Starting phenix.real_space_refine on Fri Jul 3 10:21:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g88_29843/07_2026/8g88_29843.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g88_29843/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g88_29843/07_2026/8g88_29843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g88_29843/07_2026/8g88_29843.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g88_29843/07_2026/8g88_29843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g88_29843/07_2026/8g88_29843.map" } 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-dev-6108/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: 3.15, per 1000 atoms: 0.23 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: 1.27 Conformation dependent library (CDL) restraints added in 424.6 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: 2.33 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: 3.42 Time building geometry restraints manager: 1.72 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: 21185 2.36 - 4.72: 380 4.72 - 7.07: 28 7.07 - 9.43: 2 9.43 - 11.79: 1 Bond angle restraints: 21596 Sorted by residual: angle pdb=" O3' DT J -77 " pdb=" P DG J -76 " pdb=" O5' DG J -76 " ideal model delta sigma weight residual 104.00 97.05 6.95 1.50e+00 4.44e-01 2.15e+01 angle pdb=" O3' DT J -75 " pdb=" P DG J -74 " pdb=" O5' DG J -74 " ideal model delta sigma weight residual 104.00 97.08 6.92 1.50e+00 4.44e-01 2.13e+01 angle pdb=" O3' DG J -76 " pdb=" P DT J -75 " pdb=" O5' DT J -75 " ideal model delta sigma weight residual 104.00 97.10 6.90 1.50e+00 4.44e-01 2.12e+01 angle pdb=" O3' DA J -78 " pdb=" P DT J -77 " pdb=" O5' DT J -77 " ideal model delta sigma weight residual 104.00 97.12 6.88 1.50e+00 4.44e-01 2.11e+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 ... (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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.630 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.800 ------------------------------------------------------------------------------- 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 : 0.736 11.791 21596 Z= 0.648 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 0.73577 / 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 : 0.385 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: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9112 (mt) cc_final: 0.8637 (mt) REVERT: B 62 LEU cc_start: 0.8727 (mt) cc_final: 0.8335 (mt) REVERT: C 97 LEU cc_start: 0.8888 (mt) cc_final: 0.7252 (mt) REVERT: D 66 VAL cc_start: 0.8533 (t) cc_final: 0.7908 (p) REVERT: E 97 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7046 (mt-10) REVERT: E 100 LEU cc_start: 0.8604 (mt) cc_final: 0.7877 (mm) REVERT: E 130 ILE cc_start: 0.7736 (mt) cc_final: 0.7519 (mm) REVERT: F 58 LEU cc_start: 0.7488 (tp) cc_final: 0.7112 (tp) REVERT: F 62 LEU cc_start: 0.8944 (mt) cc_final: 0.7988 (mt) REVERT: F 97 LEU cc_start: 0.7684 (tp) cc_final: 0.7412 (tp) REVERT: H 70 ILE cc_start: 0.8916 (mt) cc_final: 0.8643 (mm) REVERT: H 97 LEU cc_start: 0.7747 (mt) cc_final: 0.7464 (mt) outliers start: 7 outliers final: 0 residues processed: 148 average time/residue: 0.1731 time to fit residues: 34.2072 Evaluate side-chains 62 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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: 10.0000 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: 20.0000 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.038269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.031927 restraints weight = 230927.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.032418 restraints weight = 154278.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.032732 restraints weight = 117971.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.032928 restraints weight = 96398.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.033085 restraints weight = 84097.346| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 14927 Z= 0.224 Angle : 0.841 11.503 21596 Z= 0.467 Chirality : 0.052 0.387 2457 Planarity : 0.006 0.077 1569 Dihedral : 30.790 179.410 4747 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.13 % Allowed : 2.53 % Favored : 97.34 % 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: 2.13 (0.27), residues: 871 helix: 1.93 (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 0.008 0.001 ARG E 53 TYR 0.018 0.002 TYR C 50 PHE 0.034 0.003 PHE X 278 TRP 0.012 0.003 TRP X 277 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.22 (14927) covalent geometry : angle 0.84078 / 0.47 (21596) hydrogen bonds : bond 0.09106 / 6.14 ( 862) hydrogen bonds : angle 3.67215 / 2.58 ( 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 85 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.327 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: B 84 MET cc_start: 0.9465 (tpt) cc_final: 0.9130 (tpp) REVERT: D 59 MET cc_start: 0.9567 (mmp) cc_final: 0.9268 (mmm) REVERT: E 50 GLU cc_start: 0.9571 (mp0) cc_final: 0.9359 (mp0) REVERT: E 97 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8578 (mt-10) REVERT: H 59 MET cc_start: 0.9633 (mmp) cc_final: 0.9256 (mmm) REVERT: H 97 LEU cc_start: 0.8454 (mt) cc_final: 0.8126 (mt) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1566 time to fit residues: 18.2661 Evaluate side-chains 47 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 0.0970 chunk 103 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 74 optimal weight: 40.0000 chunk 29 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 85 optimal weight: 30.0000 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 85 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.032435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.026203 restraints weight = 243509.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.026673 restraints weight = 169273.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.026989 restraints weight = 128465.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.027206 restraints weight = 104239.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.027383 restraints weight = 89083.918| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3358 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= 0.185 Angle : 0.689 11.021 21596 Z= 0.400 Chirality : 0.044 0.245 2457 Planarity : 0.005 0.069 1569 Dihedral : 31.388 174.850 4747 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.13 % Allowed : 3.33 % Favored : 96.54 % 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: 2.08 (0.28), residues: 871 helix: 1.84 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -0.04 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 39 TYR 0.011 0.002 TYR C 50 PHE 0.027 0.002 PHE X 278 TRP 0.011 0.002 TRP X 277 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.19 (14927) covalent geometry : angle 0.68886 / 0.40 (21596) hydrogen bonds : bond 0.07006 / 4.65 ( 862) hydrogen bonds : angle 3.54311 / 2.48 ( 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 68 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.463 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: 0.9365 (tpt) cc_final: 0.8982 (tpp) REVERT: D 59 MET cc_start: 0.9568 (mmp) cc_final: 0.9241 (mmm) REVERT: E 50 GLU cc_start: 0.9569 (mp0) cc_final: 0.9332 (mp0) REVERT: E 120 MET cc_start: 0.9308 (mtm) cc_final: 0.9083 (mtt) REVERT: H 59 MET cc_start: 0.9653 (mmp) cc_final: 0.9211 (mmm) REVERT: H 97 LEU cc_start: 0.8493 (mt) cc_final: 0.8180 (mt) outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.1633 time to fit residues: 15.2118 Evaluate side-chains 34 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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: 5.9990 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 75 optimal weight: 40.0000 chunk 83 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 40.0000 chunk 47 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** 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 = 0.2894 r_free = 0.2894 target = 0.030033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.024058 restraints weight = 257802.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.024476 restraints weight = 177747.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.024769 restraints weight = 135419.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.024994 restraints weight = 110774.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.025158 restraints weight = 94293.353| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 14927 Z= 0.241 Angle : 0.767 12.668 21596 Z= 0.431 Chirality : 0.045 0.279 2457 Planarity : 0.005 0.049 1569 Dihedral : 31.840 177.849 4747 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 1.91 (0.27), residues: 871 helix: 1.67 (0.19), residues: 661 sheet: None (None), residues: 0 loop : 0.12 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 39 TYR 0.038 0.003 TYR F 88 PHE 0.017 0.003 PHE X 278 TRP 0.014 0.003 TRP X 277 HIS 0.006 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.24 (14927) covalent geometry : angle 0.76714 / 0.43 (21596) hydrogen bonds : bond 0.10782 / 7.14 ( 862) hydrogen bonds : angle 3.57711 / 2.53 ( 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 57 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.238 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: 0.9300 (tpt) cc_final: 0.8999 (tpp) REVERT: E 104 PHE cc_start: 0.9517 (m-80) cc_final: 0.9038 (m-80) REVERT: H 59 MET cc_start: 0.9692 (mmp) cc_final: 0.9318 (mmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1567 time to fit residues: 12.3142 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 : 0.351 ------------------------------------------------------------------------------- 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: 7.9990 chunk 60 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 chunk 47 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 50.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.2927 r_free = 0.2927 target = 0.030296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.024188 restraints weight = 251964.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.024698 restraints weight = 159939.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.025054 restraints weight = 114579.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.025292 restraints weight = 89639.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.025430 restraints weight = 74734.007| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14927 Z= 0.176 Angle : 0.670 10.509 21596 Z= 0.387 Chirality : 0.043 0.234 2457 Planarity : 0.005 0.060 1569 Dihedral : 31.993 175.289 4747 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.28), residues: 871 helix: 1.79 (0.19), residues: 659 sheet: None (None), residues: 0 loop : 0.05 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 89 TYR 0.012 0.002 TYR H 37 PHE 0.019 0.002 PHE E 104 TRP 0.011 0.002 TRP X 277 HIS 0.006 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.18 (14927) covalent geometry : angle 0.66979 / 0.39 (21596) hydrogen bonds : bond 0.06733 / 4.39 ( 862) hydrogen bonds : angle 3.55342 / 2.49 ( 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 52 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9243 (tpt) cc_final: 0.8838 (tpp) REVERT: E 104 PHE cc_start: 0.9516 (m-80) cc_final: 0.9061 (m-80) REVERT: H 59 MET cc_start: 0.9694 (mmp) cc_final: 0.9318 (mmm) REVERT: H 97 LEU cc_start: 0.8139 (mt) cc_final: 0.7926 (mt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1428 time to fit residues: 10.5103 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 : 0.367 ------------------------------------------------------------------------------- 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: 8.9990 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: 2.9990 chunk 51 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 91 optimal weight: 30.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 81 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.028241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.022423 restraints weight = 262594.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.022883 restraints weight = 165500.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.023191 restraints weight = 118680.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.023431 restraints weight = 93367.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.023556 restraints weight = 77135.580| |-----------------------------------------------------------------------------| r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 14927 Z= 0.257 Angle : 0.763 13.129 21596 Z= 0.435 Chirality : 0.045 0.245 2457 Planarity : 0.006 0.048 1569 Dihedral : 32.442 175.379 4747 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 23.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 1.45 (0.27), residues: 871 helix: 1.32 (0.19), residues: 663 sheet: None (None), residues: 0 loop : 0.01 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 69 TYR 0.017 0.002 TYR A 54 PHE 0.018 0.003 PHE X 194 TRP 0.013 0.003 TRP X 277 HIS 0.005 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.26 (14927) covalent geometry : angle 0.76280 / 0.43 (21596) hydrogen bonds : bond 0.12993 / 8.60 ( 862) hydrogen bonds : angle 3.78293 / 2.66 ( 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 43 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9149 (tpt) cc_final: 0.8438 (tpp) REVERT: D 62 PHE cc_start: 0.9753 (t80) cc_final: 0.9543 (t80) REVERT: E 86 SER cc_start: 0.9379 (p) cc_final: 0.8680 (p) REVERT: E 90 MET cc_start: 0.9227 (mmp) cc_final: 0.9015 (ptp) REVERT: E 104 PHE cc_start: 0.9672 (m-80) cc_final: 0.8944 (m-80) REVERT: H 59 MET cc_start: 0.9547 (mmp) cc_final: 0.8787 (mmm) REVERT: H 97 LEU cc_start: 0.8740 (mt) cc_final: 0.8455 (mt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1381 time to fit residues: 8.5033 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 : 0.319 ------------------------------------------------------------------------------- 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: 7.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 95 optimal weight: 30.0000 chunk 91 optimal weight: 30.0000 chunk 12 optimal weight: 2.9990 chunk 96 optimal weight: 30.0000 overall best weight: 10.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2808 r_free = 0.2808 target = 0.026114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.020491 restraints weight = 290209.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.020960 restraints weight = 181695.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.021278 restraints weight = 128327.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.021486 restraints weight = 98794.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.021642 restraints weight = 81453.715| |-----------------------------------------------------------------------------| r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.7250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 14927 Z= 0.345 Angle : 0.932 14.317 21596 Z= 0.518 Chirality : 0.053 0.282 2457 Planarity : 0.008 0.076 1569 Dihedral : 33.450 173.802 4747 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 36.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: 0.24 (0.27), residues: 871 helix: 0.48 (0.19), residues: 655 sheet: None (None), residues: 0 loop : -0.49 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 76 TYR 0.023 0.003 TYR D 37 PHE 0.033 0.004 PHE C 25 TRP 0.016 0.004 TRP X 277 HIS 0.008 0.003 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.35 (14927) covalent geometry : angle 0.93157 / 0.52 (21596) hydrogen bonds : bond 0.16388 / 10.95 ( 862) hydrogen bonds : angle 4.51151 / 3.19 ( 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 36 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9082 (tpt) cc_final: 0.8710 (tpp) REVERT: E 104 PHE cc_start: 0.9442 (m-80) cc_final: 0.9048 (m-80) REVERT: H 59 MET cc_start: 0.9714 (mmp) cc_final: 0.9411 (mmm) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1454 time to fit residues: 7.5335 Evaluate side-chains 24 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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: 5.9990 chunk 60 optimal weight: 5.9990 chunk 93 optimal weight: 30.0000 chunk 102 optimal weight: 40.0000 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 0.2980 chunk 77 optimal weight: 30.0000 chunk 114 optimal weight: 0.1980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.027647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.021880 restraints weight = 263707.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.022360 restraints weight = 164178.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.022682 restraints weight = 116301.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.022937 restraints weight = 89971.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.023096 restraints weight = 73212.007| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.6990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 14927 Z= 0.173 Angle : 0.750 11.307 21596 Z= 0.424 Chirality : 0.046 0.231 2457 Planarity : 0.006 0.051 1569 Dihedral : 33.068 173.822 4747 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.28), residues: 871 helix: 1.14 (0.19), residues: 653 sheet: None (None), residues: 0 loop : -0.30 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 32 TYR 0.011 0.002 TYR H 37 PHE 0.037 0.002 PHE C 25 TRP 0.013 0.002 TRP X 277 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.17 (14927) covalent geometry : angle 0.75024 / 0.42 (21596) hydrogen bonds : bond 0.06410 / 4.18 ( 862) hydrogen bonds : angle 4.02151 / 2.81 ( 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 41 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9163 (tpt) cc_final: 0.8851 (tpp) REVERT: E 104 PHE cc_start: 0.9423 (m-80) cc_final: 0.9056 (m-10) REVERT: H 59 MET cc_start: 0.9696 (mmp) cc_final: 0.9348 (mmm) REVERT: H 122 LYS cc_start: 0.9687 (mmpt) cc_final: 0.9446 (mtmm) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1306 time to fit residues: 7.9326 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 : 0.365 ------------------------------------------------------------------------------- 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: 40.0000 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 86 optimal weight: 40.0000 chunk 102 optimal weight: 40.0000 chunk 74 optimal weight: 40.0000 chunk 25 optimal weight: 9.9990 chunk 100 optimal weight: 40.0000 chunk 27 optimal weight: 10.0000 chunk 70 optimal weight: 0.0020 overall best weight: 5.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.026945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.021225 restraints weight = 277410.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.021724 restraints weight = 169027.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.022062 restraints weight = 117710.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.022292 restraints weight = 89228.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.022444 restraints weight = 72555.848| |-----------------------------------------------------------------------------| r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.7282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14927 Z= 0.212 Angle : 0.746 12.384 21596 Z= 0.422 Chirality : 0.045 0.255 2457 Planarity : 0.006 0.048 1569 Dihedral : 32.991 172.223 4747 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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: 1.14 (0.27), residues: 871 helix: 1.17 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -0.30 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 89 TYR 0.013 0.002 TYR H 37 PHE 0.031 0.002 PHE C 25 TRP 0.013 0.003 TRP X 277 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.21 (14927) covalent geometry : angle 0.74616 / 0.42 (21596) hydrogen bonds : bond 0.10292 / 6.79 ( 862) hydrogen bonds : angle 4.00649 / 2.80 ( 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 : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9218 (tpt) cc_final: 0.8604 (tpp) REVERT: E 104 PHE cc_start: 0.9656 (m-80) cc_final: 0.9000 (m-80) REVERT: F 84 MET cc_start: 0.9359 (tpp) cc_final: 0.9149 (tpp) REVERT: H 59 MET cc_start: 0.9574 (mmp) cc_final: 0.8820 (mmm) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1456 time to fit residues: 7.7411 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 : 0.542 ------------------------------------------------------------------------------- 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: 4.9990 chunk 8 optimal weight: 0.2980 chunk 40 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 101 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 chunk 103 optimal weight: 30.0000 chunk 2 optimal weight: 8.9990 chunk 88 optimal weight: 50.0000 chunk 39 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.027180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.021514 restraints weight = 271838.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.021997 restraints weight = 166297.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.022311 restraints weight = 116365.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.022567 restraints weight = 89811.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.022717 restraints weight = 72592.187| |-----------------------------------------------------------------------------| r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.7356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14927 Z= 0.170 Angle : 0.708 11.789 21596 Z= 0.401 Chirality : 0.044 0.238 2457 Planarity : 0.005 0.047 1569 Dihedral : 32.840 172.193 4747 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 1.32 (0.27), residues: 871 helix: 1.32 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -0.33 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 89 TYR 0.011 0.002 TYR H 37 PHE 0.026 0.002 PHE C 25 TRP 0.013 0.003 TRP X 277 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.17 (14927) covalent geometry : angle 0.70758 / 0.40 (21596) hydrogen bonds : bond 0.07077 / 4.63 ( 862) hydrogen bonds : angle 3.87566 / 2.70 ( 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 35 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9117 (tpt) cc_final: 0.8777 (tpp) REVERT: E 104 PHE cc_start: 0.9460 (m-80) cc_final: 0.9139 (m-10) REVERT: H 59 MET cc_start: 0.9679 (mmp) cc_final: 0.9300 (mmm) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1407 time to fit residues: 7.2820 Evaluate side-chains 30 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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: 3.9990 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 84 optimal weight: 30.0000 chunk 89 optimal weight: 50.0000 chunk 86 optimal weight: 40.0000 chunk 94 optimal weight: 40.0000 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2810 r_free = 0.2810 target = 0.026195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.020611 restraints weight = 283000.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.021092 restraints weight = 173467.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.021406 restraints weight = 121174.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.021640 restraints weight = 92882.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.021791 restraints weight = 75369.657| |-----------------------------------------------------------------------------| r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.7874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 14927 Z= 0.251 Angle : 0.788 13.238 21596 Z= 0.442 Chirality : 0.046 0.261 2457 Planarity : 0.006 0.047 1569 Dihedral : 33.046 172.030 4747 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 27.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.27), residues: 871 helix: 1.03 (0.19), residues: 657 sheet: None (None), residues: 0 loop : -0.21 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 89 TYR 0.014 0.002 TYR H 37 PHE 0.027 0.003 PHE C 25 TRP 0.013 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 0.78830 / 0.44 (21596) hydrogen bonds : bond 0.13002 / 8.63 ( 862) hydrogen bonds : angle 4.08425 / 2.87 ( 2188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1722.76 seconds wall clock time: 30 minutes 49.11 seconds (1849.11 seconds total)