Starting phenix.real_space_refine on Fri Jul 3 03:54:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k45_62046/07_2026/9k45_62046.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k45_62046/07_2026/9k45_62046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k45_62046/07_2026/9k45_62046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k45_62046/07_2026/9k45_62046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k45_62046/07_2026/9k45_62046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k45_62046/07_2026/9k45_62046.map" } resolution = 2.71 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= -0.001 sd= 0.051 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 289 5.49 5 S 10 5.16 5 C 6577 2.51 5 N 2178 2.21 5 O 2776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11830 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 778 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 778 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "I" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2950 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2992 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.29, per 1000 atoms: 0.19 Number of scatterers: 11830 At special positions: 0 Unit cell: (122.1, 80.3, 116.6, 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 10 16.00 P 289 15.00 O 2776 8.00 N 2178 7.00 C 6577 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: 0.78 Conformation dependent library (CDL) restraints added in 234.5 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 74.1% alpha, 2.7% beta 145 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.700A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.643A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.518A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) 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: 3.591A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.662A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 33 Processing helix chain 'C' and resid 37 through 49 removed outlier: 3.813A pdb=" N VAL C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 85 removed outlier: 3.762A pdb=" N ALA C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 109 Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'D' and resid 60 through 72 Processing helix chain 'D' and resid 78 through 107 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 126 through 147 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.729A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.634A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.524A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) 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: 3.592A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.710A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 33 Processing helix chain 'G' and resid 37 through 49 removed outlier: 3.831A pdb=" N VAL G 41 " --> pdb=" O PRO G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 85 removed outlier: 3.767A pdb=" N ALA G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 101 Processing helix chain 'G' and resid 102 through 109 Processing helix chain 'H' and resid 60 through 72 Processing helix chain 'H' and resid 78 through 107 Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 126 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.134A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.836A pdb=" N ARG C 54 " --> pdb=" O ILE D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 89 through 90 Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 113 removed outlier: 6.415A pdb=" N THR C 112 " --> 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: 7.163A 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 54 through 55 removed outlier: 6.730A pdb=" N ARG G 54 " --> pdb=" O ILE H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 89 through 90 403 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 696 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.14 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: 2013 1.33 - 1.45: 4213 1.45 - 1.57: 5816 1.57 - 1.69: 577 1.69 - 1.80: 18 Bond restraints: 12637 Sorted by residual: bond pdb=" C3' DC J -39 " pdb=" C2' DC J -39 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DT J -21 " pdb=" C2' DT J -21 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.07e+00 bond pdb=" C3' DC I -62 " pdb=" C2' DC I -62 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.01e+00 bond pdb=" O3' DC J -24 " pdb=" P DC J -23 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.50e-02 4.44e+03 8.96e+00 bond pdb=" C3' DC J 44 " pdb=" C2' DC J 44 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.95e+00 ... (remaining 12632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 16544 1.26 - 2.52: 1537 2.52 - 3.78: 208 3.78 - 5.04: 17 5.04 - 6.30: 5 Bond angle restraints: 18311 Sorted by residual: angle pdb=" O4' DA I 69 " pdb=" C4' DA I 69 " pdb=" C3' DA I 69 " ideal model delta sigma weight residual 106.00 102.50 3.50 6.00e-01 2.78e+00 3.39e+01 angle pdb=" N3 DT I -53 " pdb=" C4 DT I -53 " pdb=" O4 DT I -53 " ideal model delta sigma weight residual 119.90 122.72 -2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" O4' DT I -46 " pdb=" C4' DT I -46 " pdb=" C3' DT I -46 " ideal model delta sigma weight residual 106.00 103.28 2.72 6.00e-01 2.78e+00 2.06e+01 angle pdb=" N3 DT I 30 " pdb=" C4 DT I 30 " pdb=" O4 DT I 30 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 ... (remaining 18306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 4310 18.07 - 36.14: 1106 36.14 - 54.21: 1244 54.21 - 72.28: 243 72.28 - 90.35: 22 Dihedral angle restraints: 6925 sinusoidal: 4777 harmonic: 2148 Sorted by residual: dihedral pdb=" CA THR G 50 " pdb=" C THR G 50 " pdb=" N ALA G 51 " pdb=" CA ALA G 51 " ideal model delta harmonic sigma weight residual 180.00 161.57 18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CB GLU G 73 " pdb=" CG GLU G 73 " pdb=" CD GLU G 73 " pdb=" OE1 GLU G 73 " ideal model delta sinusoidal sigma weight residual 0.00 89.72 -89.72 1 3.00e+01 1.11e-03 1.06e+01 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 90.00 134.21 -44.21 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 6922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1131 0.031 - 0.062: 655 0.062 - 0.092: 227 0.092 - 0.123: 81 0.123 - 0.154: 5 Chirality restraints: 2099 Sorted by residual: chirality pdb=" P DC J 3 " pdb=" OP1 DC J 3 " pdb=" OP2 DC J 3 " pdb=" O5' DC J 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.49 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" P DA I -8 " pdb=" OP1 DA I -8 " pdb=" OP2 DA I -8 " pdb=" O5' DA I -8 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" C3' DA I -8 " pdb=" C4' DA I -8 " pdb=" O3' DA I -8 " pdb=" C2' DA I -8 " both_signs ideal model delta sigma weight residual False -2.73 -2.86 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 2096 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 48 " 0.218 9.50e-02 1.11e+02 9.78e-02 6.13e+00 pdb=" NE ARG C 48 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 48 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 48 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 48 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 88 " 0.011 2.00e-02 2.50e+03 1.33e-02 3.07e+00 pdb=" CG PHE H 88 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE H 88 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE H 88 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE H 88 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 88 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 88 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 125 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO H 126 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " 0.023 5.00e-02 4.00e+02 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1214 2.75 - 3.29: 9691 3.29 - 3.82: 21816 3.82 - 4.36: 26751 4.36 - 4.90: 39014 Nonbonded interactions: 98486 Sorted by model distance: nonbonded pdb=" OG SER G 29 " pdb=" O PHE G 36 " model vdw 2.212 3.040 nonbonded pdb=" OG SER C 29 " pdb=" O PHE C 36 " model vdw 2.228 3.040 nonbonded pdb=" N GLU G 103 " pdb=" OE1 GLU G 103 " model vdw 2.260 3.120 nonbonded pdb=" NH1 ARG B 92 " pdb=" OE1 GLU D 99 " model vdw 2.293 3.120 nonbonded pdb=" NH1 ARG F 92 " pdb=" OE1 GLU H 99 " model vdw 2.317 3.120 ... (remaining 98481 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.020 Find NCS groups from input model: 0.090 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:5.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 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 0.045 12637 Z= 0.516 Angle : 0.750 6.295 18311 Z= 0.684 Chirality : 0.043 0.154 2099 Planarity : 0.005 0.098 1298 Dihedral : 28.625 90.350 5537 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.96 % Allowed : 21.31 % Favored : 77.72 % 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: 2.50 (0.31), residues: 728 helix: 2.53 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -0.89 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 48 TYR 0.011 0.002 TYR B 51 PHE 0.030 0.001 PHE H 88 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.52 (12637) covalent geometry : angle 0.74993 / 0.68 (18311) hydrogen bonds : bond 0.11164 / 7.21 ( 751) hydrogen bonds : angle 4.41048 / 3.22 ( 1887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.308 Fit side-chains REVERT: D 91 ASP cc_start: 0.8825 (t70) cc_final: 0.8616 (t0) REVERT: G 46 LYS cc_start: 0.9400 (mtpp) cc_final: 0.9077 (mtmm) REVERT: H 91 ASP cc_start: 0.8831 (t70) cc_final: 0.8629 (t0) outliers start: 6 outliers final: 3 residues processed: 150 average time/residue: 0.7521 time to fit residues: 119.2419 Evaluate side-chains 118 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain G residue 47 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 75 HIS D 72 HIS D 107 ASN E 39 HIS E 108 ASN F 75 HIS G 121 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.067773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.048623 restraints weight = 41805.628| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.93 r_work: 0.2851 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12637 Z= 0.152 Angle : 0.638 6.650 18311 Z= 0.381 Chirality : 0.044 0.230 2099 Planarity : 0.005 0.035 1298 Dihedral : 31.007 98.356 4077 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.92 % Allowed : 26.60 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.31), residues: 728 helix: 2.78 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.77 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 105 TYR 0.012 0.001 TYR B 51 PHE 0.020 0.001 PHE D 88 HIS 0.006 0.001 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.15 (12637) covalent geometry : angle 0.63826 / 0.38 (18311) hydrogen bonds : bond 0.06213 / 4.12 ( 751) hydrogen bonds : angle 3.01301 / 2.21 ( 1887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.207 Fit side-chains REVERT: A 94 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8070 (tp30) REVERT: C 76 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8572 (tm-30) REVERT: D 58 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7901 (mt-10) REVERT: D 91 ASP cc_start: 0.9269 (t70) cc_final: 0.8949 (t0) REVERT: E 94 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8075 (tp30) REVERT: G 46 LYS cc_start: 0.9263 (mtpp) cc_final: 0.8812 (mtmm) REVERT: G 76 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8568 (tm-30) REVERT: H 91 ASP cc_start: 0.9243 (t70) cc_final: 0.8935 (t0) outliers start: 12 outliers final: 6 residues processed: 122 average time/residue: 0.7551 time to fit residues: 97.4851 Evaluate side-chains 114 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 50 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS H 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.067929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.048832 restraints weight = 42533.102| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.95 r_work: 0.2868 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12637 Z= 0.142 Angle : 0.586 6.347 18311 Z= 0.357 Chirality : 0.042 0.195 2099 Planarity : 0.004 0.043 1298 Dihedral : 30.972 98.881 4071 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.04 % Allowed : 25.80 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.17 (0.31), residues: 728 helix: 2.99 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.62 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 105 TYR 0.008 0.001 TYR D 63 PHE 0.006 0.001 PHE H 88 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.14 (12637) covalent geometry : angle 0.58565 / 0.36 (18311) hydrogen bonds : bond 0.05360 / 3.57 ( 751) hydrogen bonds : angle 2.80799 / 2.05 ( 1887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.368 Fit side-chains REVERT: A 94 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8009 (tp30) REVERT: C 48 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8303 (tpp-160) REVERT: C 76 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8581 (tm-30) REVERT: D 58 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7812 (mt-10) REVERT: D 85 MET cc_start: 0.9318 (mmm) cc_final: 0.9075 (mmm) REVERT: D 91 ASP cc_start: 0.9251 (t70) cc_final: 0.8935 (t0) REVERT: E 94 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7969 (tp30) REVERT: G 46 LYS cc_start: 0.9228 (mtpp) cc_final: 0.8785 (mtmm) REVERT: G 76 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8581 (tm-30) REVERT: H 91 ASP cc_start: 0.9237 (OUTLIER) cc_final: 0.8912 (t0) REVERT: H 116 GLU cc_start: 0.8844 (mp0) cc_final: 0.8433 (mp0) outliers start: 19 outliers final: 10 residues processed: 121 average time/residue: 0.7282 time to fit residues: 93.4154 Evaluate side-chains 122 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 91 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 95 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.068050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.048837 restraints weight = 42446.032| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.95 r_work: 0.2879 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12637 Z= 0.140 Angle : 0.580 6.636 18311 Z= 0.352 Chirality : 0.041 0.199 2099 Planarity : 0.004 0.031 1298 Dihedral : 30.916 97.559 4071 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.69 % Allowed : 24.84 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.31 (0.31), residues: 728 helix: 3.10 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.71 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 48 TYR 0.008 0.001 TYR D 63 PHE 0.009 0.001 PHE A 78 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 (12637) covalent geometry : angle 0.57957 / 0.35 (18311) hydrogen bonds : bond 0.04978 / 3.32 ( 751) hydrogen bonds : angle 2.69189 / 1.96 ( 1887) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.247 Fit side-chains REVERT: A 59 GLU cc_start: 0.8407 (pm20) cc_final: 0.8076 (pm20) REVERT: A 94 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7992 (tp30) REVERT: C 76 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8628 (tm-30) REVERT: D 58 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7855 (mt-10) REVERT: D 85 MET cc_start: 0.9324 (mmm) cc_final: 0.9080 (mmm) REVERT: D 91 ASP cc_start: 0.9269 (t70) cc_final: 0.8762 (t0) REVERT: D 99 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8795 (mm-30) REVERT: D 116 GLU cc_start: 0.8836 (mp0) cc_final: 0.8436 (mp0) REVERT: E 59 GLU cc_start: 0.8402 (pm20) cc_final: 0.8056 (pm20) REVERT: E 94 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7964 (tp30) REVERT: F 31 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8227 (ptmm) REVERT: G 46 LYS cc_start: 0.9225 (mtpp) cc_final: 0.8793 (mtmm) REVERT: G 76 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8617 (tm-30) REVERT: H 91 ASP cc_start: 0.9217 (t70) cc_final: 0.8683 (t0) REVERT: H 116 GLU cc_start: 0.8901 (mp0) cc_final: 0.8530 (mp0) outliers start: 23 outliers final: 10 residues processed: 130 average time/residue: 0.7124 time to fit residues: 98.1473 Evaluate side-chains 123 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 30.0000 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.065893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.046396 restraints weight = 42463.559| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.95 r_work: 0.2807 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12637 Z= 0.187 Angle : 0.630 7.080 18311 Z= 0.370 Chirality : 0.042 0.206 2099 Planarity : 0.004 0.039 1298 Dihedral : 31.046 93.333 4071 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.88 % Allowed : 24.52 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.31 (0.32), residues: 728 helix: 3.23 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -0.90 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 23 TYR 0.010 0.001 TYR B 51 PHE 0.024 0.002 PHE H 88 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.19 (12637) covalent geometry : angle 0.63048 / 0.37 (18311) hydrogen bonds : bond 0.06699 / 4.43 ( 751) hydrogen bonds : angle 2.93856 / 2.13 ( 1887) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.187 Fit side-chains REVERT: A 59 GLU cc_start: 0.8570 (pm20) cc_final: 0.8215 (pm20) REVERT: A 94 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8118 (tp30) REVERT: A 133 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6426 (mt-10) REVERT: C 76 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8588 (tm-30) REVERT: C 104 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8792 (mm-30) REVERT: D 58 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7978 (mt-10) REVERT: D 91 ASP cc_start: 0.9272 (t70) cc_final: 0.8978 (t0) REVERT: D 116 GLU cc_start: 0.8941 (mp0) cc_final: 0.8427 (mp0) REVERT: E 59 GLU cc_start: 0.8543 (pm20) cc_final: 0.8175 (pm20) REVERT: E 94 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8092 (tp30) REVERT: F 31 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8391 (ptmm) REVERT: G 76 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8563 (tm-30) REVERT: H 91 ASP cc_start: 0.9253 (OUTLIER) cc_final: 0.8933 (t0) REVERT: H 116 GLU cc_start: 0.8916 (mp0) cc_final: 0.8447 (mp0) outliers start: 18 outliers final: 12 residues processed: 124 average time/residue: 0.7299 time to fit residues: 95.7270 Evaluate side-chains 124 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 101 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 0.0870 chunk 74 optimal weight: 30.0000 chunk 43 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 83 optimal weight: 20.0000 chunk 87 optimal weight: 30.0000 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.067094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.048276 restraints weight = 42091.342| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.93 r_work: 0.2869 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 12637 Z= 0.143 Angle : 0.593 8.280 18311 Z= 0.356 Chirality : 0.041 0.200 2099 Planarity : 0.004 0.034 1298 Dihedral : 30.940 96.722 4071 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.01 % Allowed : 24.36 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.35 (0.31), residues: 728 helix: 3.20 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.88 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 23 TYR 0.009 0.001 TYR H 63 PHE 0.057 0.002 PHE D 88 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (12637) covalent geometry : angle 0.59283 / 0.36 (18311) hydrogen bonds : bond 0.05049 / 3.36 ( 751) hydrogen bonds : angle 2.68744 / 1.96 ( 1887) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.306 Fit side-chains REVERT: A 59 GLU cc_start: 0.8546 (pm20) cc_final: 0.8177 (pm20) REVERT: A 94 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8030 (tp30) REVERT: A 133 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6480 (mt-10) REVERT: C 76 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8627 (tm-30) REVERT: D 58 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7903 (mt-10) REVERT: D 85 MET cc_start: 0.9329 (mmm) cc_final: 0.9098 (mmm) REVERT: D 91 ASP cc_start: 0.9192 (t70) cc_final: 0.8742 (t0) REVERT: D 116 GLU cc_start: 0.8871 (mp0) cc_final: 0.8412 (mp0) REVERT: D 147 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8154 (p) REVERT: E 59 GLU cc_start: 0.8533 (pm20) cc_final: 0.8148 (pm20) REVERT: E 94 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7996 (tp30) REVERT: E 133 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6700 (mt-10) REVERT: G 76 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8644 (tm-30) REVERT: H 91 ASP cc_start: 0.9223 (t70) cc_final: 0.8724 (t0) REVERT: H 99 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8737 (mm-30) outliers start: 25 outliers final: 10 residues processed: 125 average time/residue: 0.7771 time to fit residues: 103.0668 Evaluate side-chains 123 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 146 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 0.0050 chunk 82 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 95 optimal weight: 20.0000 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.066890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.048081 restraints weight = 42209.572| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.93 r_work: 0.2864 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12637 Z= 0.145 Angle : 0.596 8.364 18311 Z= 0.357 Chirality : 0.040 0.203 2099 Planarity : 0.004 0.046 1298 Dihedral : 30.886 95.812 4071 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.56 % Allowed : 26.12 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.48 (0.31), residues: 728 helix: 3.30 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.75 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 23 TYR 0.008 0.001 TYR H 63 PHE 0.025 0.001 PHE H 88 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.15 (12637) covalent geometry : angle 0.59551 / 0.36 (18311) hydrogen bonds : bond 0.05106 / 3.40 ( 751) hydrogen bonds : angle 2.68270 / 1.95 ( 1887) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.318 Fit side-chains REVERT: A 59 GLU cc_start: 0.8564 (pm20) cc_final: 0.8225 (pm20) REVERT: A 94 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8014 (tp30) REVERT: A 120 MET cc_start: 0.8816 (mtp) cc_final: 0.8612 (mtt) REVERT: C 76 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8571 (tm-30) REVERT: D 58 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: D 85 MET cc_start: 0.9410 (mmm) cc_final: 0.9166 (mmm) REVERT: D 91 ASP cc_start: 0.9277 (t70) cc_final: 0.8818 (t0) REVERT: D 116 GLU cc_start: 0.8866 (mp0) cc_final: 0.8411 (mp0) REVERT: D 147 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8161 (p) REVERT: E 59 GLU cc_start: 0.8546 (pm20) cc_final: 0.8196 (pm20) REVERT: E 94 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7987 (tp30) REVERT: E 133 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6637 (mt-10) REVERT: G 76 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8545 (tm-30) REVERT: H 91 ASP cc_start: 0.9229 (t70) cc_final: 0.8735 (t0) REVERT: H 99 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8753 (mm-30) outliers start: 16 outliers final: 10 residues processed: 120 average time/residue: 0.7841 time to fit residues: 99.7922 Evaluate side-chains 122 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.067017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.047912 restraints weight = 42372.331| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.96 r_work: 0.2862 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12637 Z= 0.142 Angle : 0.598 9.317 18311 Z= 0.357 Chirality : 0.040 0.200 2099 Planarity : 0.004 0.040 1298 Dihedral : 30.862 95.117 4071 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.72 % Allowed : 25.96 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.43 (0.31), residues: 728 helix: 3.24 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.81 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 23 TYR 0.008 0.001 TYR H 63 PHE 0.011 0.001 PHE D 88 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (12637) covalent geometry : angle 0.59792 / 0.36 (18311) hydrogen bonds : bond 0.04943 / 3.30 ( 751) hydrogen bonds : angle 2.65053 / 1.93 ( 1887) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.344 Fit side-chains REVERT: A 59 GLU cc_start: 0.8603 (pm20) cc_final: 0.8268 (pm20) REVERT: A 94 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8017 (tp30) REVERT: A 133 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6437 (mt-10) REVERT: C 76 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8594 (tm-30) REVERT: D 58 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: D 85 MET cc_start: 0.9425 (mmm) cc_final: 0.9179 (mmm) REVERT: D 91 ASP cc_start: 0.9272 (t70) cc_final: 0.8801 (t0) REVERT: D 99 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8854 (mm-30) REVERT: D 116 GLU cc_start: 0.8876 (mp0) cc_final: 0.8409 (mp0) REVERT: D 147 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8151 (p) REVERT: E 59 GLU cc_start: 0.8590 (pm20) cc_final: 0.8301 (pm20) REVERT: E 94 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7983 (tp30) REVERT: E 133 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: G 76 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8568 (tm-30) REVERT: G 110 LYS cc_start: 0.9085 (mmpt) cc_final: 0.8863 (mmmt) REVERT: H 91 ASP cc_start: 0.9206 (t70) cc_final: 0.8726 (t0) REVERT: H 99 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8824 (mm-30) REVERT: H 116 GLU cc_start: 0.8804 (mp0) cc_final: 0.8523 (mp0) outliers start: 17 outliers final: 10 residues processed: 120 average time/residue: 0.8548 time to fit residues: 108.5184 Evaluate side-chains 124 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 135 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 0.2980 chunk 92 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 1 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 72 optimal weight: 40.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.067356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.048324 restraints weight = 42372.526| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.95 r_work: 0.2874 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12637 Z= 0.136 Angle : 0.604 9.124 18311 Z= 0.359 Chirality : 0.040 0.198 2099 Planarity : 0.004 0.054 1298 Dihedral : 30.839 95.164 4071 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.88 % Allowed : 25.96 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.31), residues: 728 helix: 3.28 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.78 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 23 TYR 0.008 0.001 TYR H 63 PHE 0.031 0.001 PHE H 88 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.14 (12637) covalent geometry : angle 0.60374 / 0.36 (18311) hydrogen bonds : bond 0.04730 / 3.17 ( 751) hydrogen bonds : angle 2.63521 / 1.92 ( 1887) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.323 Fit side-chains REVERT: A 59 GLU cc_start: 0.8614 (pm20) cc_final: 0.8334 (pm20) REVERT: A 94 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8008 (tp30) REVERT: A 133 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6404 (mt-10) REVERT: C 76 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8653 (tm-30) REVERT: D 58 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: D 85 MET cc_start: 0.9421 (mmm) cc_final: 0.9171 (mmm) REVERT: D 91 ASP cc_start: 0.9266 (t70) cc_final: 0.8798 (t0) REVERT: D 99 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8800 (mm-30) REVERT: D 147 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8150 (p) REVERT: E 59 GLU cc_start: 0.8595 (pm20) cc_final: 0.8304 (pm20) REVERT: E 94 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7960 (tp30) REVERT: E 133 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6754 (mt-10) REVERT: G 76 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8663 (tm-30) REVERT: G 110 LYS cc_start: 0.9074 (mmpt) cc_final: 0.8848 (mmmt) REVERT: H 91 ASP cc_start: 0.9193 (t70) cc_final: 0.8704 (t0) REVERT: H 116 GLU cc_start: 0.8800 (mp0) cc_final: 0.8516 (mp0) outliers start: 18 outliers final: 10 residues processed: 119 average time/residue: 0.8267 time to fit residues: 104.3433 Evaluate side-chains 122 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 14 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 72 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.067083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.048131 restraints weight = 42513.450| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.97 r_work: 0.2875 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12637 Z= 0.144 Angle : 0.609 9.403 18311 Z= 0.362 Chirality : 0.040 0.194 2099 Planarity : 0.004 0.039 1298 Dihedral : 30.827 94.162 4071 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.72 % Allowed : 26.44 % Favored : 70.83 % 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: 3.54 (0.32), residues: 728 helix: 3.32 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.75 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 23 TYR 0.008 0.001 TYR H 63 PHE 0.005 0.001 PHE F 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (12637) covalent geometry : angle 0.60905 / 0.36 (18311) hydrogen bonds : bond 0.04845 / 3.24 ( 751) hydrogen bonds : angle 2.63076 / 1.91 ( 1887) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.319 Fit side-chains REVERT: A 59 GLU cc_start: 0.8641 (pm20) cc_final: 0.8349 (pm20) REVERT: A 94 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8005 (tp30) REVERT: C 76 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8585 (tm-30) REVERT: D 58 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: D 85 MET cc_start: 0.9412 (mmm) cc_final: 0.9167 (mmm) REVERT: D 91 ASP cc_start: 0.9282 (t70) cc_final: 0.8813 (t0) REVERT: D 116 GLU cc_start: 0.8757 (mp0) cc_final: 0.8466 (mp0) REVERT: D 147 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8126 (p) REVERT: E 59 GLU cc_start: 0.8616 (pm20) cc_final: 0.8317 (pm20) REVERT: E 94 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7975 (tp30) REVERT: E 133 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6655 (mt-10) REVERT: G 76 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8598 (tm-30) REVERT: G 110 LYS cc_start: 0.9094 (mmpt) cc_final: 0.8847 (mmmt) REVERT: H 91 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8693 (t0) REVERT: H 116 GLU cc_start: 0.8849 (mp0) cc_final: 0.8534 (mp0) outliers start: 17 outliers final: 11 residues processed: 119 average time/residue: 0.8247 time to fit residues: 104.0717 Evaluate side-chains 124 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 72 optimal weight: 30.0000 chunk 47 optimal weight: 3.9990 chunk 90 optimal weight: 30.0000 chunk 36 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.067169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.048147 restraints weight = 43103.625| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.99 r_work: 0.2868 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12637 Z= 0.145 Angle : 0.608 9.452 18311 Z= 0.361 Chirality : 0.040 0.195 2099 Planarity : 0.004 0.039 1298 Dihedral : 30.827 93.441 4071 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.72 % Allowed : 26.60 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.55 (0.32), residues: 728 helix: 3.33 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.74 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 23 TYR 0.008 0.001 TYR H 63 PHE 0.031 0.001 PHE H 88 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (12637) covalent geometry : angle 0.60846 / 0.36 (18311) hydrogen bonds : bond 0.04818 / 3.22 ( 751) hydrogen bonds : angle 2.62036 / 1.90 ( 1887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3499.03 seconds wall clock time: 60 minutes 16.95 seconds (3616.95 seconds total)