Starting phenix.real_space_refine on Fri Sep 11 22:54:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wz5_21970/09_2026/6wz5_21970.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wz5_21970/09_2026/6wz5_21970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wz5_21970/09_2026/6wz5_21970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wz5_21970/09_2026/6wz5_21970.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wz5_21970/09_2026/6wz5_21970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wz5_21970/09_2026/6wz5_21970.map" } resolution = 2.2 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 306 5.49 5 S 12 5.16 5 C 6860 2.51 5 N 2349 2.21 5 O 2916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s 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: 12443 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 776 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 776 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "I" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3155 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "J" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3118 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Time building chain proxies: 2.34, per 1000 atoms: 0.19 Number of scatterers: 12443 At special positions: 0 Unit cell: (74.2, 116.6, 122.96, 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 12 16.00 P 306 15.00 O 2916 8.00 N 2349 7.00 C 6860 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: 0.92 Conformation dependent library (CDL) restraints added in 251.1 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1456 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 71.8% alpha, 3.1% beta 153 base pairs and 280 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.962A 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 132 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: 3.743A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.335A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 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 Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.987A 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 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.706A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 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: 4.370A 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 101 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.773A 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 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.695A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.928A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.556A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.789A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.055A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 414 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 392 hydrogen bonds 780 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 280 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1867 1.32 - 1.44: 4639 1.44 - 1.56: 6148 1.56 - 1.68: 610 1.68 - 1.80: 22 Bond restraints: 13286 Sorted by residual: bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.435 1.379 0.056 1.30e-02 5.92e+03 1.85e+01 bond pdb=" C3' DC I -2 " pdb=" O3' DC I -2 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.53e+01 bond pdb=" C3' DA I 16 " pdb=" O3' DA I 16 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.50e+01 bond pdb=" C3' DC I -54 " pdb=" O3' DC I -54 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.39e+01 bond pdb=" C3' DT I 69 " pdb=" O3' DT I 69 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.28e+01 ... (remaining 13281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 17969 1.71 - 3.43: 1233 3.43 - 5.14: 41 5.14 - 6.85: 4 6.85 - 8.57: 2 Bond angle restraints: 19249 Sorted by residual: angle pdb=" N3 DT I -50 " pdb=" C4 DT I -50 " pdb=" O4 DT I -50 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT J -43 " pdb=" C4 DT J -43 " pdb=" O4 DT J -43 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.91e+01 angle pdb=" O4' DG I 20 " pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " ideal model delta sigma weight residual 106.00 103.37 2.63 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I 9 " pdb=" C4 DT I 9 " pdb=" O4 DT I 9 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I 22 " pdb=" C4 DT I 22 " pdb=" O4 DT I 22 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 19244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.12: 5548 33.12 - 66.24: 1634 66.24 - 99.36: 32 99.36 - 132.48: 0 132.48 - 165.60: 2 Dihedral angle restraints: 7216 sinusoidal: 4964 harmonic: 2252 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 54.40 165.60 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 80.87 139.13 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 162.50 17.50 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 7213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1264 0.039 - 0.078: 643 0.078 - 0.117: 231 0.117 - 0.155: 50 0.155 - 0.194: 4 Chirality restraints: 2192 Sorted by residual: chirality pdb=" C3' DG I -8 " pdb=" C4' DG I -8 " pdb=" O3' DG I -8 " pdb=" C2' DG I -8 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" C3' DC I 49 " pdb=" C4' DC I 49 " pdb=" O3' DC I 49 " pdb=" C2' DC I 49 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" C3' DC J 49 " pdb=" C4' DC J 49 " pdb=" O3' DC J 49 " pdb=" C2' DC J 49 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 2189 not shown) Planarity restraints: 1372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO E 43 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " 0.028 2.00e-02 2.50e+03 1.22e-02 4.09e+00 pdb=" N9 DA I 47 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " 0.006 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 26 " -0.026 2.00e-02 2.50e+03 1.19e-02 3.92e+00 pdb=" N9 DA I 26 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 26 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 26 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 26 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA I 26 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 26 " 0.001 2.00e-02 2.50e+03 ... (remaining 1369 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2451 2.78 - 3.31: 10584 3.31 - 3.84: 26079 3.84 - 4.37: 31295 4.37 - 4.90: 42128 Nonbonded interactions: 112537 Sorted by model distance: nonbonded pdb=" OE1 GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 2.253 3.120 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.260 3.040 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.320 3.120 nonbonded pdb=" N2 DG I 38 " pdb=" O2 DC J -38 " model vdw 2.329 2.496 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.366 3.040 ... (remaining 112532 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' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.050 Find NCS groups from input model: 0.120 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:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 : 0.009 0.088 13286 Z= 0.786 Angle : 0.844 8.565 19249 Z= 0.724 Chirality : 0.051 0.194 2192 Planarity : 0.005 0.051 1372 Dihedral : 28.628 165.601 5760 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.93 % Allowed : 3.24 % Favored : 95.83 % 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: -0.00 (0.27), residues: 758 helix: 0.51 (0.20), residues: 552 sheet: None (None), residues: 0 loop : -1.19 (0.35), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 39 TYR 0.014 0.002 TYR G 57 PHE 0.017 0.002 PHE A 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00922 / 0.79 (13286) covalent geometry : angle 0.84417 / 0.72 (19249) hydrogen bonds : bond 0.08467 / 5.91 ( 806) hydrogen bonds : angle 3.42209 / 2.42 ( 1998) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 0.344 Fit side-chains REVERT: G 15 LYS cc_start: 0.7464 (mtpp) cc_final: 0.7220 (mtpt) REVERT: G 24 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7781 (mm-40) REVERT: H 68 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6886 (mp0) outliers start: 6 outliers final: 2 residues processed: 196 average time/residue: 0.8790 time to fit residues: 182.0343 Evaluate side-chains 148 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 68 GLU 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: 5.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN C 24 GLN C 31 HIS C 104 GLN D 92 GLN G 31 HIS G 68 ASN G 110 ASN H 44 GLN H 92 GLN H 106 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.119589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.096139 restraints weight = 17201.188| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 0.89 r_work: 0.3283 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 13286 Z= 0.227 Angle : 0.893 8.869 19249 Z= 0.479 Chirality : 0.056 0.292 2192 Planarity : 0.007 0.091 1372 Dihedral : 32.083 171.526 4208 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.24 % Allowed : 12.35 % Favored : 84.41 % 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: 1.16 (0.27), residues: 758 helix: 1.25 (0.20), residues: 550 sheet: None (None), residues: 0 loop : -0.37 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 129 TYR 0.022 0.003 TYR F 51 PHE 0.014 0.002 PHE E 67 HIS 0.017 0.002 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.23 (13286) covalent geometry : angle 0.89322 / 0.48 (19249) hydrogen bonds : bond 0.07202 / 4.93 ( 806) hydrogen bonds : angle 3.16884 / 2.23 ( 1998) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.291 Fit side-chains REVERT: C 15 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7679 (ttmm) REVERT: C 92 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7775 (mt-10) outliers start: 21 outliers final: 4 residues processed: 189 average time/residue: 0.8676 time to fit residues: 172.9081 Evaluate side-chains 155 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 151 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 39 optimal weight: 0.0370 chunk 87 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 125 GLN F 25 ASN G 68 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.116075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.091770 restraints weight = 17276.833| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 0.90 r_work: 0.3202 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13286 Z= 0.146 Angle : 0.669 7.626 19249 Z= 0.383 Chirality : 0.047 0.248 2192 Planarity : 0.005 0.046 1372 Dihedral : 31.789 164.498 4202 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.47 % Allowed : 14.04 % Favored : 83.49 % 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: 2.23 (0.28), residues: 758 helix: 2.09 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.15 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 42 TYR 0.013 0.001 TYR F 51 PHE 0.011 0.001 PHE E 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.15 (13286) covalent geometry : angle 0.66930 / 0.38 (19249) hydrogen bonds : bond 0.04692 / 3.21 ( 806) hydrogen bonds : angle 2.88426 / 2.05 ( 1998) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.337 Fit side-chains REVERT: B 23 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.6073 (ppt90) REVERT: C 15 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7795 (ttmm) REVERT: C 90 ASP cc_start: 0.8503 (t70) cc_final: 0.8249 (t0) REVERT: C 92 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7903 (mt-10) REVERT: G 72 ASP cc_start: 0.7740 (m-30) cc_final: 0.7530 (m-30) REVERT: G 73 ASN cc_start: 0.8141 (t0) cc_final: 0.7784 (t0) outliers start: 16 outliers final: 5 residues processed: 166 average time/residue: 0.9135 time to fit residues: 160.0003 Evaluate side-chains 161 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 60 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN A 125 GLN H 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.082987 restraints weight = 16583.560| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 0.86 r_work: 0.3047 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13286 Z= 0.229 Angle : 0.803 7.624 19249 Z= 0.430 Chirality : 0.054 0.251 2192 Planarity : 0.006 0.046 1372 Dihedral : 32.053 166.140 4202 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.85 % Allowed : 15.28 % Favored : 82.87 % 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: 2.01 (0.28), residues: 758 helix: 1.95 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.28 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 39 TYR 0.013 0.002 TYR E 54 PHE 0.011 0.002 PHE A 67 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.23 (13286) covalent geometry : angle 0.80268 / 0.43 (19249) hydrogen bonds : bond 0.06086 / 4.13 ( 806) hydrogen bonds : angle 3.07476 / 2.16 ( 1998) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: B 23 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.6367 (pmt-80) REVERT: C 15 LYS cc_start: 0.8530 (ttpp) cc_final: 0.7930 (tttm) REVERT: C 61 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8348 (mm-30) REVERT: E 129 ARG cc_start: 0.8712 (tpt90) cc_final: 0.8501 (tpt90) REVERT: G 73 ASN cc_start: 0.8322 (t0) cc_final: 0.7860 (t0) REVERT: G 104 GLN cc_start: 0.8749 (mt0) cc_final: 0.8539 (mm110) outliers start: 12 outliers final: 5 residues processed: 167 average time/residue: 0.9537 time to fit residues: 167.0889 Evaluate side-chains 159 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 0.0570 chunk 54 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN C 110 ASN E 68 GLN E 76 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.108085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.084357 restraints weight = 16769.114| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 0.87 r_work: 0.3068 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 13286 Z= 0.137 Angle : 0.710 10.861 19249 Z= 0.391 Chirality : 0.048 0.269 2192 Planarity : 0.005 0.051 1372 Dihedral : 31.984 165.657 4202 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.31 % Allowed : 14.97 % Favored : 82.72 % 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: 2.38 (0.29), residues: 758 helix: 2.24 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.20 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 42 TYR 0.018 0.001 TYR B 88 PHE 0.011 0.001 PHE A 67 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 (13286) covalent geometry : angle 0.71009 / 0.39 (19249) hydrogen bonds : bond 0.04881 / 3.31 ( 806) hydrogen bonds : angle 2.94212 / 2.08 ( 1998) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.315 Fit side-chains REVERT: A 53 ARG cc_start: 0.8683 (ttt180) cc_final: 0.8376 (ttp-110) REVERT: B 23 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.6377 (pmt-80) REVERT: C 15 LYS cc_start: 0.8511 (ttpp) cc_final: 0.7917 (tttm) REVERT: C 61 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8306 (mm-30) REVERT: E 129 ARG cc_start: 0.8683 (tpt90) cc_final: 0.8451 (tpt90) REVERT: G 73 ASN cc_start: 0.8241 (t0) cc_final: 0.7743 (t160) outliers start: 15 outliers final: 4 residues processed: 162 average time/residue: 1.0163 time to fit residues: 172.7187 Evaluate side-chains 158 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 153 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN C 110 ASN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.106686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.083268 restraints weight = 16629.671| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 0.86 r_work: 0.3045 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13286 Z= 0.177 Angle : 0.704 11.360 19249 Z= 0.390 Chirality : 0.048 0.265 2192 Planarity : 0.005 0.053 1372 Dihedral : 31.760 165.833 4202 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.85 % Allowed : 14.97 % Favored : 83.18 % 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: 2.58 (0.29), residues: 758 helix: 2.39 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.15 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 42 TYR 0.011 0.002 TYR G 57 PHE 0.011 0.002 PHE A 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.18 (13286) covalent geometry : angle 0.70356 / 0.39 (19249) hydrogen bonds : bond 0.05465 / 3.69 ( 806) hydrogen bonds : angle 2.89854 / 2.05 ( 1998) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.352 Fit side-chains REVERT: A 53 ARG cc_start: 0.8748 (ttt180) cc_final: 0.8518 (ttp-110) REVERT: C 15 LYS cc_start: 0.8523 (ttpp) cc_final: 0.7928 (ttmm) REVERT: C 90 ASP cc_start: 0.8737 (t70) cc_final: 0.8484 (t0) REVERT: E 129 ARG cc_start: 0.8635 (tpt90) cc_final: 0.8376 (tpt90) REVERT: E 131 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8387 (mtp85) REVERT: H 90 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8098 (mp0) outliers start: 12 outliers final: 5 residues processed: 157 average time/residue: 1.0023 time to fit residues: 165.2236 Evaluate side-chains 158 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 89 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 0.0570 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 44 GLN E 108 ASN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.107524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.084167 restraints weight = 16586.867| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 0.86 r_work: 0.3063 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.6899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13286 Z= 0.143 Angle : 0.677 11.509 19249 Z= 0.378 Chirality : 0.046 0.267 2192 Planarity : 0.005 0.050 1372 Dihedral : 31.752 166.233 4202 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.54 % Allowed : 16.67 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.29), residues: 758 helix: 2.53 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.05 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 23 TYR 0.011 0.001 TYR C 57 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (13286) covalent geometry : angle 0.67740 / 0.38 (19249) hydrogen bonds : bond 0.04648 / 3.15 ( 806) hydrogen bonds : angle 2.83149 / 2.01 ( 1998) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.325 Fit side-chains REVERT: A 53 ARG cc_start: 0.8802 (ttt180) cc_final: 0.8563 (ttp-110) REVERT: C 15 LYS cc_start: 0.8502 (ttpp) cc_final: 0.7917 (ttmm) REVERT: C 90 ASP cc_start: 0.8691 (t70) cc_final: 0.8450 (t0) REVERT: E 129 ARG cc_start: 0.8608 (tpt90) cc_final: 0.8379 (tpt90) outliers start: 10 outliers final: 4 residues processed: 157 average time/residue: 1.0181 time to fit residues: 167.7755 Evaluate side-chains 154 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 44 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.105460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.082129 restraints weight = 16558.233| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 0.87 r_work: 0.3023 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.7103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13286 Z= 0.198 Angle : 0.732 12.292 19249 Z= 0.400 Chirality : 0.049 0.272 2192 Planarity : 0.005 0.050 1372 Dihedral : 31.787 167.541 4202 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.39 % Allowed : 16.67 % Favored : 81.94 % 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: 2.58 (0.29), residues: 758 helix: 2.37 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.08 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 30 TYR 0.016 0.002 TYR G 57 PHE 0.012 0.002 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.20 (13286) covalent geometry : angle 0.73225 / 0.40 (19249) hydrogen bonds : bond 0.05714 / 3.86 ( 806) hydrogen bonds : angle 2.95236 / 2.09 ( 1998) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.263 Fit side-chains REVERT: C 15 LYS cc_start: 0.8516 (ttpp) cc_final: 0.7908 (ttmm) REVERT: E 129 ARG cc_start: 0.8602 (tpt90) cc_final: 0.8341 (tpt90) REVERT: E 131 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8390 (mtp85) outliers start: 9 outliers final: 4 residues processed: 156 average time/residue: 1.0091 time to fit residues: 165.3191 Evaluate side-chains 150 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 8 optimal weight: 0.0270 chunk 17 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 44 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.106247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.082957 restraints weight = 16626.145| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 0.87 r_work: 0.3046 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.7140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13286 Z= 0.152 Angle : 0.707 8.162 19249 Z= 0.390 Chirality : 0.047 0.263 2192 Planarity : 0.005 0.051 1372 Dihedral : 31.798 166.956 4202 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.77 % Allowed : 17.75 % Favored : 81.48 % 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: 2.64 (0.29), residues: 758 helix: 2.42 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.08 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.014 0.002 TYR G 57 PHE 0.011 0.002 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (13286) covalent geometry : angle 0.70659 / 0.39 (19249) hydrogen bonds : bond 0.05060 / 3.42 ( 806) hydrogen bonds : angle 2.92415 / 2.07 ( 1998) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 147 time to evaluate : 0.315 Fit side-chains REVERT: C 15 LYS cc_start: 0.8480 (ttpp) cc_final: 0.7888 (ttmm) REVERT: E 129 ARG cc_start: 0.8591 (tpt90) cc_final: 0.8389 (tpt90) outliers start: 5 outliers final: 3 residues processed: 151 average time/residue: 0.9667 time to fit residues: 153.7142 Evaluate side-chains 149 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 26 optimal weight: 0.0670 chunk 66 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 74 optimal weight: 30.0000 chunk 63 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 overall best weight: 1.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN C 104 GLN D 44 GLN E 93 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.104574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081434 restraints weight = 16801.402| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 0.87 r_work: 0.3016 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.7305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13286 Z= 0.225 Angle : 0.768 8.184 19249 Z= 0.416 Chirality : 0.051 0.272 2192 Planarity : 0.006 0.050 1372 Dihedral : 31.860 168.668 4202 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.46 % Allowed : 17.75 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.29), residues: 758 helix: 2.16 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.32 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 30 TYR 0.014 0.002 TYR G 57 PHE 0.012 0.002 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 (13286) covalent geometry : angle 0.76765 / 0.42 (19249) hydrogen bonds : bond 0.06198 / 4.18 ( 806) hydrogen bonds : angle 3.02862 / 2.14 ( 1998) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.327 Fit side-chains REVERT: C 15 LYS cc_start: 0.8450 (ttpp) cc_final: 0.7855 (ttmm) REVERT: E 129 ARG cc_start: 0.8619 (tpt90) cc_final: 0.8391 (tpt90) outliers start: 3 outliers final: 3 residues processed: 142 average time/residue: 1.0084 time to fit residues: 150.4384 Evaluate side-chains 143 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 8 optimal weight: 0.0870 chunk 71 optimal weight: 0.0770 chunk 73 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN C 104 GLN D 44 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082255 restraints weight = 16688.304| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 0.86 r_work: 0.3035 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.7315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13286 Z= 0.152 Angle : 0.740 10.833 19249 Z= 0.404 Chirality : 0.048 0.260 2192 Planarity : 0.005 0.049 1372 Dihedral : 31.874 167.871 4202 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.08 % Allowed : 16.98 % Favored : 81.94 % 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: 2.38 (0.29), residues: 758 helix: 2.24 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.30 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 30 TYR 0.013 0.002 TYR G 57 PHE 0.010 0.002 PHE A 67 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (13286) covalent geometry : angle 0.74000 / 0.40 (19249) hydrogen bonds : bond 0.05512 / 3.71 ( 806) hydrogen bonds : angle 2.99461 / 2.11 ( 1998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5715.44 seconds wall clock time: 97 minutes 49.24 seconds (5869.24 seconds total)