Starting phenix.real_space_refine on Fri Jul 3 06:01:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xzy_33534/07_2026/7xzy_33534.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xzy_33534/07_2026/7xzy_33534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xzy_33534/07_2026/7xzy_33534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xzy_33534/07_2026/7xzy_33534.map" model { file = "/net/cci-nas-00/data/ceres_data/7xzy_33534/07_2026/7xzy_33534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xzy_33534/07_2026/7xzy_33534.cif" } resolution = 3.97 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: 5 Type Number sf(0) Gaussians P 330 5.49 5 S 14 5.16 5 C 7015 2.51 5 N 2417 2.21 5 O 3045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12821 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3372 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "J" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3393 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Time building chain proxies: 2.81, per 1000 atoms: 0.22 Number of scatterers: 12821 At special positions: 0 Unit cell: (127.6, 151.8, 105.6, 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 14 16.00 P 330 15.00 O 3045 8.00 N 2417 7.00 C 7015 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: 1.07 Conformation dependent library (CDL) restraints added in 240.3 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 73.5% alpha, 2.4% beta 163 base pairs and 262 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.654A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.345A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.175A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 4.127A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.536A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.519A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 23 through 29 removed outlier: 4.152A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.723A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.306A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.699A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.602A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 removed outlier: 4.222A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 removed outlier: 3.639A pdb=" N THR C 101 " --> pdb=" O THR F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.771A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.555A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.735A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 410 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 423 hydrogen bonds 842 hydrogen bond angles 0 basepair planarities 163 basepair parallelities 262 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2094 1.33 - 1.45: 4796 1.45 - 1.57: 6152 1.57 - 1.69: 658 1.69 - 1.81: 24 Bond restraints: 13724 Sorted by residual: bond pdb=" C1' DT I 32 " pdb=" N1 DT I 32 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.47e+01 bond pdb=" C3' DT J 113 " pdb=" C2' DT J 113 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.34e+01 bond pdb=" C3' DA I 52 " pdb=" O3' DA I 52 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.25e+01 bond pdb=" N ILE H 66 " pdb=" CA ILE H 66 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" C3' DG I 35 " pdb=" C2' DG I 35 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 ... (remaining 13719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 18542 1.62 - 3.24: 1319 3.24 - 4.87: 65 4.87 - 6.49: 15 6.49 - 8.11: 7 Bond angle restraints: 19948 Sorted by residual: angle pdb=" O4' DA I 113 " pdb=" C4' DA I 113 " pdb=" C3' DA I 113 " ideal model delta sigma weight residual 106.00 103.00 3.00 6.00e-01 2.78e+00 2.50e+01 angle pdb=" O5' DT I 53 " pdb=" C5' DT I 53 " pdb=" C4' DT I 53 " ideal model delta sigma weight residual 109.40 113.39 -3.99 8.00e-01 1.56e+00 2.48e+01 angle pdb=" N3 DT J 48 " pdb=" C4 DT J 48 " pdb=" O4 DT J 48 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" O4' DG J 31 " pdb=" C1' DG J 31 " pdb=" N9 DG J 31 " ideal model delta sigma weight residual 108.00 111.10 -3.10 7.00e-01 2.04e+00 1.96e+01 ... (remaining 19943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4731 17.96 - 35.91: 1186 35.91 - 53.87: 1116 53.87 - 71.82: 317 71.82 - 89.78: 23 Dihedral angle restraints: 7373 sinusoidal: 5169 harmonic: 2204 Sorted by residual: dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -163.93 -16.07 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA ILE G 87 " pdb=" CB ILE G 87 " pdb=" CG1 ILE G 87 " pdb=" CD1 ILE G 87 " ideal model delta sinusoidal sigma weight residual 180.00 124.96 55.04 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " pdb=" NE ARG E 128 " pdb=" CZ ARG E 128 " ideal model delta sinusoidal sigma weight residual -180.00 -138.82 -41.18 2 1.50e+01 4.44e-03 9.25e+00 ... (remaining 7370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1842 0.061 - 0.123: 382 0.123 - 0.184: 37 0.184 - 0.245: 1 0.245 - 0.306: 2 Chirality restraints: 2264 Sorted by residual: chirality pdb=" CB ILE B 29 " pdb=" CA ILE B 29 " pdb=" CG1 ILE B 29 " pdb=" CG2 ILE B 29 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE F 29 " pdb=" CA ILE F 29 " pdb=" CG1 ILE F 29 " pdb=" CG2 ILE F 29 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ILE C 87 " pdb=" N ILE C 87 " pdb=" C ILE C 87 " pdb=" CB ILE C 87 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2261 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 64 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.90e+00 pdb=" C ASN B 64 " -0.054 2.00e-02 2.50e+03 pdb=" O ASN B 64 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL B 65 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 62 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C LEU B 62 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU B 62 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU B 63 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 69 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C ALA B 69 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA B 69 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 70 " -0.014 2.00e-02 2.50e+03 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 199 2.63 - 3.20: 10916 3.20 - 3.76: 24685 3.76 - 4.33: 30688 4.33 - 4.90: 43141 Nonbonded interactions: 109629 Sorted by model distance: nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 68 " model vdw 2.062 3.040 nonbonded pdb=" O ARG C 20 " pdb=" NZ LYS D 117 " model vdw 2.080 3.120 nonbonded pdb=" OG SER B 47 " pdb=" OP1 DC J 105 " model vdw 2.136 3.040 nonbonded pdb=" O2 DC I 73 " pdb=" N2 DG J 121 " model vdw 2.162 2.496 nonbonded pdb=" NH2 ARG H 30 " pdb=" OP2 DA I 146 " model vdw 2.222 3.120 ... (remaining 109624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.270 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 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 : 0.006 0.054 13724 Z= 0.541 Angle : 0.831 8.112 19948 Z= 0.707 Chirality : 0.049 0.306 2264 Planarity : 0.005 0.039 1381 Dihedral : 27.844 89.778 5953 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.16 % Allowed : 0.79 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.28), residues: 746 helix: 1.20 (0.20), residues: 542 sheet: None (None), residues: 0 loop : -0.54 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 92 TYR 0.023 0.002 TYR C 50 PHE 0.018 0.002 PHE G 25 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.54 (13724) covalent geometry : angle 0.83088 / 0.71 (19948) hydrogen bonds : bond 0.10071 / 6.93 ( 833) hydrogen bonds : angle 3.78212 / 2.69 ( 2048) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.339 Fit side-chains REVERT: B 59 LYS cc_start: 0.8792 (tttm) cc_final: 0.8221 (tttm) REVERT: B 63 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7949 (mp0) REVERT: C 64 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8299 (mm-30) REVERT: C 92 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7633 (mt-10) REVERT: F 85 ASP cc_start: 0.8274 (m-30) cc_final: 0.8031 (m-30) REVERT: G 39 TYR cc_start: 0.7474 (m-10) cc_final: 0.7231 (m-80) REVERT: G 92 GLU cc_start: 0.8786 (mp0) cc_final: 0.8585 (mp0) REVERT: H 31 LYS cc_start: 0.8302 (mmmm) cc_final: 0.7981 (mmmt) REVERT: H 73 GLU cc_start: 0.8204 (tp30) cc_final: 0.7912 (tp30) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.1023 time to fit residues: 27.5616 Evaluate side-chains 143 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 75 HIS D 44 GLN D 81 ASN E 93 GLN H 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.106317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.086069 restraints weight = 85230.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.087346 restraints weight = 47689.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.088179 restraints weight = 33440.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.088534 restraints weight = 27246.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.088790 restraints weight = 24805.787| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13724 Z= 0.185 Angle : 0.662 8.341 19948 Z= 0.399 Chirality : 0.045 0.189 2264 Planarity : 0.006 0.050 1381 Dihedral : 31.272 87.832 4432 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.52 % Allowed : 10.08 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.30), residues: 746 helix: 1.69 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.60 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 67 TYR 0.032 0.003 TYR F 88 PHE 0.022 0.002 PHE A 78 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.18 (13724) covalent geometry : angle 0.66173 / 0.40 (19948) hydrogen bonds : bond 0.06200 / 4.27 ( 833) hydrogen bonds : angle 3.27660 / 2.35 ( 2048) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.234 Fit side-chains REVERT: B 73 THR cc_start: 0.9343 (m) cc_final: 0.8872 (t) REVERT: B 88 TYR cc_start: 0.8670 (m-10) cc_final: 0.8457 (m-10) REVERT: E 50 GLU cc_start: 0.8181 (pt0) cc_final: 0.7864 (pt0) REVERT: E 67 PHE cc_start: 0.8682 (t80) cc_final: 0.8347 (t80) REVERT: F 81 VAL cc_start: 0.8928 (t) cc_final: 0.8681 (m) REVERT: G 92 GLU cc_start: 0.8897 (mp0) cc_final: 0.8479 (mp0) REVERT: H 39 TYR cc_start: 0.8449 (t80) cc_final: 0.8012 (t80) REVERT: H 65 ASP cc_start: 0.8697 (t70) cc_final: 0.8408 (t0) REVERT: H 73 GLU cc_start: 0.8330 (tp30) cc_final: 0.8106 (tp30) outliers start: 16 outliers final: 6 residues processed: 174 average time/residue: 0.0886 time to fit residues: 23.3794 Evaluate side-chains 148 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 63 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 78 optimal weight: 40.0000 chunk 82 optimal weight: 30.0000 chunk 16 optimal weight: 0.9990 chunk 91 optimal weight: 30.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.104836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.084228 restraints weight = 86865.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.085533 restraints weight = 48525.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.086393 restraints weight = 34002.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.086751 restraints weight = 27623.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.087063 restraints weight = 25131.047| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13724 Z= 0.152 Angle : 0.605 7.385 19948 Z= 0.370 Chirality : 0.042 0.183 2264 Planarity : 0.004 0.046 1381 Dihedral : 31.533 89.180 4432 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.99 % Allowed : 12.76 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.30), residues: 746 helix: 1.86 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.75 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.025 0.002 TYR D 37 PHE 0.014 0.002 PHE E 67 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.15 (13724) covalent geometry : angle 0.60458 / 0.37 (19948) hydrogen bonds : bond 0.05062 / 3.46 ( 833) hydrogen bonds : angle 3.02968 / 2.18 ( 2048) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8148 (mt-10) REVERT: B 73 THR cc_start: 0.9380 (m) cc_final: 0.9031 (t) REVERT: B 88 TYR cc_start: 0.8814 (m-10) cc_final: 0.8428 (m-10) REVERT: C 33 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8535 (mm) REVERT: C 36 LYS cc_start: 0.7884 (mmmt) cc_final: 0.7679 (mmtp) REVERT: C 56 GLU cc_start: 0.8003 (pp20) cc_final: 0.7789 (pp20) REVERT: C 91 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7831 (pm20) REVERT: E 67 PHE cc_start: 0.8729 (t80) cc_final: 0.8432 (t80) REVERT: F 93 GLN cc_start: 0.8650 (tp40) cc_final: 0.8404 (tp40) REVERT: G 92 GLU cc_start: 0.8878 (mp0) cc_final: 0.8441 (mp0) REVERT: H 65 ASP cc_start: 0.8753 (t70) cc_final: 0.8459 (t0) outliers start: 19 outliers final: 6 residues processed: 164 average time/residue: 0.0866 time to fit residues: 21.9727 Evaluate side-chains 152 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.092706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.070521 restraints weight = 85934.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.071713 restraints weight = 47686.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.072448 restraints weight = 33811.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.072947 restraints weight = 27949.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.073038 restraints weight = 25244.200| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 13724 Z= 0.220 Angle : 0.708 10.569 19948 Z= 0.416 Chirality : 0.044 0.259 2264 Planarity : 0.007 0.092 1381 Dihedral : 31.708 89.639 4432 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.99 % Allowed : 15.43 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.30), residues: 746 helix: 1.47 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -1.01 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 29 TYR 0.032 0.003 TYR D 37 PHE 0.013 0.002 PHE E 67 HIS 0.005 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.22 (13724) covalent geometry : angle 0.70797 / 0.42 (19948) hydrogen bonds : bond 0.08257 / 5.67 ( 833) hydrogen bonds : angle 3.46242 / 2.49 ( 2048) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8665 (m) REVERT: B 84 MET cc_start: 0.8723 (mmm) cc_final: 0.8467 (mmm) REVERT: C 90 ASP cc_start: 0.8894 (t0) cc_final: 0.8652 (t0) REVERT: G 39 TYR cc_start: 0.8527 (m-80) cc_final: 0.7908 (m-10) REVERT: G 50 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: G 92 GLU cc_start: 0.8833 (mp0) cc_final: 0.8548 (mp0) REVERT: H 65 ASP cc_start: 0.8890 (t70) cc_final: 0.8674 (t0) REVERT: H 73 GLU cc_start: 0.8555 (tp30) cc_final: 0.8294 (tp30) REVERT: H 81 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.7574 (t0) outliers start: 19 outliers final: 9 residues processed: 155 average time/residue: 0.1069 time to fit residues: 24.5438 Evaluate side-chains 136 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 81 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.093297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.071280 restraints weight = 85978.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.072423 restraints weight = 47680.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.073178 restraints weight = 33727.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.073536 restraints weight = 27778.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.073894 restraints weight = 25327.692| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13724 Z= 0.148 Angle : 0.605 7.993 19948 Z= 0.364 Chirality : 0.041 0.193 2264 Planarity : 0.004 0.044 1381 Dihedral : 31.789 91.127 4432 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.68 % Allowed : 19.21 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.30), residues: 746 helix: 1.97 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -1.03 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.011 0.001 TYR G 39 PHE 0.011 0.001 PHE E 67 HIS 0.013 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.15 (13724) covalent geometry : angle 0.60531 / 0.36 (19948) hydrogen bonds : bond 0.05267 / 3.60 ( 833) hydrogen bonds : angle 2.97862 / 2.14 ( 2048) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.6941 (ptpp) cc_final: 0.6601 (ptpt) REVERT: B 88 TYR cc_start: 0.8890 (m-10) cc_final: 0.8445 (m-10) REVERT: C 90 ASP cc_start: 0.8696 (t0) cc_final: 0.8446 (t0) REVERT: E 50 GLU cc_start: 0.8746 (pt0) cc_final: 0.8529 (pt0) REVERT: G 50 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: G 92 GLU cc_start: 0.8771 (mp0) cc_final: 0.8503 (mp0) REVERT: H 65 ASP cc_start: 0.8862 (t70) cc_final: 0.8652 (t0) REVERT: H 73 GLU cc_start: 0.8656 (tp30) cc_final: 0.8403 (tp30) REVERT: H 81 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7062 (t0) outliers start: 17 outliers final: 12 residues processed: 142 average time/residue: 0.1035 time to fit residues: 21.9817 Evaluate side-chains 139 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 81 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 65 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.091009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.068945 restraints weight = 84608.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.070034 restraints weight = 46758.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.070746 restraints weight = 33110.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.071182 restraints weight = 27380.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.071347 restraints weight = 24722.928| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13724 Z= 0.160 Angle : 0.600 7.008 19948 Z= 0.363 Chirality : 0.041 0.184 2264 Planarity : 0.004 0.046 1381 Dihedral : 31.741 90.936 4432 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.05 % Allowed : 20.79 % Favored : 77.17 % 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: 2.00 (0.31), residues: 746 helix: 2.13 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.05 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.011 0.001 TYR D 37 PHE 0.010 0.001 PHE E 67 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.16 (13724) covalent geometry : angle 0.59978 / 0.36 (19948) hydrogen bonds : bond 0.05288 / 3.63 ( 833) hydrogen bonds : angle 2.96265 / 2.13 ( 2048) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8876 (m-10) cc_final: 0.8421 (m-10) REVERT: C 18 SER cc_start: 0.8558 (m) cc_final: 0.8276 (p) REVERT: C 90 ASP cc_start: 0.8551 (t0) cc_final: 0.8302 (t0) REVERT: G 50 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: G 92 GLU cc_start: 0.8833 (mp0) cc_final: 0.8570 (mp0) REVERT: H 39 TYR cc_start: 0.8517 (t80) cc_final: 0.8104 (t80) REVERT: H 65 ASP cc_start: 0.8900 (t70) cc_final: 0.8690 (t0) REVERT: H 73 GLU cc_start: 0.8690 (tp30) cc_final: 0.8386 (tp30) outliers start: 13 outliers final: 10 residues processed: 143 average time/residue: 0.0989 time to fit residues: 21.3618 Evaluate side-chains 135 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 95 optimal weight: 30.0000 chunk 93 optimal weight: 30.0000 chunk 64 optimal weight: 2.9990 chunk 73 optimal weight: 50.0000 chunk 44 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.089176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.067169 restraints weight = 84672.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.068233 restraints weight = 46448.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.068956 restraints weight = 32803.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.069290 restraints weight = 27052.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.069517 restraints weight = 24682.864| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13724 Z= 0.154 Angle : 0.611 10.972 19948 Z= 0.367 Chirality : 0.041 0.204 2264 Planarity : 0.004 0.047 1381 Dihedral : 31.740 91.884 4432 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.68 % Allowed : 21.57 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.31), residues: 746 helix: 2.15 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -1.23 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 71 TYR 0.013 0.001 TYR D 37 PHE 0.012 0.001 PHE C 25 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (13724) covalent geometry : angle 0.61110 / 0.37 (19948) hydrogen bonds : bond 0.04833 / 3.32 ( 833) hydrogen bonds : angle 2.85628 / 2.06 ( 2048) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7993 (m-10) cc_final: 0.7732 (m-10) REVERT: A 120 MET cc_start: 0.8473 (mmm) cc_final: 0.8165 (mmm) REVERT: B 88 TYR cc_start: 0.8815 (m-10) cc_final: 0.8446 (m-10) REVERT: C 18 SER cc_start: 0.8549 (m) cc_final: 0.8079 (p) REVERT: C 27 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8674 (p) REVERT: C 36 LYS cc_start: 0.8958 (tppt) cc_final: 0.8513 (mmtp) REVERT: C 90 ASP cc_start: 0.8541 (t0) cc_final: 0.8169 (t0) REVERT: D 44 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8635 (tm-30) REVERT: D 113 LYS cc_start: 0.9305 (ptmm) cc_final: 0.9104 (ptpp) REVERT: G 50 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: G 92 GLU cc_start: 0.8903 (mp0) cc_final: 0.8623 (mp0) REVERT: H 39 TYR cc_start: 0.8485 (t80) cc_final: 0.8136 (t80) REVERT: H 65 ASP cc_start: 0.8901 (t70) cc_final: 0.8533 (t0) REVERT: H 73 GLU cc_start: 0.8749 (tp30) cc_final: 0.8413 (tp30) outliers start: 17 outliers final: 11 residues processed: 147 average time/residue: 0.1088 time to fit residues: 23.7725 Evaluate side-chains 137 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 9.9990 chunk 93 optimal weight: 30.0000 chunk 35 optimal weight: 0.9980 chunk 101 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 65 optimal weight: 0.7980 chunk 75 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 83 optimal weight: 30.0000 chunk 95 optimal weight: 30.0000 overall best weight: 5.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 24 GLN D 60 ASN E 93 GLN G 24 GLN H 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.072823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.049729 restraints weight = 83034.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.050566 restraints weight = 46899.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.051150 restraints weight = 34145.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.051366 restraints weight = 28806.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.051680 restraints weight = 26675.867| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.7750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.141 13724 Z= 0.324 Angle : 0.929 26.885 19948 Z= 0.526 Chirality : 0.051 0.231 2264 Planarity : 0.009 0.123 1381 Dihedral : 31.879 101.912 4432 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.08 % Favored : 96.78 % Rotamer: Outliers : 2.99 % Allowed : 22.20 % Favored : 74.80 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.29), residues: 746 helix: 1.24 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -1.66 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.002 ARG B 92 TYR 0.037 0.004 TYR D 37 PHE 0.022 0.004 PHE C 25 HIS 0.012 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.32 (13724) covalent geometry : angle 0.92858 / 0.53 (19948) hydrogen bonds : bond 0.12460 / 8.45 ( 833) hydrogen bonds : angle 4.14797 / 3.00 ( 2048) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 18 SER cc_start: 0.9087 (m) cc_final: 0.8854 (p) REVERT: C 36 LYS cc_start: 0.9338 (tppt) cc_final: 0.8970 (mmtp) REVERT: C 75 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8301 (mmmm) REVERT: H 39 TYR cc_start: 0.8885 (t80) cc_final: 0.8567 (t80) REVERT: H 65 ASP cc_start: 0.9013 (t70) cc_final: 0.8792 (t0) REVERT: H 73 GLU cc_start: 0.8928 (tp30) cc_final: 0.8546 (tp30) REVERT: H 81 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8305 (t0) outliers start: 19 outliers final: 11 residues processed: 133 average time/residue: 0.1131 time to fit residues: 21.6918 Evaluate side-chains 115 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 88 optimal weight: 50.0000 chunk 101 optimal weight: 30.0000 chunk 19 optimal weight: 6.9990 chunk 87 optimal weight: 50.0000 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 78 optimal weight: 30.0000 chunk 68 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.073980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.051127 restraints weight = 83923.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.052030 restraints weight = 46123.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.052687 restraints weight = 32919.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.052981 restraints weight = 27359.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.053176 restraints weight = 24981.726| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.7938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 13724 Z= 0.180 Angle : 0.723 15.171 19948 Z= 0.416 Chirality : 0.045 0.224 2264 Planarity : 0.005 0.044 1381 Dihedral : 32.062 95.587 4432 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.73 % Allowed : 24.88 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.31), residues: 746 helix: 1.90 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.60 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 92 TYR 0.015 0.001 TYR D 37 PHE 0.017 0.002 PHE A 78 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.18 (13724) covalent geometry : angle 0.72331 / 0.42 (19948) hydrogen bonds : bond 0.06545 / 4.41 ( 833) hydrogen bonds : angle 3.31938 / 2.39 ( 2048) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8927 (m-10) cc_final: 0.8595 (m-80) REVERT: C 18 SER cc_start: 0.8890 (m) cc_final: 0.8442 (p) REVERT: C 27 VAL cc_start: 0.9249 (OUTLIER) cc_final: 0.9012 (p) REVERT: C 36 LYS cc_start: 0.9286 (tppt) cc_final: 0.8991 (mmtp) REVERT: C 75 LYS cc_start: 0.8574 (mmmt) cc_final: 0.8253 (mmmm) REVERT: F 52 GLU cc_start: 0.8245 (mp0) cc_final: 0.7925 (mm-30) REVERT: G 91 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7677 (tm-30) REVERT: H 73 GLU cc_start: 0.8852 (tp30) cc_final: 0.8634 (tp30) outliers start: 11 outliers final: 7 residues processed: 130 average time/residue: 0.1129 time to fit residues: 21.2065 Evaluate side-chains 119 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 50 optimal weight: 0.1980 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 28 optimal weight: 0.0050 chunk 75 optimal weight: 30.0000 chunk 91 optimal weight: 30.0000 chunk 73 optimal weight: 50.0000 chunk 55 optimal weight: 0.0770 chunk 44 optimal weight: 3.9990 overall best weight: 1.0354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.074473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.052034 restraints weight = 84153.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.052956 restraints weight = 45961.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.053611 restraints weight = 32331.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.053828 restraints weight = 26701.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.054046 restraints weight = 24688.979| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.8080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13724 Z= 0.162 Angle : 0.684 13.996 19948 Z= 0.397 Chirality : 0.042 0.214 2264 Planarity : 0.004 0.046 1381 Dihedral : 31.870 92.229 4432 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.26 % Allowed : 24.41 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.31), residues: 746 helix: 2.09 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.60 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 29 TYR 0.017 0.001 TYR D 37 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (13724) covalent geometry : angle 0.68399 / 0.40 (19948) hydrogen bonds : bond 0.05546 / 3.77 ( 833) hydrogen bonds : angle 3.04419 / 2.21 ( 2048) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8855 (m-10) cc_final: 0.8625 (m-80) REVERT: C 18 SER cc_start: 0.8848 (m) cc_final: 0.8640 (p) REVERT: C 36 LYS cc_start: 0.9246 (tppt) cc_final: 0.8964 (mmtp) REVERT: C 64 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8475 (tm-30) REVERT: C 75 LYS cc_start: 0.8455 (mmmt) cc_final: 0.8139 (mmmm) REVERT: E 59 GLU cc_start: 0.8289 (pm20) cc_final: 0.7945 (pm20) REVERT: H 73 GLU cc_start: 0.8866 (tp30) cc_final: 0.8549 (tp30) REVERT: H 81 ASN cc_start: 0.8527 (t0) cc_final: 0.8169 (t0) outliers start: 8 outliers final: 5 residues processed: 127 average time/residue: 0.1105 time to fit residues: 20.1323 Evaluate side-chains 119 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 89 optimal weight: 50.0000 chunk 98 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 73 optimal weight: 50.0000 chunk 76 optimal weight: 30.0000 chunk 79 optimal weight: 30.0000 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 overall best weight: 12.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN E 113 HIS H 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.061319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.038450 restraints weight = 85285.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.039185 restraints weight = 48397.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.039661 restraints weight = 35014.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.040047 restraints weight = 29345.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.040070 restraints weight = 26492.837| |-----------------------------------------------------------------------------| r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 1.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.140 13724 Z= 0.541 Angle : 1.254 17.137 19948 Z= 0.673 Chirality : 0.067 0.319 2264 Planarity : 0.011 0.105 1381 Dihedral : 32.108 114.154 4432 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.36 % Allowed : 24.57 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.28), residues: 746 helix: 0.13 (0.20), residues: 544 sheet: None (None), residues: 0 loop : -2.63 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG G 35 TYR 0.040 0.005 TYR D 80 PHE 0.037 0.005 PHE E 84 HIS 0.011 0.004 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.01190 / 0.54 (13724) covalent geometry : angle 1.25363 / 0.67 (19948) hydrogen bonds : bond 0.15966 / 10.68 ( 833) hydrogen bonds : angle 5.41296 / 3.93 ( 2048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2170.56 seconds wall clock time: 38 minutes 4.06 seconds (2284.06 seconds total)