Starting phenix.real_space_refine on Sat Sep 12 00:15:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xzy_33534/09_2026/7xzy_33534.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xzy_33534/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xzy_33534/09_2026/7xzy_33534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xzy_33534/09_2026/7xzy_33534.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xzy_33534/09_2026/7xzy_33534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xzy_33534/09_2026/7xzy_33534.map" } 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-2.2.1-6174/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: 2.64, per 1000 atoms: 0.21 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: 0.80 Conformation dependent library (CDL) restraints added in 266.6 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: 1.62 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: 2.18 Time building geometry restraints manager: 1.17 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: 18527 1.62 - 3.24: 1334 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: 0.700 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.880 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- 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 : 0.836 8.112 19948 Z= 0.711 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 0.83592 / 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 : 0.287 Fit side-chains revert: symmetry clash 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: 0.7950 (mp0) REVERT: C 64 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8301 (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: 0.8024 (m-30) REVERT: G 39 TYR cc_start: 0.7474 (m-10) cc_final: 0.7232 (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: 0.7913 (tp30) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.0946 time to fit residues: 25.5879 Evaluate side-chains 144 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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: 20.0000 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: 7.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 75 HIS C 82 HIS D 44 GLN D 81 ASN E 93 GLN H 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.105620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.085159 restraints weight = 85013.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.086417 restraints weight = 47832.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.087237 restraints weight = 33756.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.087638 restraints weight = 27628.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.087824 restraints weight = 24991.990| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13724 Z= 0.185 Angle : 0.673 8.898 19948 Z= 0.405 Chirality : 0.043 0.187 2264 Planarity : 0.006 0.052 1381 Dihedral : 31.246 87.578 4432 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.68 % Allowed : 9.45 % Favored : 87.87 % 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: 1.57 (0.29), residues: 746 helix: 1.64 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.61 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 40 TYR 0.040 0.003 TYR F 88 PHE 0.019 0.002 PHE A 78 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.18 (13724) covalent geometry : angle 0.67298 / 0.41 (19948) hydrogen bonds : bond 0.06353 / 4.38 ( 833) hydrogen bonds : angle 3.30879 / 2.38 ( 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 186 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8731 (m-10) cc_final: 0.8528 (m-10) REVERT: E 50 GLU cc_start: 0.8212 (pt0) cc_final: 0.7877 (pt0) REVERT: E 67 PHE cc_start: 0.8736 (t80) cc_final: 0.8414 (t80) REVERT: F 81 VAL cc_start: 0.9018 (t) cc_final: 0.8795 (m) REVERT: G 50 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7470 (m-80) REVERT: G 92 GLU cc_start: 0.8901 (mp0) cc_final: 0.8442 (mp0) REVERT: H 65 ASP cc_start: 0.8716 (t70) cc_final: 0.8419 (t0) outliers start: 17 outliers final: 6 residues processed: 178 average time/residue: 0.1038 time to fit residues: 27.6112 Evaluate side-chains 151 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain G residue 50 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 78 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 16 optimal weight: 0.8980 chunk 91 optimal weight: 30.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS D 44 GLN D 81 ASN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.103587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.082793 restraints weight = 86758.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.084028 restraints weight = 48454.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.084879 restraints weight = 34197.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.085305 restraints weight = 27857.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.085576 restraints weight = 25156.898| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13724 Z= 0.160 Angle : 0.618 7.463 19948 Z= 0.377 Chirality : 0.042 0.188 2264 Planarity : 0.004 0.047 1381 Dihedral : 31.466 88.498 4432 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.68 % Allowed : 13.86 % Favored : 83.46 % 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: 1.79 (0.30), residues: 746 helix: 1.87 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.72 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 35 TYR 0.022 0.002 TYR H 80 PHE 0.014 0.002 PHE E 67 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.16 (13724) covalent geometry : angle 0.61807 / 0.38 (19948) hydrogen bonds : bond 0.05192 / 3.55 ( 833) hydrogen bonds : angle 3.06258 / 2.21 ( 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 172 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7522 (mt-10) REVERT: B 63 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7938 (mp0) REVERT: B 73 THR cc_start: 0.9379 (m) cc_final: 0.9044 (t) REVERT: B 88 TYR cc_start: 0.8848 (m-10) cc_final: 0.8446 (m-10) REVERT: C 36 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7746 (mmtp) REVERT: C 56 GLU cc_start: 0.8038 (pp20) cc_final: 0.7806 (pp20) REVERT: E 50 GLU cc_start: 0.8384 (pt0) cc_final: 0.8050 (pt0) REVERT: F 34 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.9031 (mp) REVERT: F 93 GLN cc_start: 0.8655 (tp40) cc_final: 0.8421 (tp40) REVERT: G 36 LYS cc_start: 0.8956 (tppt) cc_final: 0.8719 (tppt) REVERT: G 92 GLU cc_start: 0.8785 (mp0) cc_final: 0.8401 (mp0) REVERT: H 65 ASP cc_start: 0.8752 (t70) cc_final: 0.8505 (t0) outliers start: 17 outliers final: 8 residues processed: 163 average time/residue: 0.1025 time to fit residues: 25.2752 Evaluate side-chains 150 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 110 ASN Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 81 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 85 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 80 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS D 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.092105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.069805 restraints weight = 85428.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.070934 restraints weight = 47457.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.071622 restraints weight = 33865.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.071951 restraints weight = 28287.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.072352 restraints weight = 25931.352| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 13724 Z= 0.241 Angle : 0.696 9.497 19948 Z= 0.416 Chirality : 0.043 0.200 2264 Planarity : 0.006 0.092 1381 Dihedral : 31.642 88.647 4432 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.99 % Allowed : 16.85 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.61 (0.30), residues: 746 helix: 1.73 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.79 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 83 TYR 0.030 0.003 TYR H 80 PHE 0.014 0.002 PHE E 67 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.24 (13724) covalent geometry : angle 0.69649 / 0.42 (19948) hydrogen bonds : bond 0.07821 / 5.36 ( 833) hydrogen bonds : angle 3.34959 / 2.41 ( 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 154 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8677 (m) REVERT: B 84 MET cc_start: 0.8853 (mmm) cc_final: 0.8508 (mmm) REVERT: E 50 GLU cc_start: 0.8677 (pt0) cc_final: 0.8462 (pt0) REVERT: F 34 ILE cc_start: 0.9522 (OUTLIER) cc_final: 0.9298 (mp) REVERT: G 36 LYS cc_start: 0.9257 (tppt) cc_final: 0.9009 (tppt) REVERT: G 39 TYR cc_start: 0.8524 (m-80) cc_final: 0.7866 (m-10) REVERT: G 56 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8678 (mm-30) REVERT: G 92 GLU cc_start: 0.8836 (mp0) cc_final: 0.8535 (mp0) REVERT: H 51 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9175 (mp) REVERT: H 65 ASP cc_start: 0.8893 (t70) cc_final: 0.8665 (t0) outliers start: 19 outliers final: 9 residues processed: 148 average time/residue: 0.1014 time to fit residues: 22.4115 Evaluate side-chains 132 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 51 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.092297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.070186 restraints weight = 85947.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.071309 restraints weight = 47792.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.072056 restraints weight = 33780.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.072412 restraints weight = 27914.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.072620 restraints weight = 25454.106| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13724 Z= 0.151 Angle : 0.623 7.964 19948 Z= 0.370 Chirality : 0.042 0.202 2264 Planarity : 0.004 0.045 1381 Dihedral : 31.717 89.963 4432 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.83 % Allowed : 19.69 % Favored : 77.48 % 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: 1.85 (0.31), residues: 746 helix: 2.00 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -1.05 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 28 TYR 0.037 0.002 TYR D 37 PHE 0.012 0.001 PHE E 67 HIS 0.014 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.15 (13724) covalent geometry : angle 0.62272 / 0.37 (19948) hydrogen bonds : bond 0.05291 / 3.61 ( 833) hydrogen bonds : angle 3.00574 / 2.17 ( 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: 18 poor density : 129 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7769 (mt-10) REVERT: C 36 LYS cc_start: 0.8670 (mmmt) cc_final: 0.8329 (mmtp) REVERT: C 90 ASP cc_start: 0.8525 (t0) cc_final: 0.8310 (t0) REVERT: E 50 GLU cc_start: 0.8665 (pt0) cc_final: 0.8291 (pt0) REVERT: F 34 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9285 (mp) REVERT: G 36 LYS cc_start: 0.9225 (tppt) cc_final: 0.8975 (tppt) REVERT: G 50 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: G 56 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8531 (mm-30) REVERT: G 92 GLU cc_start: 0.8754 (mp0) cc_final: 0.8496 (mp0) REVERT: H 39 TYR cc_start: 0.8493 (t80) cc_final: 0.8075 (t80) REVERT: H 65 ASP cc_start: 0.8863 (t70) cc_final: 0.8646 (t0) outliers start: 18 outliers final: 12 residues processed: 140 average time/residue: 0.1045 time to fit residues: 22.1780 Evaluate side-chains 138 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 92 GLU 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 34 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 44 GLN Chi-restraints excluded: chain H residue 80 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 99 optimal weight: 30.0000 chunk 96 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 65 optimal weight: 0.8980 chunk 95 optimal weight: 30.0000 chunk 6 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN E 93 GLN H 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.077180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.054126 restraints weight = 83826.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055077 restraints weight = 47551.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.055695 restraints weight = 34487.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.056025 restraints weight = 28962.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.056124 restraints weight = 26517.892| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.173 13724 Z= 0.270 Angle : 0.827 11.918 19948 Z= 0.472 Chirality : 0.048 0.230 2264 Planarity : 0.007 0.094 1381 Dihedral : 31.728 97.552 4432 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.31 % Allowed : 19.37 % Favored : 77.32 % 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: 1.08 (0.30), residues: 746 helix: 1.42 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -1.25 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 32 TYR 0.028 0.003 TYR D 37 PHE 0.029 0.003 PHE C 25 HIS 0.010 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.27 (13724) covalent geometry : angle 0.82665 / 0.47 (19948) hydrogen bonds : bond 0.10692 / 7.33 ( 833) hydrogen bonds : angle 3.77769 / 2.73 ( 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 147 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8393 (mp0) REVERT: B 84 MET cc_start: 0.8923 (mmm) cc_final: 0.8671 (mmm) REVERT: C 18 SER cc_start: 0.8678 (m) cc_final: 0.8430 (p) REVERT: C 90 ASP cc_start: 0.8592 (t0) cc_final: 0.8340 (t0) REVERT: D 44 GLN cc_start: 0.9159 (tm-30) cc_final: 0.8910 (tm-30) REVERT: F 30 THR cc_start: 0.8658 (p) cc_final: 0.8458 (p) REVERT: F 31 LYS cc_start: 0.8566 (tttm) cc_final: 0.8350 (tttm) REVERT: F 53 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8614 (mp0) REVERT: G 13 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6239 (ptmm) REVERT: G 36 LYS cc_start: 0.9318 (tppt) cc_final: 0.9063 (tppt) REVERT: G 39 TYR cc_start: 0.8791 (m-80) cc_final: 0.8544 (m-10) REVERT: G 56 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8378 (mm-30) REVERT: H 65 ASP cc_start: 0.9007 (t70) cc_final: 0.8638 (t0) REVERT: H 73 GLU cc_start: 0.8906 (tp30) cc_final: 0.8628 (tp30) outliers start: 21 outliers final: 13 residues processed: 140 average time/residue: 0.1195 time to fit residues: 23.8516 Evaluate side-chains 126 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 80 TYR 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: 4.9990 chunk 95 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 73 optimal weight: 50.0000 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.077768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.055047 restraints weight = 83709.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.055977 restraints weight = 46714.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.056638 restraints weight = 33450.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.056973 restraints weight = 27808.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.057038 restraints weight = 25337.906| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.7065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13724 Z= 0.167 Angle : 0.663 9.314 19948 Z= 0.391 Chirality : 0.043 0.213 2264 Planarity : 0.004 0.039 1381 Dihedral : 31.877 92.115 4432 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.99 % Allowed : 21.57 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.30), residues: 746 helix: 1.88 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.32 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 40 TYR 0.020 0.001 TYR D 37 PHE 0.010 0.001 PHE D 67 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.17 (13724) covalent geometry : angle 0.66342 / 0.39 (19948) hydrogen bonds : bond 0.06141 / 4.16 ( 833) hydrogen bonds : angle 3.23066 / 2.31 ( 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 143 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8567 (mmm) cc_final: 0.8256 (mmm) REVERT: B 88 TYR cc_start: 0.8956 (m-10) cc_final: 0.8682 (m-10) REVERT: C 50 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8482 (m-80) REVERT: C 90 ASP cc_start: 0.8499 (t0) cc_final: 0.8091 (t0) REVERT: D 44 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8907 (tm-30) REVERT: E 79 LYS cc_start: 0.8699 (tptp) cc_final: 0.8415 (tptm) REVERT: G 56 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8397 (mm-30) REVERT: G 92 GLU cc_start: 0.8900 (mp0) cc_final: 0.8695 (pm20) REVERT: H 39 TYR cc_start: 0.8569 (t80) cc_final: 0.8313 (t80) REVERT: H 73 GLU cc_start: 0.8890 (tp30) cc_final: 0.8601 (tp30) outliers start: 19 outliers final: 9 residues processed: 136 average time/residue: 0.1115 time to fit residues: 22.2479 Evaluate side-chains 124 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 50 TYR 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 51 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 80 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 6.9990 chunk 93 optimal weight: 30.0000 chunk 35 optimal weight: 0.9990 chunk 101 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 83 optimal weight: 30.0000 chunk 95 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS E 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.066462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.043116 restraints weight = 78820.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.043888 restraints weight = 43805.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.044432 restraints weight = 31258.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.044751 restraints weight = 25991.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.044843 restraints weight = 23580.568| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.8904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 13724 Z= 0.291 Angle : 0.852 11.528 19948 Z= 0.482 Chirality : 0.050 0.271 2264 Planarity : 0.007 0.077 1381 Dihedral : 31.838 102.256 4432 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.94 % Allowed : 20.00 % Favored : 76.06 % 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: 0.94 (0.30), residues: 746 helix: 1.44 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -1.68 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG F 39 TYR 0.019 0.002 TYR D 37 PHE 0.016 0.003 PHE E 84 HIS 0.008 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.29 (13724) covalent geometry : angle 0.85221 / 0.48 (19948) hydrogen bonds : bond 0.10376 / 7.06 ( 833) hydrogen bonds : angle 3.94281 / 2.83 ( 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 135 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 53 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8499 (mm-30) REVERT: G 56 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8410 (mm-30) REVERT: G 92 GLU cc_start: 0.9064 (mp0) cc_final: 0.8807 (pm20) REVERT: H 81 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8637 (t0) REVERT: H 90 GLU cc_start: 0.9109 (pm20) cc_final: 0.8758 (pm20) outliers start: 25 outliers final: 13 residues processed: 127 average time/residue: 0.1120 time to fit residues: 20.9038 Evaluate side-chains 115 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 73 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 99 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.7980 chunk 98 optimal weight: 30.0000 chunk 88 optimal weight: 50.0000 chunk 101 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 87 optimal weight: 50.0000 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 78 optimal weight: 30.0000 chunk 68 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.066359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.043113 restraints weight = 80022.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.043884 restraints weight = 43692.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.044450 restraints weight = 30736.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.044747 restraints weight = 25431.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.044969 restraints weight = 23124.064| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.9263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 13724 Z= 0.199 Angle : 0.727 14.785 19948 Z= 0.418 Chirality : 0.045 0.239 2264 Planarity : 0.005 0.048 1381 Dihedral : 31.997 97.143 4432 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.68 % Allowed : 22.99 % 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: 1.41 (0.31), residues: 746 helix: 1.85 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.69 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 96 TYR 0.016 0.001 TYR D 37 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.20 (13724) covalent geometry : angle 0.72721 / 0.42 (19948) hydrogen bonds : bond 0.06578 / 4.44 ( 833) hydrogen bonds : angle 3.45918 / 2.48 ( 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 130 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8964 (m-10) cc_final: 0.8636 (m-80) REVERT: C 64 GLU cc_start: 0.8736 (tp30) cc_final: 0.8527 (tm-30) REVERT: C 92 GLU cc_start: 0.8608 (tp30) cc_final: 0.8353 (tp30) REVERT: G 56 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8393 (mm-30) REVERT: G 92 GLU cc_start: 0.9015 (mp0) cc_final: 0.8773 (pm20) REVERT: H 81 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8589 (t0) outliers start: 17 outliers final: 12 residues processed: 125 average time/residue: 0.1210 time to fit residues: 21.5125 Evaluate side-chains 116 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 50 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 40.0000 chunk 91 optimal weight: 30.0000 chunk 73 optimal weight: 50.0000 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.069378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.046766 restraints weight = 83992.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.047633 restraints weight = 46124.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.048248 restraints weight = 32386.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.048650 restraints weight = 26644.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.048776 restraints weight = 23977.179| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.9458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 13724 Z= 0.167 Angle : 0.727 14.294 19948 Z= 0.415 Chirality : 0.044 0.240 2264 Planarity : 0.005 0.056 1381 Dihedral : 31.854 93.809 4432 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.20 % Allowed : 23.46 % 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: 1.72 (0.31), residues: 746 helix: 2.14 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.76 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 40 TYR 0.014 0.001 TYR H 34 PHE 0.009 0.001 PHE E 67 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 (13724) covalent geometry : angle 0.72664 / 0.42 (19948) hydrogen bonds : bond 0.05800 / 3.96 ( 833) hydrogen bonds : angle 3.14277 / 2.25 ( 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 128 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8570 (mmm) cc_final: 0.8368 (mmm) REVERT: B 88 TYR cc_start: 0.8925 (m-10) cc_final: 0.8646 (m-80) REVERT: C 64 GLU cc_start: 0.8723 (tp30) cc_final: 0.8474 (tm-30) REVERT: G 56 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8328 (mm-30) REVERT: H 81 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8516 (t0) REVERT: H 90 GLU cc_start: 0.8987 (pm20) cc_final: 0.8680 (pm20) outliers start: 14 outliers final: 11 residues processed: 123 average time/residue: 0.0990 time to fit residues: 18.3040 Evaluate side-chains 121 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 46 HIS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 ASN 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: 30.0000 chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 40.0000 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: 2.9990 chunk 95 optimal weight: 40.0000 chunk 82 optimal weight: 30.0000 overall best weight: 12.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN G 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.060114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.037162 restraints weight = 85141.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.037881 restraints weight = 48273.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.038410 restraints weight = 34664.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.038607 restraints weight = 28786.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.038817 restraints weight = 26373.157| |-----------------------------------------------------------------------------| r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 1.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.119 13724 Z= 0.528 Angle : 1.173 16.523 19948 Z= 0.625 Chirality : 0.065 0.307 2264 Planarity : 0.010 0.095 1381 Dihedral : 31.984 106.289 4432 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.99 % Allowed : 22.83 % Favored : 74.17 % 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: -0.36 (0.29), residues: 746 helix: 0.66 (0.20), residues: 543 sheet: None (None), residues: 0 loop : -2.70 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG E 116 TYR 0.033 0.004 TYR D 80 PHE 0.021 0.004 PHE A 104 HIS 0.007 0.003 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.01143 / 0.53 (13724) covalent geometry : angle 1.17267 / 0.63 (19948) hydrogen bonds : bond 0.13822 / 9.24 ( 833) hydrogen bonds : angle 5.17165 / 3.73 ( 2048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2189.41 seconds wall clock time: 38 minutes 28.44 seconds (2308.44 seconds total)