=" C SER C 23 " pdb=" N PRO C 24 " ideal model delta sigma weight residual 1.326 1.338 -0.012 1.44e-02 4.82e+03 7.27e-01 ... (remaining 4345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.66: 5097 0.66 - 1.31: 644 1.31 - 1.97: 106 1.97 - 2.63: 20 2.63 - 3.28: 55 Bond angle restraints: 5922 Sorted by residual: angle pdb=" N PRO C 24 " pdb=" CA PRO C 24 " pdb=" C PRO C 24 " ideal model delta sigma weight residual 110.40 113.67 -3.27 1.61e+00 3.86e-01 4.13e+00 angle pdb=" N PRO A 24 " pdb=" CA PRO A 24 " pdb=" C PRO A 24 " ideal model delta sigma weight residual 110.40 113.64 -3.24 1.61e+00 3.86e-01 4.06e+00 angle pdb=" N PRO F 24 " pdb=" CA PRO F 24 " pdb=" C PRO F 24 " ideal model delta sigma weight residual 110.40 113.62 -3.22 1.61e+00 3.86e-01 4.00e+00 angle pdb=" N PRO B 24 " pdb=" CA PRO B 24 " pdb=" C PRO B 24 " ideal model delta sigma weight residual 110.40 113.58 -3.18 1.61e+00 3.86e-01 3.90e+00 angle pdb=" N PRO D 24 " pdb=" CA PRO D 24 " pdb=" C PRO D 24 " ideal model delta sigma weight residual 110.40 113.57 -3.17 1.61e+00 3.86e-01 3.89e+00 ... (remaining 5917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 2250 16.88 - 33.76: 246 33.76 - 50.64: 72 50.64 - 67.52: 12 67.52 - 84.40: 6 Dihedral angle restraints: 2586 sinusoidal: 978 harmonic: 1608 Sorted by residual: dihedral pdb=" CB GLU E 72 " pdb=" CG GLU E 72 " pdb=" CD GLU E 72 " pdb=" OE1 GLU E 72 " ideal model delta sinusoidal sigma weight residual 0.00 84.40 -84.40 1 3.00e+01 1.11e-03 9.62e+00 dihedral pdb=" CB GLU D 72 " pdb=" CG GLU D 72 " pdb=" CD GLU D 72 " pdb=" OE1 GLU D 72 " ideal model delta sinusoidal sigma weight residual 0.00 84.39 -84.39 1 3.00e+01 1.11e-03 9.62e+00 dihedral pdb=" CB GLU B 72 " pdb=" CG GLU B 72 " pdb=" CD GLU B 72 " pdb=" OE1 GLU B 72 " ideal model delta sinusoidal sigma weight residual 0.00 84.38 -84.38 1 3.00e+01 1.11e-03 9.62e+00 ... (remaining 2583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 317 0.023 - 0.046: 184 0.046 - 0.069: 99 0.069 - 0.092: 41 0.092 - 0.115: 67 Chirality restraints: 708 Sorted by residual: chirality pdb=" CA ILE E 73 " pdb=" N ILE E 73 " pdb=" C ILE E 73 " pdb=" CB ILE E 73 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.32e-01 chirality pdb=" CA VAL B 65 " pdb=" N VAL B 65 " pdb=" C VAL B 65 " pdb=" CB VAL B 65 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.24e-01 chirality pdb=" CA ILE A 73 " pdb=" N ILE A 73 " pdb=" C ILE A 73 " pdb=" CB ILE A 73 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 ... (remaining 705 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 23 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO D 24 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO D 24 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 24 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 23 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO E 24 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO E 24 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 24 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 23 " 0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO B 24 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 24 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 24 " 0.015 5.00e-02 4.00e+02 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1244 2.83 - 3.34: 3401 3.34 - 3.86: 7398 3.86 - 4.38: 7963 4.38 - 4.90: 15369 Nonbonded interactions: 35375 Sorted by model distance: nonbonded pdb=" O SER C 23 " pdb=" OG SER C 115 " model vdw 2.307 3.040 nonbonded pdb=" O SER E 23 " pdb=" OG SER E 115 " model vdw 2.307 3.040 nonbonded pdb=" O SER A 23 " pdb=" OG SER A 115 " model vdw 2.307 3.040 nonbonded pdb=" O SER B 23 " pdb=" OG SER B 115 " model vdw 2.307 3.040 nonbonded pdb=" O SER D 23 " pdb=" OG SER D 115 " model vdw 2.307 3.040 ... (remaining 35370 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: 0.01 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.700 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:5.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 0.024 4350 Z= 0.118 Angle : 0.533 3.283 5922 Z= 0.303 Chirality : 0.046 0.115 708 Planarity : 0.003 0.026 726 Dihedral : 16.223 84.395 1542 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 28.21 % Favored : 71.79 % 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: -3.82 (0.31), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 21 TYR 0.011 0.001 TYR D 114 PHE 0.003 0.001 PHE A 95 TRP 0.002 0.001 TRP F 79 HIS 0.002 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 ( 4350) covalent geometry : angle 0.53344 / 0.30 ( 5922) hydrogen bonds : bond 0.16085 / 10.04 ( 48) hydrogen bonds : angle 8.97280 / 6.33 ( 144) *********************** 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 104 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.102 Fit side-chains REVERT: A 99 ASP cc_start: 0.7370 (m-30) cc_final: 0.6881 (m-30) REVERT: A 104 ARG cc_start: 0.7464 (mtt90) cc_final: 0.7086 (mtt180) REVERT: B 99 ASP cc_start: 0.7370 (m-30) cc_final: 0.6879 (m-30) REVERT: B 104 ARG cc_start: 0.7453 (mtt90) cc_final: 0.7083 (mtt180) REVERT: C 21 ARG cc_start: 0.7639 (tmm160) cc_final: 0.6713 (pmt170) REVERT: C 61 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7174 (tt0) REVERT: C 63 GLU cc_start: 0.7833 (mp0) cc_final: 0.6916 (mp0) REVERT: C 99 ASP cc_start: 0.7660 (m-30) cc_final: 0.7415 (m-30) REVERT: C 104 ARG cc_start: 0.7469 (mtt90) cc_final: 0.7173 (mtt180) REVERT: D 21 ARG cc_start: 0.7639 (tmm160) cc_final: 0.6713 (pmt170) REVERT: D 61 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7174 (tt0) REVERT: D 63 GLU cc_start: 0.7832 (mp0) cc_final: 0.6912 (mp0) REVERT: D 99 ASP cc_start: 0.7660 (m-30) cc_final: 0.7413 (m-30) REVERT: D 104 ARG cc_start: 0.7465 (mtt90) cc_final: 0.7170 (mtt180) REVERT: F 63 GLU cc_start: 0.7986 (mp0) cc_final: 0.7765 (mp0) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.5431 time to fit residues: 58.1365 Evaluate side-chains 93 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 19 optimal weight: 0.4980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.196691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.171965 restraints weight = 4663.621| |-----------------------------------------------------------------------------| r_work (start): 0.4615 rms_B_bonded: 2.42 r_work: 0.4517 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4396 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 4350 Z= 0.108 Angle : 0.489 3.756 5922 Z= 0.258 Chirality : 0.046 0.119 708 Planarity : 0.003 0.020 726 Dihedral : 4.219 13.318 588 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.56 % Allowed : 27.35 % Favored : 70.09 % 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: -3.72 (0.32), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 103 TYR 0.010 0.001 TYR B 114 PHE 0.006 0.001 PHE E 87 TRP 0.005 0.001 TRP B 79 HIS 0.002 0.001 HIS D 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 4350) covalent geometry : angle 0.48863 / 0.26 ( 5922) hydrogen bonds : bond 0.02694 / 1.82 ( 48) hydrogen bonds : angle 5.15059 / 3.85 ( 144) *********************** 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 107 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.144 Fit side-chains REVERT: A 21 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6915 (tmm-80) REVERT: A 104 ARG cc_start: 0.7718 (mtt90) cc_final: 0.7378 (mtt180) REVERT: B 21 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6864 (tmm-80) REVERT: B 104 ARG cc_start: 0.7707 (mtt90) cc_final: 0.7367 (mtt180) REVERT: C 21 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6800 (pmt170) REVERT: C 61 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7292 (tt0) REVERT: C 63 GLU cc_start: 0.7856 (mp0) cc_final: 0.7105 (mp0) REVERT: C 66 GLU cc_start: 0.8172 (tt0) cc_final: 0.7840 (tt0) REVERT: C 104 ARG cc_start: 0.7739 (mtt90) cc_final: 0.7508 (mtt180) REVERT: D 21 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6778 (pmt170) REVERT: D 61 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7269 (tt0) REVERT: D 63 GLU cc_start: 0.7846 (mp0) cc_final: 0.7086 (mp0) REVERT: D 66 GLU cc_start: 0.8060 (tt0) cc_final: 0.7739 (tt0) REVERT: D 104 ARG cc_start: 0.7741 (mtt90) cc_final: 0.7508 (mtt180) REVERT: E 21 ARG cc_start: 0.7394 (tmm160) cc_final: 0.6745 (tpm170) REVERT: E 63 GLU cc_start: 0.8096 (mp0) cc_final: 0.7828 (mp0) REVERT: F 21 ARG cc_start: 0.7320 (tmm160) cc_final: 0.6702 (tpm170) REVERT: F 63 GLU cc_start: 0.8110 (mp0) cc_final: 0.7842 (mp0) outliers start: 12 outliers final: 6 residues processed: 105 average time/residue: 0.5025 time to fit residues: 54.3614 Evaluate side-chains 96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 85 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 30.0000 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.181921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.156642 restraints weight = 4511.532| |-----------------------------------------------------------------------------| r_work (start): 0.4418 rms_B_bonded: 2.48 r_work: 0.4294 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4163 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 4350 Z= 0.323 Angle : 0.680 4.514 5922 Z= 0.368 Chirality : 0.051 0.135 708 Planarity : 0.004 0.025 726 Dihedral : 5.295 14.583 588 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 7.69 % Allowed : 24.15 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.29), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.22), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 103 TYR 0.014 0.002 TYR B 114 PHE 0.014 0.003 PHE F 95 TRP 0.012 0.003 TRP B 79 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00741 / 0.32 ( 4350) covalent geometry : angle 0.67980 / 0.37 ( 5922) hydrogen bonds : bond 0.03080 / 1.88 ( 48) hydrogen bonds : angle 4.76667 / 3.67 ( 144) *********************** 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 132 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.178 Fit side-chains REVERT: A 21 ARG cc_start: 0.7784 (tmm160) cc_final: 0.7536 (tmm-80) REVERT: A 104 ARG cc_start: 0.7765 (mtt90) cc_final: 0.7382 (mtt180) REVERT: B 21 ARG cc_start: 0.7794 (tmm160) cc_final: 0.7546 (tmm-80) REVERT: B 104 ARG cc_start: 0.7772 (mtt90) cc_final: 0.7391 (mtt180) REVERT: C 12 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8435 (tp) REVERT: C 21 ARG cc_start: 0.8229 (tmm160) cc_final: 0.7285 (ppt170) REVERT: C 66 GLU cc_start: 0.8222 (tt0) cc_final: 0.7969 (tt0) REVERT: C 104 ARG cc_start: 0.7960 (mtt90) cc_final: 0.7689 (mtt180) REVERT: D 12 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8438 (tp) REVERT: D 21 ARG cc_start: 0.8225 (tmm160) cc_final: 0.7296 (ppt170) REVERT: D 66 GLU cc_start: 0.8221 (tt0) cc_final: 0.7965 (tt0) REVERT: D 104 ARG cc_start: 0.7957 (mtt90) cc_final: 0.7686 (mtt180) REVERT: E 21 ARG cc_start: 0.7630 (tmm160) cc_final: 0.6980 (tpm170) REVERT: F 21 ARG cc_start: 0.7631 (tmm160) cc_final: 0.6989 (tpm170) REVERT: F 63 GLU cc_start: 0.8471 (mp0) cc_final: 0.8271 (mp0) outliers start: 36 outliers final: 20 residues processed: 112 average time/residue: 0.5146 time to fit residues: 59.3449 Evaluate side-chains 110 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 0.0020 chunk 48 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 42 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 37 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.201108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.176386 restraints weight = 4298.251| |-----------------------------------------------------------------------------| r_work (start): 0.4610 rms_B_bonded: 2.33 r_work: 0.4497 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4366 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4350 Z= 0.105 Angle : 0.502 4.118 5922 Z= 0.263 Chirality : 0.046 0.119 708 Planarity : 0.003 0.025 726 Dihedral : 4.297 12.785 588 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.21 % Allowed : 29.06 % Favored : 67.74 % 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: -3.88 (0.30), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.23), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 103 TYR 0.015 0.001 TYR B 114 PHE 0.006 0.001 PHE A 95 TRP 0.001 0.001 TRP C 79 HIS 0.002 0.001 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.10 ( 4350) covalent geometry : angle 0.50202 / 0.26 ( 5922) hydrogen bonds : bond 0.01776 / 1.15 ( 48) hydrogen bonds : angle 4.06447 / 3.07 ( 144) *********************** 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 101 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.174 Fit side-chains REVERT: A 21 ARG cc_start: 0.7618 (tmm160) cc_final: 0.7245 (tmm-80) REVERT: A 104 ARG cc_start: 0.7801 (mtt90) cc_final: 0.7423 (mtt180) REVERT: B 21 ARG cc_start: 0.7628 (tmm160) cc_final: 0.7254 (tmm-80) REVERT: B 104 ARG cc_start: 0.7798 (mtt90) cc_final: 0.7423 (mtt180) REVERT: C 12 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8319 (tp) REVERT: C 21 ARG cc_start: 0.8030 (tmm160) cc_final: 0.7163 (ppt170) REVERT: C 66 GLU cc_start: 0.8094 (tt0) cc_final: 0.7603 (pm20) REVERT: C 104 ARG cc_start: 0.7887 (mtt90) cc_final: 0.7603 (mtt180) REVERT: D 12 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8323 (tp) REVERT: D 21 ARG cc_start: 0.8022 (tmm160) cc_final: 0.7181 (ppt170) REVERT: D 66 GLU cc_start: 0.8051 (tt0) cc_final: 0.7651 (pm20) REVERT: D 104 ARG cc_start: 0.7902 (mtt90) cc_final: 0.7618 (mtt180) REVERT: E 21 ARG cc_start: 0.7516 (tmm160) cc_final: 0.6855 (tpm170) REVERT: F 21 ARG cc_start: 0.7538 (tmm160) cc_final: 0.6878 (tpm170) REVERT: F 63 GLU cc_start: 0.8448 (mp0) cc_final: 0.8235 (mp0) outliers start: 15 outliers final: 6 residues processed: 96 average time/residue: 0.4998 time to fit residues: 49.4157 Evaluate side-chains 88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 85 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.0040 chunk 20 optimal weight: 10.0000 chunk 50 optimal weight: 0.0980 chunk 37 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.205483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.180557 restraints weight = 4596.414| |-----------------------------------------------------------------------------| r_work (start): 0.4628 rms_B_bonded: 2.42 r_work: 0.4525 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4407 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4350 Z= 0.106 Angle : 0.495 4.189 5922 Z= 0.259 Chirality : 0.046 0.116 708 Planarity : 0.003 0.023 726 Dihedral : 4.149 13.406 588 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.78 % Allowed : 27.78 % Favored : 69.44 % 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: -3.75 (0.30), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.23), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 103 TYR 0.017 0.001 TYR A 114 PHE 0.006 0.001 PHE B 95 TRP 0.002 0.001 TRP B 79 HIS 0.002 0.001 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 4350) covalent geometry : angle 0.49469 / 0.26 ( 5922) hydrogen bonds : bond 0.01707 / 1.11 ( 48) hydrogen bonds : angle 3.89011 / 2.95 ( 144) *********************** 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 93 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.094 Fit side-chains REVERT: A 21 ARG cc_start: 0.7583 (tmm160) cc_final: 0.7288 (tmm-80) REVERT: A 104 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7456 (mtt180) REVERT: B 21 ARG cc_start: 0.7548 (tmm160) cc_final: 0.7252 (tmm-80) REVERT: B 104 ARG cc_start: 0.7820 (mtt90) cc_final: 0.7458 (mtt180) REVERT: C 12 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8352 (tp) REVERT: C 21 ARG cc_start: 0.8043 (tmm160) cc_final: 0.7165 (ppt170) REVERT: C 66 GLU cc_start: 0.7959 (tt0) cc_final: 0.7587 (pm20) REVERT: C 104 ARG cc_start: 0.7936 (mtt90) cc_final: 0.7680 (mtt180) REVERT: D 12 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8359 (tp) REVERT: D 21 ARG cc_start: 0.8030 (tmm160) cc_final: 0.6925 (pmt170) REVERT: D 66 GLU cc_start: 0.7940 (tt0) cc_final: 0.7573 (pm20) REVERT: D 104 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7663 (mtt180) REVERT: E 21 ARG cc_start: 0.7716 (tmm160) cc_final: 0.7018 (tpm170) REVERT: F 21 ARG cc_start: 0.7663 (tmm160) cc_final: 0.6983 (tpm170) REVERT: F 63 GLU cc_start: 0.8415 (mp0) cc_final: 0.8096 (mp0) outliers start: 13 outliers final: 8 residues processed: 89 average time/residue: 0.5320 time to fit residues: 48.6310 Evaluate side-chains 86 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.0270 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 overall best weight: 3.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.193159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.167496 restraints weight = 4448.631| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 2.41 r_work: 0.4365 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4228 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4350 Z= 0.172 Angle : 0.552 4.911 5922 Z= 0.291 Chirality : 0.047 0.120 708 Planarity : 0.003 0.025 726 Dihedral : 4.560 13.934 588 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.77 % Allowed : 25.21 % Favored : 69.02 % 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: -3.80 (0.30), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.23), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 103 TYR 0.018 0.002 TYR A 114 PHE 0.009 0.002 PHE B 95 TRP 0.004 0.001 TRP A 79 HIS 0.003 0.001 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 4350) covalent geometry : angle 0.55172 / 0.29 ( 5922) hydrogen bonds : bond 0.01955 / 1.28 ( 48) hydrogen bonds : angle 3.96801 / 3.06 ( 144) *********************** 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 113 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.160 Fit side-chains REVERT: A 21 ARG cc_start: 0.7668 (tmm160) cc_final: 0.7394 (tmm-80) REVERT: A 104 ARG cc_start: 0.7745 (mtt90) cc_final: 0.7369 (mtt180) REVERT: B 21 ARG cc_start: 0.7677 (tmm160) cc_final: 0.7403 (tmm-80) REVERT: B 104 ARG cc_start: 0.7742 (mtt90) cc_final: 0.7369 (mtt180) REVERT: C 12 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8332 (tp) REVERT: C 21 ARG cc_start: 0.8121 (tmm160) cc_final: 0.7257 (ppt170) REVERT: C 66 GLU cc_start: 0.8094 (tt0) cc_final: 0.7814 (tt0) REVERT: C 104 ARG cc_start: 0.7917 (mtt90) cc_final: 0.7636 (mtt180) REVERT: D 12 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8334 (tp) REVERT: D 21 ARG cc_start: 0.8135 (tmm160) cc_final: 0.7020 (pmt170) REVERT: D 66 GLU cc_start: 0.8097 (tt0) cc_final: 0.7818 (tt0) REVERT: D 104 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7637 (mtt180) REVERT: E 21 ARG cc_start: 0.7708 (tmm160) cc_final: 0.7060 (tpm170) REVERT: F 21 ARG cc_start: 0.7714 (tmm160) cc_final: 0.7074 (tpm170) REVERT: F 63 GLU cc_start: 0.8460 (mp0) cc_final: 0.8147 (mp0) outliers start: 27 outliers final: 15 residues processed: 100 average time/residue: 0.6613 time to fit residues: 68.0225 Evaluate side-chains 99 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.186003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.160338 restraints weight = 4480.707| |-----------------------------------------------------------------------------| r_work (start): 0.4474 rms_B_bonded: 2.43 r_work: 0.4355 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4221 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4350 Z= 0.233 Angle : 0.615 5.105 5922 Z= 0.329 Chirality : 0.048 0.125 708 Planarity : 0.004 0.026 726 Dihedral : 5.028 15.319 588 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 5.77 % Allowed : 25.64 % Favored : 68.59 % 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: -3.80 (0.30), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.23), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 103 TYR 0.021 0.002 TYR B 114 PHE 0.011 0.002 PHE B 95 TRP 0.006 0.002 TRP A 79 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 ( 4350) covalent geometry : angle 0.61452 / 0.33 ( 5922) hydrogen bonds : bond 0.02191 / 1.42 ( 48) hydrogen bonds : angle 4.17025 / 3.23 ( 144) *********************** 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 125 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ARG cc_start: 0.7741 (mtt90) cc_final: 0.7339 (mtt180) REVERT: B 104 ARG cc_start: 0.7751 (mtt90) cc_final: 0.7358 (mtt180) REVERT: C 12 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8322 (tp) REVERT: C 21 ARG cc_start: 0.8063 (tmm160) cc_final: 0.7262 (ppt170) REVERT: C 63 GLU cc_start: 0.8521 (mp0) cc_final: 0.7684 (mp0) REVERT: C 66 GLU cc_start: 0.8084 (tt0) cc_final: 0.7855 (tt0) REVERT: C 104 ARG cc_start: 0.7967 (mtt90) cc_final: 0.7674 (mtt180) REVERT: D 12 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8333 (tp) REVERT: D 21 ARG cc_start: 0.8068 (tmm160) cc_final: 0.7269 (ppt170) REVERT: D 63 GLU cc_start: 0.8508 (mp0) cc_final: 0.7683 (mp0) REVERT: D 66 GLU cc_start: 0.8083 (tt0) cc_final: 0.7866 (tt0) REVERT: D 104 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7653 (mtt180) REVERT: E 21 ARG cc_start: 0.7780 (tmm160) cc_final: 0.7146 (tpm170) REVERT: F 21 ARG cc_start: 0.7795 (tmm160) cc_final: 0.7166 (tpm170) REVERT: F 63 GLU cc_start: 0.8542 (mp0) cc_final: 0.8197 (mp0) outliers start: 27 outliers final: 19 residues processed: 111 average time/residue: 0.6200 time to fit residues: 70.8160 Evaluate side-chains 113 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.190286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.165179 restraints weight = 4386.903| |-----------------------------------------------------------------------------| r_work (start): 0.4448 rms_B_bonded: 2.34 r_work: 0.4331 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4196 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4350 Z= 0.223 Angle : 0.611 5.613 5922 Z= 0.324 Chirality : 0.049 0.126 708 Planarity : 0.004 0.027 726 Dihedral : 4.982 14.784 588 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 5.77 % Allowed : 25.85 % Favored : 68.38 % 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: -3.82 (0.30), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.23), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 103 TYR 0.020 0.002 TYR B 114 PHE 0.011 0.002 PHE A 95 TRP 0.006 0.002 TRP E 79 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 ( 4350) covalent geometry : angle 0.61106 / 0.32 ( 5922) hydrogen bonds : bond 0.02112 / 1.37 ( 48) hydrogen bonds : angle 4.09630 / 3.17 ( 144) *********************** 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 123 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8335 (mp0) cc_final: 0.7713 (mp0) REVERT: A 104 ARG cc_start: 0.7794 (mtt90) cc_final: 0.7411 (mtt180) REVERT: B 104 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7420 (mtt180) REVERT: C 12 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8370 (tp) REVERT: C 21 ARG cc_start: 0.8003 (tmm160) cc_final: 0.7283 (ppt170) REVERT: C 63 GLU cc_start: 0.8541 (mp0) cc_final: 0.7724 (mp0) REVERT: C 66 GLU cc_start: 0.8014 (tt0) cc_final: 0.7796 (tt0) REVERT: C 104 ARG cc_start: 0.7979 (mtt90) cc_final: 0.7709 (mtt180) REVERT: D 12 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8385 (tp) REVERT: D 21 ARG cc_start: 0.8010 (tmm160) cc_final: 0.7292 (ppt170) REVERT: D 63 GLU cc_start: 0.8521 (mp0) cc_final: 0.7713 (mp0) REVERT: D 66 GLU cc_start: 0.7998 (tt0) cc_final: 0.7769 (tt0) REVERT: D 104 ARG cc_start: 0.7967 (mtt90) cc_final: 0.7703 (mtt180) REVERT: E 21 ARG cc_start: 0.7844 (tmm160) cc_final: 0.7263 (tpm170) REVERT: E 122 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8078 (t) REVERT: F 21 ARG cc_start: 0.7863 (tmm160) cc_final: 0.7283 (tpm170) REVERT: F 63 GLU cc_start: 0.8528 (mp0) cc_final: 0.8209 (mp0) REVERT: F 122 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.8079 (t) outliers start: 27 outliers final: 20 residues processed: 106 average time/residue: 0.6565 time to fit residues: 71.5421 Evaluate side-chains 120 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 11 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.201806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.176976 restraints weight = 4317.465| |-----------------------------------------------------------------------------| r_work (start): 0.4629 rms_B_bonded: 2.32 r_work: 0.4521 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4390 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4350 Z= 0.096 Angle : 0.507 5.710 5922 Z= 0.261 Chirality : 0.047 0.120 708 Planarity : 0.004 0.029 726 Dihedral : 4.281 14.337 588 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.78 % Allowed : 28.63 % Favored : 68.59 % 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: -3.68 (0.31), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.23), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 103 TYR 0.017 0.002 TYR B 114 PHE 0.006 0.001 PHE A 95 TRP 0.002 0.000 TRP D 79 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 4350) covalent geometry : angle 0.50744 / 0.26 ( 5922) hydrogen bonds : bond 0.01559 / 1.02 ( 48) hydrogen bonds : angle 3.70059 / 2.75 ( 144) *********************** 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 93 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8097 (mp0) cc_final: 0.7570 (mp0) REVERT: A 104 ARG cc_start: 0.7872 (mtt90) cc_final: 0.7447 (mtt180) REVERT: B 104 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7450 (mtt180) REVERT: C 12 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8308 (tp) REVERT: C 21 ARG cc_start: 0.7899 (tmm160) cc_final: 0.6963 (tmm160) REVERT: C 104 ARG cc_start: 0.7945 (mtt90) cc_final: 0.7687 (mtt180) REVERT: D 12 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8305 (tp) REVERT: D 21 ARG cc_start: 0.7901 (tmm160) cc_final: 0.6959 (tmm160) REVERT: D 104 ARG cc_start: 0.7942 (mtt90) cc_final: 0.7694 (mtt180) REVERT: E 21 ARG cc_start: 0.7759 (tmm160) cc_final: 0.7310 (tpm170) REVERT: E 122 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.7969 (t) REVERT: F 21 ARG cc_start: 0.7741 (tmm160) cc_final: 0.7303 (tpm170) REVERT: F 63 GLU cc_start: 0.8406 (mp0) cc_final: 0.8150 (mp0) outliers start: 13 outliers final: 10 residues processed: 87 average time/residue: 0.6625 time to fit residues: 59.2824 Evaluate side-chains 90 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 0.0570 chunk 16 optimal weight: 0.5980 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 overall best weight: 2.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.198243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.173091 restraints weight = 4309.869| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 2.32 r_work: 0.4418 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4280 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4350 Z= 0.128 Angle : 0.547 6.173 5922 Z= 0.279 Chirality : 0.047 0.119 708 Planarity : 0.004 0.029 726 Dihedral : 4.417 13.932 588 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.21 % Allowed : 28.21 % Favored : 68.59 % 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: -3.59 (0.31), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 103 TYR 0.019 0.002 TYR B 114 PHE 0.007 0.001 PHE A 95 TRP 0.002 0.001 TRP D 79 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 4350) covalent geometry : angle 0.54701 / 0.28 ( 5922) hydrogen bonds : bond 0.01640 / 1.07 ( 48) hydrogen bonds : angle 3.77759 / 2.87 ( 144) ********************** 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 98 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ARG cc_start: 0.7851 (mtt90) cc_final: 0.7419 (mtt180) REVERT: B 104 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7429 (mtt180) REVERT: C 12 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8298 (tp) REVERT: C 21 ARG cc_start: 0.7969 (tmm160) cc_final: 0.7023 (tmm160) REVERT: C 104 ARG cc_start: 0.7934 (mtt90) cc_final: 0.7680 (mtt180) REVERT: D 12 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8302 (tp) REVERT: D 21 ARG cc_start: 0.7970 (tmm160) cc_final: 0.7024 (tmm160) REVERT: D 104 ARG cc_start: 0.7928 (mtt90) cc_final: 0.7676 (mtt180) REVERT: E 21 ARG cc_start: 0.7835 (tmm160) cc_final: 0.7358 (tpm170) REVERT: E 122 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8033 (t) REVERT: F 21 ARG cc_start: 0.7824 (tmm160) cc_final: 0.7356 (tpm170) REVERT: F 63 GLU cc_start: 0.8364 (mp0) cc_final: 0.8095 (mp0) REVERT: F 122 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.8031 (t) outliers start: 15 outliers final: 10 residues processed: 92 average time/residue: 0.5969 time to fit residues: 56.5425 Evaluate side-chains 94 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.188726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.163525 restraints weight = 4380.126| |-----------------------------------------------------------------------------| r_work (start): 0.4468 rms_B_bonded: 2.35 r_work: 0.4353 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4221 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 4350 Z= 0.268 Angle : 0.666 6.204 5922 Z= 0.350 Chirality : 0.050 0.128 708 Planarity : 0.004 0.026 726 Dihedral : 5.135 14.394 588 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 4.06 % Allowed : 27.35 % Favored : 68.59 % 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: -3.67 (0.30), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.23), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 103 TYR 0.026 0.002 TYR B 114 PHE 0.012 0.002 PHE A 95 TRP 0.007 0.002 TRP F 79 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.27 ( 4350) covalent geometry : angle 0.66558 / 0.35 ( 5922) hydrogen bonds : bond 0.02227 / 1.42 ( 48) hydrogen bonds : angle 4.18011 / 3.24 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2168.44 seconds wall clock time: 37 minutes 35.54 seconds (2255.54 seconds total)