Starting phenix.real_space_refine on Fri Jul 3 12:19:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8g_29850/07_2026/8g8g_29850.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8g_29850/07_2026/8g8g_29850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g8g_29850/07_2026/8g8g_29850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8g_29850/07_2026/8g8g_29850.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8g_29850/07_2026/8g8g_29850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8g_29850/07_2026/8g8g_29850.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 348 5.49 5 S 17 5.16 5 C 8089 2.51 5 N 2711 2.21 5 O 3393 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 14558 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 895 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} 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: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 756 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" 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: "F" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 915 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 3539 Classifications: {'DNA': 174} Link IDs: {'rna3p': 173} Chain: "J" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 3595 Classifications: {'DNA': 174} Link IDs: {'rna3p': 173} Chain: "X" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1152 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Time building chain proxies: 3.04, per 1000 atoms: 0.21 Number of scatterers: 14558 At special positions: 0 Unit cell: (97.52, 116.6, 189.74, 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 348 15.00 O 3393 8.00 N 2711 7.00 C 8089 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 416.1 milliseconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1752 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 10 sheets defined 71.5% alpha, 2.6% beta 157 base pairs and 325 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 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 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.335A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.572A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.220A 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 removed outlier: 3.537A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 122 Processing 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: 3.554A 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 238 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: 6.873A 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: 6.630A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.964A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.919A 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: 7.035A 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 78 493 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 379 hydrogen bonds 758 hydrogen bond angles 0 basepair planarities 157 basepair parallelities 325 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 1.61 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: 2787 1.33 - 1.45: 5064 1.45 - 1.57: 6948 1.57 - 1.69: 694 1.69 - 1.81: 28 Bond restraints: 15521 Sorted by residual: bond pdb=" C LEU G 116 " pdb=" N PRO G 117 " ideal model delta sigma weight residual 1.332 1.213 0.119 1.34e-02 5.57e+03 7.87e+01 bond pdb=" C LEU F 22 " pdb=" N ARG F 23 " ideal model delta sigma weight residual 1.330 1.384 -0.054 1.22e-02 6.72e+03 1.98e+01 bond pdb=" C3' DC I 95 " pdb=" C2' DC I 95 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DA J 67 " pdb=" C2' DA J 67 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT I 26 " pdb=" C2' DT I 26 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 ... (remaining 15516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 22021 2.38 - 4.76: 398 4.76 - 7.14: 13 7.14 - 9.52: 2 9.52 - 11.90: 1 Bond angle restraints: 22435 Sorted by residual: angle pdb=" N3 DT J -53 " pdb=" C4 DT J -53 " pdb=" O4 DT J -53 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" O4' DG I 85 " pdb=" C4' DG I 85 " pdb=" C3' DG I 85 " ideal model delta sigma weight residual 106.00 103.44 2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT I 90 " pdb=" C4 DT I 90 " pdb=" O4 DT I 90 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT I 76 " pdb=" C4 DT I 76 " pdb=" O4 DT I 76 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT J 28 " pdb=" C4 DT J 28 " pdb=" O4 DT J 28 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 22430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 6918 35.91 - 71.82: 1652 71.82 - 107.73: 18 107.73 - 143.64: 2 143.64 - 179.55: 1 Dihedral angle restraints: 8591 sinusoidal: 5887 harmonic: 2704 Sorted by residual: dihedral pdb=" C4' DC I 20 " pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " pdb=" P DT I 21 " ideal model delta sinusoidal sigma weight residual 220.00 40.45 179.55 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J -93 " pdb=" C3' DG J -93 " pdb=" O3' DG J -93 " pdb=" P DG J -92 " ideal model delta sinusoidal sigma weight residual 220.00 81.86 138.14 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" C4' DA I 52 " pdb=" C3' DA I 52 " pdb=" O3' DA I 52 " pdb=" P DA I 53 " ideal model delta sinusoidal sigma weight residual 220.00 84.27 135.73 1 3.50e+01 8.16e-04 1.34e+01 ... (remaining 8588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1674 0.038 - 0.076: 552 0.076 - 0.114: 288 0.114 - 0.152: 33 0.152 - 0.190: 3 Chirality restraints: 2550 Sorted by residual: chirality pdb=" CA ILE B 26 " pdb=" N ILE B 26 " pdb=" C ILE B 26 " pdb=" CB ILE B 26 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" C3' DA I 74 " pdb=" C4' DA I 74 " pdb=" O3' DA I 74 " pdb=" C2' DA I 74 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.75e-01 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 5.83e-01 ... (remaining 2547 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 22 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.00e+01 pdb=" C LEU F 22 " -0.077 2.00e-02 2.50e+03 pdb=" O LEU F 22 " 0.030 2.00e-02 2.50e+03 pdb=" N ARG F 23 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.98e+00 pdb=" N PRO E 43 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 40 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C ARG A 40 " -0.031 2.00e-02 2.50e+03 pdb=" O ARG A 40 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 41 " 0.010 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 7 2.28 - 2.93: 5418 2.93 - 3.59: 21629 3.59 - 4.24: 41392 4.24 - 4.90: 59753 Nonbonded interactions: 128199 Sorted by model distance: nonbonded pdb=" O SER G 123 " pdb=" OP1 DG J -75 " model vdw 1.622 3.040 nonbonded pdb=" CD LYS G 124 " pdb=" O3' DA J -76 " model vdw 1.932 3.440 nonbonded pdb=" C SER G 123 " pdb=" OP1 DG J -75 " model vdw 2.057 3.270 nonbonded pdb=" NH1 ARG A 26 " pdb=" OP1 DA J 2 " model vdw 2.165 3.120 nonbonded pdb=" O HIS F 75 " pdb=" NH2 ARG H 89 " model vdw 2.238 3.120 ... (remaining 128194 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 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and resid 28 through 122) 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.350 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4950 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 0.119 15521 Z= 0.550 Angle : 0.747 11.899 22435 Z= 0.659 Chirality : 0.046 0.190 2550 Planarity : 0.004 0.050 1630 Dihedral : 27.409 179.553 6839 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.64 % Allowed : 14.27 % Favored : 85.10 % 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: -0.50 (0.25), residues: 911 helix: 0.14 (0.19), residues: 648 sheet: None (None), residues: 0 loop : -1.29 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 42 TYR 0.009 0.001 TYR G 57 PHE 0.011 0.001 PHE X 187 TRP 0.022 0.003 TRP X 277 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.55 (15521) covalent geometry : angle 0.74715 / 0.66 (22435) hydrogen bonds : bond 0.20972 / 13.80 ( 872) hydrogen bonds : angle 6.94673 / 5.00 ( 2216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 271 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.5202 (mt) cc_final: 0.4916 (mt) REVERT: F 19 ARG cc_start: 0.7804 (mtt-85) cc_final: 0.7445 (ptp-170) REVERT: F 20 LYS cc_start: 0.7435 (tppt) cc_final: 0.7205 (tppt) outliers start: 5 outliers final: 0 residues processed: 273 average time/residue: 0.1386 time to fit residues: 52.7515 Evaluate side-chains 135 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 40.0000 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN C 24 GLN C 112 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 76 GLN H 46 HIS H 81 ASN H 92 GLN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.086450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.061556 restraints weight = 98734.770| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 3.70 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 15521 Z= 0.236 Angle : 0.889 9.990 22435 Z= 0.484 Chirality : 0.055 0.266 2550 Planarity : 0.006 0.070 1630 Dihedral : 31.106 175.808 4949 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.46 % Allowed : 18.85 % Favored : 76.69 % 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: 0.79 (0.26), residues: 911 helix: 1.17 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -1.19 (0.34), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 116 TYR 0.024 0.003 TYR B 88 PHE 0.013 0.002 PHE D 67 TRP 0.007 0.001 TRP X 277 HIS 0.012 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.24 (15521) covalent geometry : angle 0.88859 / 0.48 (22435) hydrogen bonds : bond 0.06336 / 4.20 ( 872) hydrogen bonds : angle 3.77069 / 2.73 ( 2216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.7331 (t) cc_final: 0.7086 (t) REVERT: A 104 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8438 (t80) REVERT: B 88 TYR cc_start: 0.7927 (m-10) cc_final: 0.7706 (m-10) REVERT: C 59 THR cc_start: 0.9454 (m) cc_final: 0.9092 (p) REVERT: C 90 ASP cc_start: 0.7776 (t0) cc_final: 0.7521 (t0) REVERT: E 73 GLU cc_start: 0.8632 (tt0) cc_final: 0.8432 (tt0) REVERT: E 90 MET cc_start: 0.8793 (mmm) cc_final: 0.8586 (mmt) REVERT: F 19 ARG cc_start: 0.8071 (mtt-85) cc_final: 0.7544 (ptp-170) REVERT: F 96 THR cc_start: 0.9388 (m) cc_final: 0.9099 (p) REVERT: G 118 LYS cc_start: 0.6871 (mmpt) cc_final: 0.5804 (tptp) REVERT: H 90 GLU cc_start: 0.8931 (mp0) cc_final: 0.8181 (mp0) outliers start: 35 outliers final: 19 residues processed: 177 average time/residue: 0.1136 time to fit residues: 29.5535 Evaluate side-chains 139 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 86 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 30.0000 chunk 45 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 107 optimal weight: 30.0000 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 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 = 0.4172 r_free = 0.4172 target = 0.084688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.058979 restraints weight = 97924.904| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.68 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15521 Z= 0.167 Angle : 0.678 8.863 22435 Z= 0.400 Chirality : 0.045 0.284 2550 Planarity : 0.005 0.053 1630 Dihedral : 30.969 179.753 4949 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.04 % Allowed : 20.38 % Favored : 77.58 % 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: 1.30 (0.27), residues: 911 helix: 1.60 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.17 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 45 TYR 0.025 0.002 TYR H 37 PHE 0.029 0.002 PHE B 61 TRP 0.005 0.001 TRP X 277 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.17 (15521) covalent geometry : angle 0.67776 / 0.40 (22435) hydrogen bonds : bond 0.05566 / 3.69 ( 872) hydrogen bonds : angle 3.47624 / 2.51 ( 2216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7966 (ttmt) REVERT: B 88 TYR cc_start: 0.7993 (m-10) cc_final: 0.7666 (m-80) REVERT: B 91 LYS cc_start: 0.9200 (tttp) cc_final: 0.8990 (tttt) REVERT: C 90 ASP cc_start: 0.7952 (t0) cc_final: 0.7637 (t0) REVERT: E 90 MET cc_start: 0.8946 (mmm) cc_final: 0.8741 (mmt) REVERT: F 19 ARG cc_start: 0.8023 (mtt-85) cc_final: 0.7451 (ptp-170) REVERT: F 96 THR cc_start: 0.9372 (m) cc_final: 0.9057 (p) REVERT: G 118 LYS cc_start: 0.7195 (mmpt) cc_final: 0.6122 (tptp) REVERT: H 56 MET cc_start: 0.8074 (mmm) cc_final: 0.7641 (mmm) REVERT: H 73 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8119 (mm-30) REVERT: H 90 GLU cc_start: 0.8971 (mp0) cc_final: 0.8094 (mp0) outliers start: 16 outliers final: 7 residues processed: 143 average time/residue: 0.1168 time to fit residues: 25.3879 Evaluate side-chains 129 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 0.0030 chunk 19 optimal weight: 8.9990 chunk 91 optimal weight: 50.0000 chunk 82 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 22 optimal weight: 0.2980 chunk 65 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 overall best weight: 3.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 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 = 0.3919 r_free = 0.3919 target = 0.072762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.045795 restraints weight = 95526.451| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.61 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 15521 Z= 0.276 Angle : 0.888 14.867 22435 Z= 0.499 Chirality : 0.053 0.274 2550 Planarity : 0.006 0.053 1630 Dihedral : 31.335 176.838 4949 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.44 % Allowed : 19.49 % Favored : 77.07 % 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: 0.80 (0.27), residues: 911 helix: 1.30 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.55 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 116 TYR 0.013 0.002 TYR H 37 PHE 0.022 0.002 PHE D 67 TRP 0.005 0.001 TRP X 277 HIS 0.010 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.28 (15521) covalent geometry : angle 0.88843 / 0.50 (22435) hydrogen bonds : bond 0.07709 / 5.11 ( 872) hydrogen bonds : angle 3.81394 / 2.80 ( 2216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8374 (ttmt) REVERT: A 96 SER cc_start: 0.9373 (OUTLIER) cc_final: 0.8987 (p) REVERT: A 97 GLU cc_start: 0.7866 (tp30) cc_final: 0.7654 (tp30) REVERT: A 133 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: B 88 TYR cc_start: 0.8544 (m-10) cc_final: 0.8238 (m-10) REVERT: C 90 ASP cc_start: 0.8434 (t0) cc_final: 0.8147 (t0) REVERT: F 19 ARG cc_start: 0.7903 (mtt-85) cc_final: 0.7241 (ptp-170) REVERT: F 63 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8376 (mt-10) REVERT: F 79 LYS cc_start: 0.8543 (mppt) cc_final: 0.7936 (mppt) REVERT: G 64 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8166 (tm-30) REVERT: G 92 GLU cc_start: 0.8927 (mp0) cc_final: 0.8617 (mp0) REVERT: H 56 MET cc_start: 0.8636 (mmm) cc_final: 0.8366 (mmm) REVERT: H 90 GLU cc_start: 0.8944 (mp0) cc_final: 0.8111 (mp0) outliers start: 27 outliers final: 12 residues processed: 150 average time/residue: 0.1296 time to fit residues: 28.1966 Evaluate side-chains 126 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 36 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 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 = 0.3919 r_free = 0.3919 target = 0.073106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.046218 restraints weight = 93999.226| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.58 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.6948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15521 Z= 0.159 Angle : 0.666 8.241 22435 Z= 0.396 Chirality : 0.044 0.235 2550 Planarity : 0.005 0.035 1630 Dihedral : 31.147 179.437 4949 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.68 % Allowed : 21.53 % Favored : 75.80 % 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: 1.37 (0.27), residues: 911 helix: 1.82 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -1.59 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.017 0.001 TYR H 37 PHE 0.010 0.001 PHE D 67 TRP 0.005 0.001 TRP X 277 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 (15521) covalent geometry : angle 0.66569 / 0.40 (22435) hydrogen bonds : bond 0.04777 / 3.19 ( 872) hydrogen bonds : angle 3.35333 / 2.43 ( 2216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.9479 (OUTLIER) cc_final: 0.9049 (p) REVERT: A 97 GLU cc_start: 0.8113 (tp30) cc_final: 0.7746 (tp30) REVERT: B 88 TYR cc_start: 0.8508 (m-10) cc_final: 0.8254 (m-10) REVERT: C 90 ASP cc_start: 0.8363 (t0) cc_final: 0.8016 (t0) REVERT: E 56 LYS cc_start: 0.9261 (ptmm) cc_final: 0.9039 (ttpp) REVERT: E 120 MET cc_start: 0.6788 (mmt) cc_final: 0.6082 (mtt) REVERT: F 19 ARG cc_start: 0.7848 (mtt-85) cc_final: 0.7246 (ptp-170) REVERT: F 24 ASP cc_start: 0.8712 (t0) cc_final: 0.8449 (t0) REVERT: F 79 LYS cc_start: 0.8702 (mppt) cc_final: 0.8015 (mppt) REVERT: G 61 GLU cc_start: 0.8866 (tp30) cc_final: 0.8627 (tp30) REVERT: G 64 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8001 (tm-30) REVERT: G 90 ASP cc_start: 0.8345 (t70) cc_final: 0.7992 (t70) REVERT: G 92 GLU cc_start: 0.8506 (mp0) cc_final: 0.8065 (mp0) REVERT: H 56 MET cc_start: 0.8739 (mmm) cc_final: 0.8500 (mmm) REVERT: H 90 GLU cc_start: 0.9026 (mp0) cc_final: 0.8171 (mp0) outliers start: 21 outliers final: 10 residues processed: 141 average time/residue: 0.1314 time to fit residues: 27.0446 Evaluate side-chains 119 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 27 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 40.0000 chunk 78 optimal weight: 30.0000 chunk 63 optimal weight: 0.0050 overall best weight: 2.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** 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 = 0.3825 r_free = 0.3825 target = 0.068805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.042429 restraints weight = 94158.443| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.93 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.8250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 15521 Z= 0.215 Angle : 0.760 9.353 22435 Z= 0.430 Chirality : 0.046 0.279 2550 Planarity : 0.005 0.039 1630 Dihedral : 31.269 179.865 4949 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.04 % Allowed : 21.53 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.27), residues: 911 helix: 1.85 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -1.70 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 42 TYR 0.011 0.001 TYR H 37 PHE 0.021 0.002 PHE X 194 TRP 0.006 0.001 TRP X 277 HIS 0.011 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.22 (15521) covalent geometry : angle 0.76009 / 0.43 (22435) hydrogen bonds : bond 0.06199 / 4.10 ( 872) hydrogen bonds : angle 3.49030 / 2.51 ( 2216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.7765 (pp30) cc_final: 0.7504 (pp30) REVERT: A 79 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8192 (mttt) REVERT: A 96 SER cc_start: 0.9532 (OUTLIER) cc_final: 0.9170 (p) REVERT: B 88 TYR cc_start: 0.8709 (m-10) cc_final: 0.8311 (m-10) REVERT: C 90 ASP cc_start: 0.8589 (t0) cc_final: 0.8048 (t70) REVERT: E 56 LYS cc_start: 0.9342 (ptmm) cc_final: 0.9120 (ttpp) REVERT: E 59 GLU cc_start: 0.8067 (pm20) cc_final: 0.7678 (pm20) REVERT: E 120 MET cc_start: 0.7486 (mmt) cc_final: 0.6084 (mtt) REVERT: E 123 ASP cc_start: 0.8605 (m-30) cc_final: 0.8182 (m-30) REVERT: F 19 ARG cc_start: 0.7780 (mtt-85) cc_final: 0.7541 (mtm180) REVERT: F 24 ASP cc_start: 0.8693 (t0) cc_final: 0.8456 (t0) REVERT: F 63 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8370 (mt-10) REVERT: F 79 LYS cc_start: 0.8712 (mppt) cc_final: 0.7943 (mppt) REVERT: G 64 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7908 (tm-30) REVERT: G 90 ASP cc_start: 0.8592 (t70) cc_final: 0.8316 (t70) REVERT: G 92 GLU cc_start: 0.8805 (mp0) cc_final: 0.8227 (mp0) REVERT: H 90 GLU cc_start: 0.9068 (mp0) cc_final: 0.8218 (mp0) outliers start: 16 outliers final: 8 residues processed: 122 average time/residue: 0.1376 time to fit residues: 24.0439 Evaluate side-chains 105 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 116 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 40.0000 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 114 optimal weight: 0.0470 chunk 99 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 40.0000 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** 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 = 0.3833 r_free = 0.3833 target = 0.069247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.041665 restraints weight = 94524.231| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.56 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.8510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15521 Z= 0.153 Angle : 0.649 7.689 22435 Z= 0.386 Chirality : 0.043 0.238 2550 Planarity : 0.004 0.038 1630 Dihedral : 31.134 179.683 4949 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.04 % Allowed : 21.91 % Favored : 76.05 % 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: 1.74 (0.28), residues: 911 helix: 2.15 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -1.70 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 40 TYR 0.014 0.001 TYR H 37 PHE 0.009 0.001 PHE E 67 TRP 0.005 0.001 TRP X 277 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (15521) covalent geometry : angle 0.64927 / 0.39 (22435) hydrogen bonds : bond 0.04365 / 2.91 ( 872) hydrogen bonds : angle 3.22884 / 2.33 ( 2216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.9576 (OUTLIER) cc_final: 0.9194 (p) REVERT: B 88 TYR cc_start: 0.8712 (m-10) cc_final: 0.8329 (m-10) REVERT: C 90 ASP cc_start: 0.8455 (t0) cc_final: 0.7915 (t70) REVERT: E 56 LYS cc_start: 0.9304 (ptmm) cc_final: 0.9080 (ttpp) REVERT: E 59 GLU cc_start: 0.7946 (pm20) cc_final: 0.7628 (pm20) REVERT: E 120 MET cc_start: 0.7286 (mmt) cc_final: 0.5958 (mtt) REVERT: E 123 ASP cc_start: 0.8542 (m-30) cc_final: 0.8142 (m-30) REVERT: F 19 ARG cc_start: 0.7761 (mtt-85) cc_final: 0.7548 (mtm180) REVERT: F 24 ASP cc_start: 0.8743 (t0) cc_final: 0.8494 (t0) REVERT: F 63 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8184 (mt-10) REVERT: G 64 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7870 (tm-30) REVERT: G 90 ASP cc_start: 0.8635 (t70) cc_final: 0.8115 (t70) REVERT: G 92 GLU cc_start: 0.8670 (mp0) cc_final: 0.8132 (mp0) REVERT: H 90 GLU cc_start: 0.9073 (mp0) cc_final: 0.8310 (mp0) outliers start: 16 outliers final: 7 residues processed: 124 average time/residue: 0.1285 time to fit residues: 23.4118 Evaluate side-chains 108 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 126 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 50 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 75 optimal weight: 40.0000 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 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 ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 GLN ** 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 = 0.3733 r_free = 0.3733 target = 0.064765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.038822 restraints weight = 92645.233| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.83 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.9721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 15521 Z= 0.247 Angle : 0.775 12.197 22435 Z= 0.444 Chirality : 0.046 0.295 2550 Planarity : 0.005 0.074 1630 Dihedral : 31.363 178.811 4949 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.17 % Allowed : 22.04 % Favored : 75.80 % 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 (0.28), residues: 911 helix: 1.92 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.73 (0.33), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 23 TYR 0.015 0.001 TYR H 37 PHE 0.009 0.002 PHE D 67 TRP 0.006 0.002 TRP X 277 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.25 (15521) covalent geometry : angle 0.77546 / 0.44 (22435) hydrogen bonds : bond 0.06778 / 4.47 ( 872) hydrogen bonds : angle 3.56766 / 2.57 ( 2216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.9565 (OUTLIER) cc_final: 0.9328 (p) REVERT: A 120 MET cc_start: 0.8767 (mtt) cc_final: 0.8506 (mtt) REVERT: B 84 MET cc_start: 0.9234 (mmm) cc_final: 0.8650 (mmm) REVERT: B 88 TYR cc_start: 0.8878 (m-10) cc_final: 0.8380 (m-10) REVERT: C 90 ASP cc_start: 0.8719 (t0) cc_final: 0.8248 (t0) REVERT: E 120 MET cc_start: 0.7784 (mmt) cc_final: 0.6611 (mtt) REVERT: E 123 ASP cc_start: 0.8847 (m-30) cc_final: 0.8463 (m-30) REVERT: F 63 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8304 (mt-10) REVERT: F 79 LYS cc_start: 0.9212 (mppt) cc_final: 0.8639 (mppt) REVERT: G 64 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7837 (tm-30) REVERT: G 90 ASP cc_start: 0.8841 (t70) cc_final: 0.8311 (t0) REVERT: G 92 GLU cc_start: 0.8799 (mp0) cc_final: 0.8349 (mp0) REVERT: H 90 GLU cc_start: 0.9059 (mp0) cc_final: 0.8073 (mp0) outliers start: 17 outliers final: 14 residues processed: 118 average time/residue: 0.1322 time to fit residues: 22.6917 Evaluate side-chains 108 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain G residue 116 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 85 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 121 optimal weight: 40.0000 chunk 58 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 30.0000 chunk 9 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 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 = 0.3735 r_free = 0.3735 target = 0.065234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.038064 restraints weight = 90997.118| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.73 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 1.0006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15521 Z= 0.181 Angle : 0.675 7.650 22435 Z= 0.400 Chirality : 0.043 0.264 2550 Planarity : 0.004 0.038 1630 Dihedral : 31.294 179.464 4949 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.04 % Allowed : 21.66 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.28), residues: 911 helix: 2.04 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -1.70 (0.33), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 23 TYR 0.016 0.001 TYR H 37 PHE 0.010 0.001 PHE E 78 TRP 0.007 0.002 TRP X 207 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.18 (15521) covalent geometry : angle 0.67544 / 0.40 (22435) hydrogen bonds : bond 0.04586 / 3.05 ( 872) hydrogen bonds : angle 3.31366 / 2.39 ( 2216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9427 (pm20) cc_final: 0.9158 (pm20) REVERT: A 96 SER cc_start: 0.9565 (OUTLIER) cc_final: 0.9324 (p) REVERT: B 74 GLU cc_start: 0.8637 (mp0) cc_final: 0.8167 (mp0) REVERT: B 88 TYR cc_start: 0.8885 (m-10) cc_final: 0.8404 (m-10) REVERT: C 90 ASP cc_start: 0.8632 (t0) cc_final: 0.8202 (t70) REVERT: E 81 ASP cc_start: 0.8578 (t0) cc_final: 0.8281 (t0) REVERT: E 97 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8542 (mm-30) REVERT: E 120 MET cc_start: 0.7735 (mmt) cc_final: 0.6583 (mtt) REVERT: E 123 ASP cc_start: 0.8751 (m-30) cc_final: 0.8359 (m-30) REVERT: F 79 LYS cc_start: 0.9200 (mppt) cc_final: 0.8757 (mmmm) REVERT: G 64 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7805 (tm-30) REVERT: H 90 GLU cc_start: 0.9058 (mp0) cc_final: 0.8042 (mp0) outliers start: 16 outliers final: 9 residues processed: 113 average time/residue: 0.1191 time to fit residues: 19.9352 Evaluate side-chains 109 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain G residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 68 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 30.0000 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 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 = 0.3699 r_free = 0.3699 target = 0.063726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.035965 restraints weight = 94139.197| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.48 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 1.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 15521 Z= 0.221 Angle : 0.753 11.561 22435 Z= 0.429 Chirality : 0.045 0.278 2550 Planarity : 0.005 0.089 1630 Dihedral : 31.394 178.099 4949 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.66 % Allowed : 22.55 % Favored : 75.80 % 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: 1.51 (0.28), residues: 911 helix: 1.95 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.69 (0.33), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG X 240 TYR 0.011 0.001 TYR H 37 PHE 0.013 0.002 PHE X 194 TRP 0.007 0.002 TRP X 207 HIS 0.009 0.002 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.22 (15521) covalent geometry : angle 0.75318 / 0.43 (22435) hydrogen bonds : bond 0.05920 / 3.89 ( 872) hydrogen bonds : angle 3.42435 / 2.47 ( 2216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9377 (pm20) cc_final: 0.9126 (pm20) REVERT: A 87 SER cc_start: 0.9396 (t) cc_final: 0.9136 (t) REVERT: B 88 TYR cc_start: 0.8948 (m-10) cc_final: 0.8517 (m-10) REVERT: C 90 ASP cc_start: 0.8780 (t0) cc_final: 0.8373 (t0) REVERT: E 81 ASP cc_start: 0.8657 (t0) cc_final: 0.8404 (t0) REVERT: F 63 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8374 (mt-10) REVERT: F 79 LYS cc_start: 0.9218 (mppt) cc_final: 0.8808 (mmmm) REVERT: G 64 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7808 (tm-30) REVERT: G 92 GLU cc_start: 0.8940 (mp0) cc_final: 0.8700 (mp0) REVERT: H 90 GLU cc_start: 0.9052 (mp0) cc_final: 0.8122 (mp0) outliers start: 13 outliers final: 10 residues processed: 108 average time/residue: 0.1204 time to fit residues: 19.3534 Evaluate side-chains 107 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain G residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 40.0000 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN F 75 HIS ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 283 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 = 0.3705 r_free = 0.3705 target = 0.064125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.035953 restraints weight = 92572.107| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.37 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 1.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15521 Z= 0.164 Angle : 0.678 10.672 22435 Z= 0.395 Chirality : 0.043 0.270 2550 Planarity : 0.004 0.055 1630 Dihedral : 31.333 178.839 4949 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.53 % Allowed : 23.31 % Favored : 75.16 % 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: 1.71 (0.28), residues: 911 helix: 2.11 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.68 (0.33), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.013 0.001 TYR H 37 PHE 0.013 0.001 PHE A 67 TRP 0.009 0.002 TRP X 207 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (15521) covalent geometry : angle 0.67769 / 0.40 (22435) hydrogen bonds : bond 0.04280 / 2.83 ( 872) hydrogen bonds : angle 3.24932 / 2.34 ( 2216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3309.03 seconds wall clock time: 57 minutes 26.13 seconds (3446.13 seconds total)