Starting phenix.real_space_refine on Thu Aug 6 07:05:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8g_29850/08_2026/8g8g_29850.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8g_29850/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g8g_29850/08_2026/8g8g_29850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8g_29850/08_2026/8g8g_29850.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g8g_29850/08_2026/8g8g_29850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8g_29850/08_2026/8g8g_29850.map" } 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-2.2rc3-6140/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: 2.88, per 1000 atoms: 0.20 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: 0.86 Conformation dependent library (CDL) restraints added in 413.1 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: 2.04 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: 3.22 Time building geometry restraints manager: 1.26 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: 22018 2.38 - 4.76: 401 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: 1.180 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.620 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.560 ------------------------------------------------------------------------------- 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 : 0.753 11.899 22435 Z= 0.663 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 0.75299 / 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 : 0.363 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: 0.4901 (mt) REVERT: F 19 ARG cc_start: 0.7804 (mtt-85) cc_final: 0.7443 (ptp-170) REVERT: F 20 LYS cc_start: 0.7435 (tppt) cc_final: 0.7201 (tppt) outliers start: 5 outliers final: 0 residues processed: 273 average time/residue: 0.1300 time to fit residues: 49.7969 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 : 0.372 ------------------------------------------------------------------------------- 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: 9.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.085603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.060526 restraints weight = 97485.462| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.64 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 15521 Z= 0.248 Angle : 0.920 9.763 22435 Z= 0.500 Chirality : 0.055 0.271 2550 Planarity : 0.007 0.061 1630 Dihedral : 31.054 177.084 4949 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.59 % Allowed : 18.60 % Favored : 76.82 % 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: 0.77 (0.26), residues: 911 helix: 1.16 (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 0.015 0.001 ARG A 116 TYR 0.028 0.003 TYR A 54 PHE 0.014 0.002 PHE D 67 TRP 0.007 0.001 TRP X 277 HIS 0.014 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.25 (15521) covalent geometry : angle 0.91989 / 0.50 (22435) hydrogen bonds : bond 0.06475 / 4.31 ( 872) hydrogen bonds : angle 3.83708 / 2.78 ( 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 193 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.7444 (t) cc_final: 0.7212 (t) REVERT: A 104 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8549 (t80) REVERT: B 88 TYR cc_start: 0.7958 (m-10) cc_final: 0.7751 (m-10) REVERT: C 90 ASP cc_start: 0.7836 (t0) cc_final: 0.7604 (t0) REVERT: E 73 GLU cc_start: 0.8674 (tt0) cc_final: 0.8473 (tt0) REVERT: E 90 MET cc_start: 0.8848 (mmm) cc_final: 0.8618 (mmt) REVERT: F 19 ARG cc_start: 0.8072 (mtt-85) cc_final: 0.7527 (ptp-170) REVERT: F 96 THR cc_start: 0.9389 (m) cc_final: 0.9073 (p) REVERT: G 118 LYS cc_start: 0.7077 (mmpt) cc_final: 0.5963 (tptp) REVERT: H 90 GLU cc_start: 0.8914 (mp0) cc_final: 0.8155 (mp0) outliers start: 36 outliers final: 19 residues processed: 179 average time/residue: 0.0989 time to fit residues: 26.1764 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 : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL 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: 0.9990 chunk 80 optimal weight: 40.0000 chunk 45 optimal weight: 0.8980 chunk 119 optimal weight: 0.0070 chunk 117 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 107 optimal weight: 30.0000 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.085205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.059983 restraints weight = 99777.295| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.58 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15521 Z= 0.156 Angle : 0.681 9.336 22435 Z= 0.398 Chirality : 0.045 0.256 2550 Planarity : 0.005 0.043 1630 Dihedral : 30.882 179.848 4949 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.29 % Allowed : 20.89 % Favored : 76.82 % 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: 1.47 (0.28), residues: 911 helix: 1.75 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.16 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 116 TYR 0.027 0.002 TYR H 37 PHE 0.034 0.002 PHE B 61 TRP 0.005 0.001 TRP X 277 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.16 (15521) covalent geometry : angle 0.68142 / 0.40 (22435) hydrogen bonds : bond 0.05051 / 3.36 ( 872) hydrogen bonds : angle 3.44288 / 2.49 ( 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 154 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7988 (ttmt) REVERT: B 88 TYR cc_start: 0.7920 (m-10) cc_final: 0.7595 (m-80) REVERT: C 90 ASP cc_start: 0.7881 (t0) cc_final: 0.7591 (t0) REVERT: E 90 MET cc_start: 0.8812 (mmm) cc_final: 0.8605 (mmt) REVERT: F 19 ARG cc_start: 0.7992 (mtt-85) cc_final: 0.7443 (ptp-170) REVERT: F 96 THR cc_start: 0.9351 (m) cc_final: 0.9098 (p) REVERT: G 63 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8901 (mm) REVERT: G 118 LYS cc_start: 0.7084 (mmpt) cc_final: 0.6003 (tptp) REVERT: H 90 GLU cc_start: 0.8865 (mp0) cc_final: 0.8151 (mp0) outliers start: 18 outliers final: 10 residues processed: 149 average time/residue: 0.0941 time to fit residues: 21.4333 Evaluate side-chains 132 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR 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 E residue 56 LYS Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain X residue 260 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 0.0770 chunk 19 optimal weight: 9.9990 chunk 91 optimal weight: 50.0000 chunk 82 optimal weight: 30.0000 chunk 4 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 overall best weight: 4.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.073039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.046872 restraints weight = 96016.307| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.99 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.6382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 15521 Z= 0.282 Angle : 0.897 18.112 22435 Z= 0.496 Chirality : 0.052 0.317 2550 Planarity : 0.006 0.041 1630 Dihedral : 31.151 179.413 4949 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.82 % Allowed : 19.87 % 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: 0.85 (0.27), residues: 911 helix: 1.31 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -1.46 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 116 TYR 0.022 0.002 TYR H 37 PHE 0.017 0.002 PHE D 67 TRP 0.004 0.001 TRP X 277 HIS 0.011 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.28 (15521) covalent geometry : angle 0.89745 / 0.50 (22435) hydrogen bonds : bond 0.07910 / 5.28 ( 872) hydrogen bonds : angle 3.90644 / 2.85 ( 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 154 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8177 (mt-10) REVERT: A 60 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8274 (mm) REVERT: A 79 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8394 (ttmt) REVERT: B 88 TYR cc_start: 0.8541 (m-10) cc_final: 0.8254 (m-10) REVERT: C 36 LYS cc_start: 0.8920 (mmtm) cc_final: 0.8625 (mmtm) REVERT: C 90 ASP cc_start: 0.8518 (t0) cc_final: 0.8232 (t0) REVERT: F 19 ARG cc_start: 0.7930 (mtt-85) cc_final: 0.7329 (ptp-170) REVERT: G 64 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8299 (tm-30) REVERT: G 92 GLU cc_start: 0.8874 (mp0) cc_final: 0.8559 (mp0) REVERT: H 90 GLU cc_start: 0.8958 (mp0) cc_final: 0.8121 (mp0) outliers start: 30 outliers final: 16 residues processed: 145 average time/residue: 0.1028 time to fit residues: 22.5207 Evaluate side-chains 127 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 89 VAL 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 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 50 ILE 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 63 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN ** E 113 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.074139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.046944 restraints weight = 95214.238| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.71 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15521 Z= 0.149 Angle : 0.680 9.111 22435 Z= 0.398 Chirality : 0.044 0.257 2550 Planarity : 0.004 0.047 1630 Dihedral : 31.044 179.610 4949 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.29 % Allowed : 21.66 % 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: 1.53 (0.28), residues: 911 helix: 1.89 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -1.42 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.021 0.001 TYR H 37 PHE 0.013 0.001 PHE X 194 TRP 0.005 0.001 TRP X 277 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 (15521) covalent geometry : angle 0.67985 / 0.40 (22435) hydrogen bonds : bond 0.04698 / 3.14 ( 872) hydrogen bonds : angle 3.39212 / 2.46 ( 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 148 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7972 (mt-10) REVERT: A 79 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8413 (ttmt) REVERT: B 88 TYR cc_start: 0.8471 (m-10) cc_final: 0.8227 (m-10) REVERT: C 90 ASP cc_start: 0.8339 (t0) cc_final: 0.7976 (t0) REVERT: F 19 ARG cc_start: 0.7933 (mtt-85) cc_final: 0.7345 (ptp-170) REVERT: F 24 ASP cc_start: 0.8744 (t0) cc_final: 0.8490 (t0) REVERT: F 53 GLU cc_start: 0.8743 (tp30) cc_final: 0.8508 (tp30) REVERT: F 63 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8191 (mt-10) REVERT: G 64 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8063 (tm-30) REVERT: G 92 GLU cc_start: 0.8589 (mp0) cc_final: 0.8303 (mp0) REVERT: H 90 GLU cc_start: 0.8958 (mp0) cc_final: 0.8133 (mp0) outliers start: 18 outliers final: 8 residues processed: 144 average time/residue: 0.1029 time to fit residues: 22.1066 Evaluate side-chains 118 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE 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 E residue 71 VAL Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 27 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 chunk 50 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 94 optimal weight: 40.0000 chunk 78 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 196 ASN ** 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 = 0.3780 r_free = 0.3780 target = 0.066556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.038986 restraints weight = 95751.006| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.58 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.8886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 15521 Z= 0.277 Angle : 0.871 15.850 22435 Z= 0.478 Chirality : 0.051 0.295 2550 Planarity : 0.006 0.051 1630 Dihedral : 31.282 178.695 4949 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.18 % Allowed : 22.29 % Favored : 74.52 % 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: 0.98 (0.27), residues: 911 helix: 1.45 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -1.55 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 131 TYR 0.015 0.002 TYR H 39 PHE 0.012 0.002 PHE D 67 TRP 0.006 0.002 TRP X 277 HIS 0.010 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.28 (15521) covalent geometry : angle 0.87053 / 0.48 (22435) hydrogen bonds : bond 0.08197 / 5.42 ( 872) hydrogen bonds : angle 3.85115 / 2.82 ( 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 139 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8817 (m-10) cc_final: 0.8383 (m-10) REVERT: C 90 ASP cc_start: 0.8749 (t0) cc_final: 0.8292 (t0) REVERT: E 59 GLU cc_start: 0.8390 (pm20) cc_final: 0.8077 (pm20) REVERT: E 120 MET cc_start: 0.7952 (mmt) cc_final: 0.6549 (mtt) REVERT: E 123 ASP cc_start: 0.8706 (m-30) cc_final: 0.8102 (m-30) REVERT: F 24 ASP cc_start: 0.8641 (t0) cc_final: 0.8401 (t0) REVERT: F 63 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8274 (mt-10) REVERT: G 64 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8105 (tm-30) REVERT: G 73 ASN cc_start: 0.8276 (m-40) cc_final: 0.7889 (m-40) REVERT: G 92 GLU cc_start: 0.8867 (mp0) cc_final: 0.8467 (mp0) REVERT: H 90 GLU cc_start: 0.9079 (mp0) cc_final: 0.8141 (mp0) REVERT: X 200 LEU cc_start: -0.5008 (OUTLIER) cc_final: -0.5221 (mp) outliers start: 25 outliers final: 11 residues processed: 135 average time/residue: 0.1152 time to fit residues: 22.9238 Evaluate side-chains 109 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 87 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 C residue 59 THR Chi-restraints excluded: chain D residue 33 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 Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain X residue 200 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 50.0000 chunk 39 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 99 optimal weight: 30.0000 chunk 52 optimal weight: 7.9990 chunk 108 optimal weight: 40.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.066455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.038921 restraints weight = 91954.297| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.32 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.9178 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= 0.171 Angle : 0.693 8.106 22435 Z= 0.405 Chirality : 0.044 0.253 2550 Planarity : 0.005 0.051 1630 Dihedral : 31.192 179.398 4949 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.42 % Allowed : 23.18 % Favored : 74.39 % 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: 2.00 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.59 (0.33), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 40 TYR 0.014 0.001 TYR H 37 PHE 0.012 0.001 PHE X 194 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 0.00309 / 0.17 (15521) covalent geometry : angle 0.69293 / 0.40 (22435) hydrogen bonds : bond 0.04750 / 3.17 ( 872) hydrogen bonds : angle 3.34400 / 2.43 ( 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 130 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8952 (mm-30) REVERT: B 88 TYR cc_start: 0.8826 (m-10) cc_final: 0.8438 (m-10) REVERT: C 90 ASP cc_start: 0.8632 (t0) cc_final: 0.8153 (t70) REVERT: E 59 GLU cc_start: 0.8345 (pm20) cc_final: 0.8039 (pm20) REVERT: E 120 MET cc_start: 0.7735 (mmt) cc_final: 0.6180 (mtt) REVERT: E 123 ASP cc_start: 0.8690 (m-30) cc_final: 0.8053 (m-30) REVERT: F 24 ASP cc_start: 0.8710 (t0) cc_final: 0.8450 (t0) REVERT: F 63 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8385 (mt-10) REVERT: G 64 GLU cc_start: 0.8473 (tm-30) cc_final: 0.7890 (tm-30) REVERT: G 92 GLU cc_start: 0.8790 (mp0) cc_final: 0.8376 (mp0) REVERT: H 90 GLU cc_start: 0.9055 (mp0) cc_final: 0.8086 (mp0) outliers start: 19 outliers final: 9 residues processed: 126 average time/residue: 0.1136 time to fit residues: 20.8604 Evaluate side-chains 109 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 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 C residue 102 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 75 optimal weight: 40.0000 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 ** 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 = 0.3766 r_free = 0.3766 target = 0.066122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.038768 restraints weight = 91898.351| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.41 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.9589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15521 Z= 0.158 Angle : 0.686 8.819 22435 Z= 0.398 Chirality : 0.043 0.245 2550 Planarity : 0.005 0.061 1630 Dihedral : 31.111 178.162 4949 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.29 % Allowed : 22.55 % 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: 1.83 (0.28), residues: 911 helix: 2.15 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -1.48 (0.33), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 40 TYR 0.010 0.001 TYR H 37 PHE 0.013 0.001 PHE A 67 TRP 0.008 0.002 TRP X 207 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (15521) covalent geometry : angle 0.68643 / 0.40 (22435) hydrogen bonds : bond 0.04573 / 3.01 ( 872) hydrogen bonds : angle 3.22377 / 2.32 ( 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 125 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8834 (m-10) cc_final: 0.8408 (m-10) REVERT: B 93 GLN cc_start: 0.9021 (tt0) cc_final: 0.8765 (tt0) REVERT: C 90 ASP cc_start: 0.8575 (t0) cc_final: 0.8126 (t0) REVERT: E 59 GLU cc_start: 0.8294 (pm20) cc_final: 0.7992 (pm20) REVERT: E 123 ASP cc_start: 0.8680 (m-30) cc_final: 0.8106 (m-30) REVERT: F 63 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8297 (mt-10) REVERT: G 64 GLU cc_start: 0.8446 (tm-30) cc_final: 0.7922 (tm-30) REVERT: H 90 GLU cc_start: 0.9071 (mp0) cc_final: 0.8248 (mp0) outliers start: 18 outliers final: 11 residues processed: 117 average time/residue: 0.1133 time to fit residues: 19.5048 Evaluate side-chains 112 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 87 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 109 SER 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: 5.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 104 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 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 = 0.3768 r_free = 0.3768 target = 0.066409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.038236 restraints weight = 92350.410| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.40 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.9827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15521 Z= 0.149 Angle : 0.664 8.925 22435 Z= 0.390 Chirality : 0.042 0.251 2550 Planarity : 0.005 0.050 1630 Dihedral : 31.006 178.296 4949 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.02 % Allowed : 23.31 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.28), residues: 911 helix: 2.19 (0.20), residues: 665 sheet: None (None), residues: 0 loop : -1.56 (0.33), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 40 TYR 0.012 0.001 TYR H 37 PHE 0.011 0.001 PHE X 194 TRP 0.008 0.002 TRP X 207 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.15 (15521) covalent geometry : angle 0.66383 / 0.39 (22435) hydrogen bonds : bond 0.04243 / 2.81 ( 872) hydrogen bonds : angle 3.15123 / 2.28 ( 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 118 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8830 (m-10) cc_final: 0.8423 (m-10) REVERT: B 93 GLN cc_start: 0.9013 (tt0) cc_final: 0.8778 (tt0) REVERT: C 38 ASN cc_start: 0.8029 (t0) cc_final: 0.7773 (t0) REVERT: C 90 ASP cc_start: 0.8531 (t0) cc_final: 0.8121 (t0) REVERT: E 59 GLU cc_start: 0.8196 (pm20) cc_final: 0.7904 (pm20) REVERT: E 81 ASP cc_start: 0.8630 (t0) cc_final: 0.8113 (p0) REVERT: E 123 ASP cc_start: 0.8717 (m-30) cc_final: 0.8248 (m-30) REVERT: F 63 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8270 (mt-10) REVERT: G 64 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7780 (tm-30) REVERT: G 92 GLU cc_start: 0.9043 (mp0) cc_final: 0.8373 (mp0) REVERT: H 48 ASP cc_start: 0.9313 (p0) cc_final: 0.9112 (p0) REVERT: H 90 GLU cc_start: 0.9035 (mp0) cc_final: 0.8258 (mp0) outliers start: 8 outliers final: 6 residues processed: 115 average time/residue: 0.1063 time to fit residues: 18.3648 Evaluate side-chains 107 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 68 optimal weight: 0.0040 chunk 119 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 90 optimal weight: 30.0000 chunk 64 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 96 optimal weight: 30.0000 chunk 20 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 overall best weight: 2.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS H 81 ASN ** 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 = 0.3724 r_free = 0.3724 target = 0.064392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.036955 restraints weight = 92524.239| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.43 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 1.0387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 15521 Z= 0.190 Angle : 0.721 12.107 22435 Z= 0.412 Chirality : 0.043 0.244 2550 Planarity : 0.005 0.104 1630 Dihedral : 31.090 177.592 4949 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.15 % Allowed : 24.33 % Favored : 74.52 % 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: 1.90 (0.28), residues: 911 helix: 2.21 (0.20), residues: 665 sheet: None (None), residues: 0 loop : -1.51 (0.33), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 30 TYR 0.012 0.001 TYR H 37 PHE 0.011 0.001 PHE A 67 TRP 0.007 0.002 TRP X 277 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 (15521) covalent geometry : angle 0.72125 / 0.41 (22435) hydrogen bonds : bond 0.05153 / 3.37 ( 872) hydrogen bonds : angle 3.26914 / 2.35 ( 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 119 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8878 (m-10) cc_final: 0.8436 (m-10) REVERT: B 93 GLN cc_start: 0.9024 (tt0) cc_final: 0.8784 (tt0) REVERT: C 38 ASN cc_start: 0.8105 (t0) cc_final: 0.7821 (t0) REVERT: C 90 ASP cc_start: 0.8708 (t0) cc_final: 0.8278 (t0) REVERT: D 98 LEU cc_start: 0.9093 (mt) cc_final: 0.8877 (mt) REVERT: E 59 GLU cc_start: 0.8284 (pm20) cc_final: 0.7989 (pm20) REVERT: E 123 ASP cc_start: 0.8697 (m-30) cc_final: 0.8255 (m-30) REVERT: F 63 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8311 (mt-10) REVERT: G 64 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7809 (tm-30) REVERT: H 90 GLU cc_start: 0.9040 (mp0) cc_final: 0.8035 (mp0) outliers start: 9 outliers final: 8 residues processed: 115 average time/residue: 0.1168 time to fit residues: 19.8023 Evaluate side-chains 114 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain G residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 40.0000 chunk 56 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** 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 = 0.3697 r_free = 0.3697 target = 0.063687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.035837 restraints weight = 92703.692| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.94 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 1.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15521 Z= 0.193 Angle : 0.712 11.808 22435 Z= 0.412 Chirality : 0.044 0.246 2550 Planarity : 0.005 0.043 1630 Dihedral : 31.196 177.812 4949 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.53 % Allowed : 23.82 % Favored : 74.65 % 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: 1.64 (0.27), residues: 911 helix: 2.00 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.49 (0.33), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 69 TYR 0.011 0.001 TYR H 37 PHE 0.015 0.002 PHE H 67 TRP 0.008 0.002 TRP X 207 HIS 0.007 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.19 (15521) covalent geometry : angle 0.71224 / 0.41 (22435) hydrogen bonds : bond 0.04699 / 3.10 ( 872) hydrogen bonds : angle 3.24334 / 2.36 ( 2216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2985.17 seconds wall clock time: 51 minutes 45.32 seconds (3105.32 seconds total)