Starting phenix.real_space_refine on Thu Aug 6 05:00:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g88_29843/08_2026/8g88_29843.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g88_29843/08_2026/8g88_29843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g88_29843/08_2026/8g88_29843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g88_29843/08_2026/8g88_29843.map" model { file = "/net/cci-nas-00/data/ceres_data/8g88_29843/08_2026/8g88_29843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g88_29843/08_2026/8g88_29843.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 336 5.49 5 S 17 5.16 5 C 7773 2.51 5 N 2598 2.21 5 O 3271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13995 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} 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: 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: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3417 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "J" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3471 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "X" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1080 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 1 Time building chain proxies: 2.90, per 1000 atoms: 0.21 Number of scatterers: 13995 At special positions: 0 Unit cell: (82.11, 119.14, 175.49, 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 17 16.00 P 336 15.00 O 3271 8.00 N 2598 7.00 C 7773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 412.8 milliseconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1674 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 75.2% alpha, 2.5% beta 155 base pairs and 306 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.145A 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 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.236A 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 100 through 122 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.829A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.386A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'X' and resid 141 through 161 Processing helix chain 'X' and resid 163 through 176 Processing helix chain 'X' and resid 180 through 189 removed outlier: 3.552A pdb=" N ILE X 184 " --> pdb=" O SER X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 193 through 211 Proline residue: X 202 - end of helix Processing helix chain 'X' and resid 215 through 220 Processing helix chain 'X' and resid 239 through 249 Processing helix chain 'X' and resid 256 through 268 removed outlier: 3.681A pdb=" N HIS X 262 " --> pdb=" O GLN X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 288 removed outlier: 4.058A pdb=" N SER X 288 " --> pdb=" O LYS X 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.003A 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: 6.691A 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: 7.144A 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 101 through 102 removed outlier: 6.770A 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: 6.763A 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: 7.057A 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 78 492 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 155 basepair parallelities 306 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 1.57 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: 2767 1.33 - 1.45: 4835 1.45 - 1.57: 6627 1.57 - 1.69: 670 1.69 - 1.81: 28 Bond restraints: 14927 Sorted by residual: bond pdb=" C1' DC J -95 " pdb=" N1 DC J -95 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.36e+01 bond pdb=" C1' DT J -75 " pdb=" N1 DT J -75 " ideal model delta sigma weight residual 1.468 1.543 -0.075 1.40e-02 5.10e+03 2.86e+01 bond pdb=" C1' DT J -77 " pdb=" N1 DT J -77 " ideal model delta sigma weight residual 1.468 1.542 -0.074 1.40e-02 5.10e+03 2.81e+01 bond pdb=" C3' DA I -31 " pdb=" C2' DA I -31 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DT J 41 " pdb=" C2' DT J 41 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 ... (remaining 14922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 21184 2.36 - 4.72: 381 4.72 - 7.07: 28 7.07 - 9.43: 2 9.43 - 11.79: 1 Bond angle restraints: 21596 Sorted by residual: angle pdb=" C3' DC I 80 " pdb=" O3' DC I 80 " pdb=" P DA I 81 " ideal model delta sigma weight residual 119.70 125.35 -5.65 1.20e+00 6.94e-01 2.21e+01 angle pdb=" O4' DG J -90 " pdb=" C4' DG J -90 " pdb=" C3' DG J -90 " ideal model delta sigma weight residual 106.00 103.39 2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J -91 " pdb=" C4 DT J -91 " pdb=" O4 DT J -91 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT I -71 " pdb=" C4 DT I -71 " pdb=" O4 DT I -71 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT J -93 " pdb=" C4 DT J -93 " pdb=" O4 DT J -93 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 ... (remaining 21591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 6595 35.89 - 71.78: 1596 71.78 - 107.66: 18 107.66 - 143.55: 0 143.55 - 179.44: 3 Dihedral angle restraints: 8212 sinusoidal: 5626 harmonic: 2586 Sorted by residual: dihedral pdb=" C4' DT I 20 " pdb=" C3' DT I 20 " pdb=" O3' DT I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual -140.00 39.44 -179.44 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA I 81 " pdb=" C3' DA I 81 " pdb=" O3' DA I 81 " pdb=" P DC I 82 " ideal model delta sinusoidal sigma weight residual -140.00 36.15 -176.15 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 80 " pdb=" C3' DC I 80 " pdb=" O3' DC I 80 " pdb=" P DA I 81 " ideal model delta sinusoidal sigma weight residual -140.00 16.00 -156.00 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 8209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1432 0.031 - 0.061: 621 0.061 - 0.092: 243 0.092 - 0.122: 146 0.122 - 0.153: 15 Chirality restraints: 2457 Sorted by residual: chirality pdb=" CG LEU X 190 " pdb=" CB LEU X 190 " pdb=" CD1 LEU X 190 " pdb=" CD2 LEU X 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" C3' DT J -93 " pdb=" C4' DT J -93 " pdb=" O3' DT J -93 " pdb=" C2' DT J -93 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" C1' DC J -95 " pdb=" O4' DC J -95 " pdb=" C2' DC J -95 " pdb=" N1 DC J -95 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 2454 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO G 80 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO C 80 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS X 254 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO X 255 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO X 255 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO X 255 " -0.023 5.00e-02 4.00e+02 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2950 2.80 - 3.33: 12263 3.33 - 3.85: 28072 3.85 - 4.38: 34764 4.38 - 4.90: 46610 Nonbonded interactions: 124659 Sorted by model distance: nonbonded pdb=" O GLN X 155 " pdb=" OG1 THR X 159 " model vdw 2.277 3.040 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.288 3.040 nonbonded pdb=" NE ARG X 157 " pdb=" OE2 GLU X 188 " model vdw 2.303 3.120 nonbonded pdb=" OP2 DA I 88 " pdb=" ND2 ASN X 196 " model vdw 2.303 3.120 nonbonded pdb=" NH2 ARG X 157 " pdb=" OE1 GLU X 188 " model vdw 2.305 3.120 ... (remaining 124654 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' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 22 through 101) selection = (chain 'F' and resid 22 through 101) } 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=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.520 Find NCS groups from input model: 0.140 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 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 0.081 14927 Z= 0.524 Angle : 0.742 11.791 21596 Z= 0.652 Chirality : 0.045 0.153 2457 Planarity : 0.004 0.047 1569 Dihedral : 27.716 179.439 6538 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.93 % Allowed : 16.78 % Favored : 82.29 % 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: 1.45 (0.26), residues: 871 helix: 1.36 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.12 (0.38), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.010 0.001 TYR B 51 PHE 0.011 0.001 PHE X 187 TRP 0.022 0.003 TRP X 277 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.52 (14927) covalent geometry : angle 0.74207 / 0.65 (21596) hydrogen bonds : bond 0.22233 / 15.04 ( 862) hydrogen bonds : angle 8.29165 / 5.93 ( 2188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9112 (mt) cc_final: 0.8638 (mt) REVERT: B 62 LEU cc_start: 0.8727 (mt) cc_final: 0.8325 (mt) REVERT: C 97 LEU cc_start: 0.8888 (mt) cc_final: 0.7239 (mt) REVERT: D 66 VAL cc_start: 0.8533 (t) cc_final: 0.7899 (p) REVERT: E 97 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7044 (mt-10) REVERT: E 100 LEU cc_start: 0.8604 (mt) cc_final: 0.7869 (mm) REVERT: E 130 ILE cc_start: 0.7736 (mt) cc_final: 0.7517 (mm) REVERT: F 58 LEU cc_start: 0.7488 (tp) cc_final: 0.7125 (tp) REVERT: F 62 LEU cc_start: 0.8944 (mt) cc_final: 0.7990 (mt) REVERT: F 97 LEU cc_start: 0.7684 (tp) cc_final: 0.7415 (tp) REVERT: H 70 ILE cc_start: 0.8916 (mt) cc_final: 0.8618 (mm) REVERT: H 97 LEU cc_start: 0.7747 (mt) cc_final: 0.7446 (mt) outliers start: 7 outliers final: 0 residues processed: 148 average time/residue: 0.1655 time to fit residues: 32.7494 Evaluate side-chains 59 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 30.0000 chunk 113 optimal weight: 0.0470 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 30.0000 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN B 75 HIS D 81 ASN E 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** 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 = 0.3033 r_free = 0.3033 target = 0.038232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.031903 restraints weight = 230593.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.032397 restraints weight = 154163.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.032743 restraints weight = 118238.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.032897 restraints weight = 96359.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.033037 restraints weight = 82443.929| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 14927 Z= 0.225 Angle : 0.870 12.177 21596 Z= 0.473 Chirality : 0.055 0.432 2457 Planarity : 0.006 0.066 1569 Dihedral : 30.795 179.748 4747 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.13 % Allowed : 2.93 % Favored : 96.94 % 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: 2.09 (0.27), residues: 871 helix: 1.90 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -0.20 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 53 TYR 0.018 0.002 TYR C 50 PHE 0.033 0.003 PHE X 175 TRP 0.013 0.003 TRP X 277 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.22 (14927) covalent geometry : angle 0.86970 / 0.47 (21596) hydrogen bonds : bond 0.09160 / 6.19 ( 862) hydrogen bonds : angle 3.68877 / 2.59 ( 2188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9039 (mtm) cc_final: 0.8695 (mpp) REVERT: B 84 MET cc_start: 0.9433 (tpt) cc_final: 0.8995 (tpp) REVERT: D 59 MET cc_start: 0.9559 (mmp) cc_final: 0.9252 (mmm) REVERT: E 50 GLU cc_start: 0.9576 (mp0) cc_final: 0.9336 (mp0) REVERT: E 97 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8593 (mt-10) REVERT: H 59 MET cc_start: 0.9636 (mmp) cc_final: 0.9243 (mmm) REVERT: H 97 LEU cc_start: 0.8518 (mt) cc_final: 0.8192 (mt) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1466 time to fit residues: 16.6749 Evaluate side-chains 46 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 103 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 74 optimal weight: 50.0000 chunk 29 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN H 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.032085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.025841 restraints weight = 246775.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.026304 restraints weight = 170994.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.026614 restraints weight = 130064.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.026839 restraints weight = 106086.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.027003 restraints weight = 90239.122| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14927 Z= 0.189 Angle : 0.708 11.434 21596 Z= 0.406 Chirality : 0.044 0.271 2457 Planarity : 0.006 0.098 1569 Dihedral : 31.432 174.896 4747 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.27 % Allowed : 3.33 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.27), residues: 871 helix: 1.77 (0.19), residues: 664 sheet: None (None), residues: 0 loop : 0.07 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG B 39 TYR 0.011 0.002 TYR C 50 PHE 0.027 0.002 PHE X 278 TRP 0.013 0.002 TRP X 277 HIS 0.006 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.19 (14927) covalent geometry : angle 0.70848 / 0.41 (21596) hydrogen bonds : bond 0.07994 / 5.35 ( 862) hydrogen bonds : angle 3.62677 / 2.55 ( 2188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9429 (tpt) cc_final: 0.9045 (tpp) REVERT: D 59 MET cc_start: 0.9575 (mmp) cc_final: 0.9234 (mmm) REVERT: E 50 GLU cc_start: 0.9589 (mp0) cc_final: 0.9335 (mp0) REVERT: E 120 MET cc_start: 0.9292 (mtm) cc_final: 0.9061 (mtt) REVERT: H 59 MET cc_start: 0.9670 (mmp) cc_final: 0.9228 (mmm) outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.1515 time to fit residues: 13.5794 Evaluate side-chains 32 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 0.4980 chunk 75 optimal weight: 40.0000 chunk 83 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 98 optimal weight: 40.0000 chunk 47 optimal weight: 30.0000 chunk 12 optimal weight: 3.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.029747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.023769 restraints weight = 259846.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.024193 restraints weight = 177611.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.024487 restraints weight = 135066.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.024705 restraints weight = 110658.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.024866 restraints weight = 94298.595| |-----------------------------------------------------------------------------| r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 14927 Z= 0.229 Angle : 0.796 12.894 21596 Z= 0.437 Chirality : 0.046 0.280 2457 Planarity : 0.006 0.062 1569 Dihedral : 31.860 179.211 4747 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.27), residues: 871 helix: 1.54 (0.19), residues: 661 sheet: None (None), residues: 0 loop : 0.13 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 32 TYR 0.026 0.003 TYR A 54 PHE 0.027 0.002 PHE E 104 TRP 0.013 0.003 TRP X 277 HIS 0.006 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.23 (14927) covalent geometry : angle 0.79610 / 0.44 (21596) hydrogen bonds : bond 0.10239 / 6.77 ( 862) hydrogen bonds : angle 3.62188 / 2.55 ( 2188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9379 (tpt) cc_final: 0.9066 (tpp) REVERT: E 104 PHE cc_start: 0.9493 (m-80) cc_final: 0.9163 (m-10) REVERT: H 59 MET cc_start: 0.9700 (mmp) cc_final: 0.9327 (mmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1612 time to fit residues: 12.7207 Evaluate side-chains 29 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 31 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 91 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.028696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.022784 restraints weight = 262699.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.023250 restraints weight = 166785.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.023585 restraints weight = 120262.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.023800 restraints weight = 94057.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.023968 restraints weight = 78728.668| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14927 Z= 0.235 Angle : 0.758 10.287 21596 Z= 0.427 Chirality : 0.045 0.251 2457 Planarity : 0.006 0.079 1569 Dihedral : 32.398 172.858 4747 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: 1.61 (0.27), residues: 871 helix: 1.43 (0.19), residues: 659 sheet: None (None), residues: 0 loop : 0.14 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 69 TYR 0.016 0.002 TYR B 51 PHE 0.015 0.002 PHE D 67 TRP 0.014 0.003 TRP X 277 HIS 0.008 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.23 (14927) covalent geometry : angle 0.75781 / 0.43 (21596) hydrogen bonds : bond 0.10020 / 6.63 ( 862) hydrogen bonds : angle 3.83711 / 2.68 ( 2188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9266 (tpt) cc_final: 0.8629 (tpp) REVERT: D 62 PHE cc_start: 0.9775 (t80) cc_final: 0.9569 (t80) REVERT: E 86 SER cc_start: 0.9377 (p) cc_final: 0.8936 (p) REVERT: E 90 MET cc_start: 0.9285 (mmp) cc_final: 0.9071 (ptp) REVERT: E 104 PHE cc_start: 0.9652 (m-80) cc_final: 0.8904 (m-80) REVERT: H 59 MET cc_start: 0.9557 (mmp) cc_final: 0.8801 (mmm) REVERT: H 97 LEU cc_start: 0.8651 (mt) cc_final: 0.8396 (mt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1486 time to fit residues: 11.0560 Evaluate side-chains 31 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 36 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 chunk 78 optimal weight: 40.0000 chunk 56 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 34 optimal weight: 0.7980 chunk 91 optimal weight: 30.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.028289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.022404 restraints weight = 261085.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.022874 restraints weight = 165024.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.023188 restraints weight = 118364.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.023428 restraints weight = 93159.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.023590 restraints weight = 77352.895| |-----------------------------------------------------------------------------| r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 14927 Z= 0.200 Angle : 0.729 11.740 21596 Z= 0.408 Chirality : 0.044 0.250 2457 Planarity : 0.005 0.040 1569 Dihedral : 32.455 175.920 4747 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: 1.76 (0.28), residues: 871 helix: 1.57 (0.19), residues: 659 sheet: None (None), residues: 0 loop : 0.06 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 77 TYR 0.013 0.002 TYR A 54 PHE 0.020 0.002 PHE E 104 TRP 0.011 0.002 TRP X 277 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.20 (14927) covalent geometry : angle 0.72865 / 0.41 (21596) hydrogen bonds : bond 0.08785 / 5.81 ( 862) hydrogen bonds : angle 3.71785 / 2.59 ( 2188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9181 (tpt) cc_final: 0.8770 (tpp) REVERT: E 86 SER cc_start: 0.9418 (p) cc_final: 0.9213 (p) REVERT: E 90 MET cc_start: 0.9498 (mmp) cc_final: 0.9285 (ptp) REVERT: E 104 PHE cc_start: 0.9510 (m-80) cc_final: 0.9044 (m-80) REVERT: H 59 MET cc_start: 0.9683 (mmp) cc_final: 0.9281 (mmm) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1433 time to fit residues: 9.8221 Evaluate side-chains 31 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 103 optimal weight: 30.0000 chunk 90 optimal weight: 30.0000 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 95 optimal weight: 40.0000 chunk 91 optimal weight: 40.0000 chunk 12 optimal weight: 0.9990 chunk 96 optimal weight: 30.0000 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.027198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.021498 restraints weight = 273862.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.021963 restraints weight = 173096.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.022274 restraints weight = 123814.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.022500 restraints weight = 96457.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.022608 restraints weight = 79650.122| |-----------------------------------------------------------------------------| r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 14927 Z= 0.252 Angle : 0.780 12.708 21596 Z= 0.436 Chirality : 0.046 0.258 2457 Planarity : 0.006 0.052 1569 Dihedral : 32.712 173.847 4747 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 25.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 1.29 (0.27), residues: 871 helix: 1.20 (0.19), residues: 655 sheet: None (None), residues: 0 loop : 0.04 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 40 TYR 0.025 0.002 TYR H 37 PHE 0.029 0.003 PHE C 25 TRP 0.014 0.003 TRP X 277 HIS 0.005 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.25 (14927) covalent geometry : angle 0.78031 / 0.44 (21596) hydrogen bonds : bond 0.12272 / 8.15 ( 862) hydrogen bonds : angle 3.93608 / 2.75 ( 2188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8945 (pm20) cc_final: 0.8740 (pm20) REVERT: B 84 MET cc_start: 0.9152 (tpt) cc_final: 0.8776 (tpp) REVERT: E 104 PHE cc_start: 0.9500 (m-80) cc_final: 0.9040 (m-80) REVERT: H 59 MET cc_start: 0.9698 (mmp) cc_final: 0.9305 (mmm) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1298 time to fit residues: 8.0681 Evaluate side-chains 27 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 100 optimal weight: 30.0000 chunk 18 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 93 optimal weight: 40.0000 chunk 102 optimal weight: 40.0000 chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 77 optimal weight: 30.0000 chunk 114 optimal weight: 5.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.027127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.021446 restraints weight = 271007.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.021896 restraints weight = 171563.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.022216 restraints weight = 122068.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.022440 restraints weight = 94053.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.022608 restraints weight = 77689.618| |-----------------------------------------------------------------------------| r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 14927 Z= 0.215 Angle : 0.754 12.029 21596 Z= 0.421 Chirality : 0.046 0.254 2457 Planarity : 0.006 0.059 1569 Dihedral : 32.850 174.382 4747 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: 1.50 (0.28), residues: 871 helix: 1.37 (0.19), residues: 656 sheet: None (None), residues: 0 loop : 0.03 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 69 TYR 0.009 0.002 TYR G 57 PHE 0.040 0.003 PHE C 25 TRP 0.012 0.003 TRP X 277 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.21 (14927) covalent geometry : angle 0.75392 / 0.42 (21596) hydrogen bonds : bond 0.08951 / 5.92 ( 862) hydrogen bonds : angle 3.93936 / 2.75 ( 2188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9168 (tpt) cc_final: 0.8463 (tpp) REVERT: E 104 PHE cc_start: 0.9651 (m-80) cc_final: 0.8992 (m-10) REVERT: H 59 MET cc_start: 0.9591 (mmp) cc_final: 0.8820 (mmm) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1273 time to fit residues: 8.0850 Evaluate side-chains 28 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 83 optimal weight: 30.0000 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 86 optimal weight: 40.0000 chunk 102 optimal weight: 40.0000 chunk 74 optimal weight: 40.0000 chunk 25 optimal weight: 7.9990 chunk 100 optimal weight: 40.0000 chunk 27 optimal weight: 9.9990 chunk 70 optimal weight: 30.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.025950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.020394 restraints weight = 291257.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.020865 restraints weight = 181148.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.021196 restraints weight = 127720.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.021399 restraints weight = 97588.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.021564 restraints weight = 80077.839| |-----------------------------------------------------------------------------| r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.7784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 14927 Z= 0.280 Angle : 0.832 12.968 21596 Z= 0.460 Chirality : 0.048 0.276 2457 Planarity : 0.007 0.112 1569 Dihedral : 33.148 173.043 4747 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 31.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.27), residues: 871 helix: 0.99 (0.19), residues: 657 sheet: None (None), residues: 0 loop : -0.12 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 96 TYR 0.015 0.002 TYR G 57 PHE 0.019 0.003 PHE B 61 TRP 0.012 0.003 TRP X 277 HIS 0.007 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.28 (14927) covalent geometry : angle 0.83238 / 0.46 (21596) hydrogen bonds : bond 0.14352 / 9.56 ( 862) hydrogen bonds : angle 4.20813 / 2.95 ( 2188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8990 (pm20) cc_final: 0.8781 (pm20) REVERT: B 84 MET cc_start: 0.9060 (tpt) cc_final: 0.8696 (tpp) REVERT: E 104 PHE cc_start: 0.9399 (m-80) cc_final: 0.9118 (m-10) REVERT: H 59 MET cc_start: 0.9694 (mmp) cc_final: 0.9330 (mmm) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1370 time to fit residues: 7.2524 Evaluate side-chains 25 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 101 optimal weight: 40.0000 chunk 53 optimal weight: 7.9990 chunk 103 optimal weight: 30.0000 chunk 2 optimal weight: 8.9990 chunk 88 optimal weight: 50.0000 chunk 39 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.026395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.020739 restraints weight = 282498.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.021231 restraints weight = 172986.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.021571 restraints weight = 120637.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.021783 restraints weight = 91630.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.021944 restraints weight = 74955.175| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.7931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14927 Z= 0.210 Angle : 0.771 12.017 21596 Z= 0.425 Chirality : 0.046 0.258 2457 Planarity : 0.005 0.059 1569 Dihedral : 33.158 173.275 4747 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.28), residues: 871 helix: 1.20 (0.19), residues: 657 sheet: None (None), residues: 0 loop : -0.14 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 89 TYR 0.015 0.002 TYR H 80 PHE 0.023 0.002 PHE C 25 TRP 0.012 0.003 TRP X 277 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.21 (14927) covalent geometry : angle 0.77053 / 0.43 (21596) hydrogen bonds : bond 0.09043 / 6.00 ( 862) hydrogen bonds : angle 4.08905 / 2.87 ( 2188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9098 (tpt) cc_final: 0.8740 (tpp) REVERT: E 104 PHE cc_start: 0.9396 (m-80) cc_final: 0.9102 (m-10) REVERT: H 59 MET cc_start: 0.9684 (mmp) cc_final: 0.9308 (mmm) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1298 time to fit residues: 7.0849 Evaluate side-chains 28 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 84 optimal weight: 40.0000 chunk 89 optimal weight: 50.0000 chunk 86 optimal weight: 40.0000 chunk 94 optimal weight: 30.0000 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.026279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.020674 restraints weight = 284436.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.021158 restraints weight = 173996.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.021497 restraints weight = 121487.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.021716 restraints weight = 92057.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.021883 restraints weight = 74895.258| |-----------------------------------------------------------------------------| r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.8166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14927 Z= 0.207 Angle : 0.763 15.112 21596 Z= 0.422 Chirality : 0.046 0.262 2457 Planarity : 0.005 0.049 1569 Dihedral : 32.976 171.935 4747 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.28), residues: 871 helix: 1.34 (0.19), residues: 657 sheet: None (None), residues: 0 loop : -0.24 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 89 TYR 0.012 0.002 TYR G 57 PHE 0.031 0.003 PHE C 25 TRP 0.013 0.003 TRP X 277 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.21 (14927) covalent geometry : angle 0.76270 / 0.42 (21596) hydrogen bonds : bond 0.09992 / 6.62 ( 862) hydrogen bonds : angle 3.95360 / 2.77 ( 2188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1694.45 seconds wall clock time: 30 minutes 19.41 seconds (1819.41 seconds total)