Starting phenix.real_space_refine on Wed Aug 5 19:48:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k40_62036/08_2026/9k40_62036.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k40_62036/08_2026/9k40_62036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k40_62036/08_2026/9k40_62036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k40_62036/08_2026/9k40_62036.map" model { file = "/net/cci-nas-00/data/ceres_data/9k40_62036/08_2026/9k40_62036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k40_62036/08_2026/9k40_62036.cif" } resolution = 3.15 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 289 5.49 5 S 12 5.16 5 C 6575 2.51 5 N 2168 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 11824 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 783 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 783 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "I" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2950 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2992 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.21, per 1000 atoms: 0.19 Number of scatterers: 11824 At special positions: 0 Unit cell: (104.5, 119.9, 115.5, 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 12 16.00 P 289 15.00 O 2780 8.00 N 2168 7.00 C 6575 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: 0.95 Conformation dependent library (CDL) restraints added in 187.8 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 74.1% alpha, 2.7% beta 144 base pairs and 251 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.632A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.890A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.503A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.536A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 60 through 72 Processing helix chain 'D' and resid 78 through 107 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 126 through 147 removed outlier: 3.715A pdb=" N SER D 147 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.570A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.832A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.552A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.541A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 47 through 75 Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 60 through 72 Processing helix chain 'H' and resid 78 through 107 Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 126 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.035A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.851A pdb=" N ARG C 43 " --> pdb=" O ILE D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 7.092A pdb=" N THR C 102 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.035A 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 43 through 44 removed outlier: 6.985A pdb=" N ARG G 43 " --> pdb=" O ILE H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 408 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 346 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.32 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: 2039 1.33 - 1.45: 4192 1.45 - 1.57: 5799 1.57 - 1.69: 577 1.69 - 1.80: 22 Bond restraints: 12629 Sorted by residual: bond pdb=" O3' DG I -26 " pdb=" P DT I -25 " ideal model delta sigma weight residual 1.607 1.657 -0.050 1.20e-02 6.94e+03 1.74e+01 bond pdb=" O3' DA J -46 " pdb=" P DA J -45 " ideal model delta sigma weight residual 1.607 1.655 -0.048 1.20e-02 6.94e+03 1.62e+01 bond pdb=" O3' DC J -24 " pdb=" P DC J -23 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.20e-02 6.94e+03 1.57e+01 bond pdb=" O3' DT J -36 " pdb=" P DG J -35 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.20e-02 6.94e+03 1.56e+01 bond pdb=" C3' DG I -40 " pdb=" C2' DG I -40 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 ... (remaining 12624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 16828 1.43 - 2.86: 1381 2.86 - 4.28: 79 4.28 - 5.71: 12 5.71 - 7.14: 3 Bond angle restraints: 18303 Sorted by residual: angle pdb=" N ASN F 25 " pdb=" CA ASN F 25 " pdb=" C ASN F 25 " ideal model delta sigma weight residual 112.92 106.83 6.09 1.23e+00 6.61e-01 2.45e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT I 30 " pdb=" C4 DT I 30 " pdb=" O4 DT I 30 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 8 " pdb=" C4 DT I 8 " pdb=" O4 DT I 8 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 13 " pdb=" C4 DT I 13 " pdb=" O4 DT I 13 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 ... (remaining 18298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.21: 4295 18.21 - 36.42: 1209 36.42 - 54.64: 1118 54.64 - 72.85: 287 72.85 - 91.06: 22 Dihedral angle restraints: 6931 sinusoidal: 4773 harmonic: 2158 Sorted by residual: dihedral pdb=" CA ASN G 69 " pdb=" CB ASN G 69 " pdb=" CG ASN G 69 " pdb=" OD1 ASN G 69 " ideal model delta sinusoidal sigma weight residual 120.00 -173.40 -66.60 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA PRO H 126 " pdb=" C PRO H 126 " pdb=" N GLY H 127 " pdb=" CA GLY H 127 " ideal model delta harmonic sigma weight residual 180.00 164.14 15.86 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA PRO D 126 " pdb=" C PRO D 126 " pdb=" N GLY D 127 " pdb=" CA GLY D 127 " ideal model delta harmonic sigma weight residual 180.00 164.51 15.49 0 5.00e+00 4.00e-02 9.60e+00 ... (remaining 6928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1146 0.032 - 0.064: 653 0.064 - 0.096: 204 0.096 - 0.128: 78 0.128 - 0.161: 8 Chirality restraints: 2089 Sorted by residual: chirality pdb=" CA ASP F 24 " pdb=" N ASP F 24 " pdb=" C ASP F 24 " pdb=" CB ASP F 24 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CG LEU A 61 " pdb=" CB LEU A 61 " pdb=" CD1 LEU A 61 " pdb=" CD2 LEU A 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" C3' DG J -37 " pdb=" C4' DG J -37 " pdb=" O3' DG J -37 " pdb=" C2' DG J -37 " both_signs ideal model delta sigma weight residual False -2.73 -2.88 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 2086 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 74 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" C ASN G 74 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN G 74 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS G 75 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 125 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO D 126 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 126 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 126 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 125 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO H 126 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " 0.023 5.00e-02 4.00e+02 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1553 2.75 - 3.29: 10323 3.29 - 3.83: 23082 3.83 - 4.36: 27355 4.36 - 4.90: 39301 Nonbonded interactions: 101614 Sorted by model distance: nonbonded pdb=" OG SER G 19 " pdb=" O PHE G 26 " model vdw 2.219 3.040 nonbonded pdb=" NH2 ARG C 33 " pdb=" OE1 GLU D 58 " model vdw 2.282 3.120 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH1 ARG A 131 " model vdw 2.295 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.310 3.120 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.334 3.040 ... (remaining 101609 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.910 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 0.050 12629 Z= 0.517 Angle : 0.773 7.139 18303 Z= 0.698 Chirality : 0.045 0.161 2089 Planarity : 0.004 0.042 1310 Dihedral : 28.829 91.058 5535 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.65 % Allowed : 11.33 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.30), residues: 730 helix: 2.37 (0.22), residues: 534 sheet: None (None), residues: 0 loop : 0.25 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 72 TYR 0.019 0.001 TYR F 98 PHE 0.008 0.001 PHE H 88 HIS 0.002 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.52 (12629) covalent geometry : angle 0.77337 / 0.70 (18303) hydrogen bonds : bond 0.11525 / 8.02 ( 754) hydrogen bonds : angle 3.89656 / 2.91 ( 1895) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 228 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 230 average time/residue: 0.1170 time to fit residues: 37.3045 Evaluate side-chains 196 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 75 HIS G 69 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.070073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.048977 restraints weight = 49324.251| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.33 r_work: 0.2775 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12629 Z= 0.146 Angle : 0.657 7.164 18303 Z= 0.388 Chirality : 0.045 0.204 2089 Planarity : 0.004 0.039 1310 Dihedral : 31.580 97.266 4071 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.46 % Allowed : 16.67 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.30), residues: 730 helix: 2.52 (0.21), residues: 542 sheet: None (None), residues: 0 loop : 0.10 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 122 TYR 0.012 0.002 TYR F 88 PHE 0.015 0.001 PHE H 93 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.15 (12629) covalent geometry : angle 0.65727 / 0.39 (18303) hydrogen bonds : bond 0.05145 / 3.54 ( 754) hydrogen bonds : angle 3.12205 / 2.35 ( 1895) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9488 (tttm) cc_final: 0.9259 (tttm) REVERT: A 59 GLU cc_start: 0.8260 (pt0) cc_final: 0.7961 (pm20) REVERT: A 81 ASP cc_start: 0.8533 (t0) cc_final: 0.8271 (t0) REVERT: B 84 MET cc_start: 0.9012 (mmm) cc_final: 0.8593 (mmm) REVERT: C 65 GLU cc_start: 0.8634 (tp30) cc_final: 0.8412 (tp30) REVERT: D 91 ASP cc_start: 0.9291 (t0) cc_final: 0.9076 (t0) REVERT: E 53 LYS cc_start: 0.9490 (tttm) cc_final: 0.9280 (tttm) REVERT: E 59 GLU cc_start: 0.8068 (pt0) cc_final: 0.7767 (pm20) REVERT: G 91 ASP cc_start: 0.8278 (t70) cc_final: 0.7952 (t70) REVERT: H 82 MET cc_start: 0.9133 (tpp) cc_final: 0.8837 (tpp) REVERT: H 94 GLU cc_start: 0.9012 (tp30) cc_final: 0.8666 (tp30) REVERT: H 98 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8411 (mm-40) outliers start: 9 outliers final: 4 residues processed: 214 average time/residue: 0.1217 time to fit residues: 36.2946 Evaluate side-chains 203 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 199 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 92 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN D 107 ASN E 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.069904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.048793 restraints weight = 49829.452| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.28 r_work: 0.2775 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12629 Z= 0.137 Angle : 0.617 6.786 18303 Z= 0.367 Chirality : 0.043 0.192 2089 Planarity : 0.004 0.037 1310 Dihedral : 31.688 95.537 4071 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.94 % Allowed : 16.18 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.30), residues: 730 helix: 2.81 (0.21), residues: 542 sheet: None (None), residues: 0 loop : 0.05 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 105 TYR 0.013 0.002 TYR C 51 PHE 0.007 0.001 PHE A 67 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.14 (12629) covalent geometry : angle 0.61737 / 0.37 (18303) hydrogen bonds : bond 0.04552 / 3.16 ( 754) hydrogen bonds : angle 2.91937 / 2.20 ( 1895) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9471 (tttm) cc_final: 0.9225 (tttm) REVERT: A 59 GLU cc_start: 0.8300 (pt0) cc_final: 0.8021 (pm20) REVERT: B 88 TYR cc_start: 0.9469 (m-10) cc_final: 0.9113 (m-10) REVERT: C 65 GLU cc_start: 0.8681 (tp30) cc_final: 0.8406 (tp30) REVERT: D 91 ASP cc_start: 0.9311 (t0) cc_final: 0.9061 (t0) REVERT: D 129 LEU cc_start: 0.9385 (tp) cc_final: 0.9130 (tp) REVERT: E 53 LYS cc_start: 0.9479 (tttm) cc_final: 0.9271 (tttm) REVERT: E 59 GLU cc_start: 0.8227 (pt0) cc_final: 0.7985 (pm20) REVERT: G 91 ASP cc_start: 0.8132 (t70) cc_final: 0.7187 (t70) REVERT: G 93 GLU cc_start: 0.9337 (mp0) cc_final: 0.8795 (pm20) REVERT: H 94 GLU cc_start: 0.9059 (tp30) cc_final: 0.8790 (tp30) REVERT: H 98 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8597 (mm-40) outliers start: 12 outliers final: 7 residues processed: 211 average time/residue: 0.1081 time to fit residues: 31.7678 Evaluate side-chains 205 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 198 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 86 optimal weight: 40.0000 chunk 82 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 85 optimal weight: 40.0000 chunk 35 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.067806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.046630 restraints weight = 50013.158| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.27 r_work: 0.2714 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12629 Z= 0.209 Angle : 0.670 7.856 18303 Z= 0.384 Chirality : 0.044 0.203 2089 Planarity : 0.004 0.038 1310 Dihedral : 31.911 92.660 4071 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.07 % Allowed : 15.53 % Favored : 81.39 % 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: 3.36 (0.30), residues: 730 helix: 2.97 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.14 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 105 TYR 0.026 0.002 TYR D 106 PHE 0.013 0.001 PHE D 93 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 (12629) covalent geometry : angle 0.67022 / 0.38 (18303) hydrogen bonds : bond 0.05704 / 3.98 ( 754) hydrogen bonds : angle 3.10034 / 2.34 ( 1895) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9455 (tttm) cc_final: 0.9163 (tttm) REVERT: A 59 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8162 (pm20) REVERT: B 84 MET cc_start: 0.9063 (mmm) cc_final: 0.8491 (mmm) REVERT: B 88 TYR cc_start: 0.9401 (m-10) cc_final: 0.8951 (m-10) REVERT: C 65 GLU cc_start: 0.8756 (tp30) cc_final: 0.8431 (tp30) REVERT: D 91 ASP cc_start: 0.9341 (t0) cc_final: 0.9109 (t0) REVERT: D 94 GLU cc_start: 0.9051 (tp30) cc_final: 0.8517 (tp30) REVERT: D 98 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8485 (mm-40) REVERT: D 106 TYR cc_start: 0.8531 (m-10) cc_final: 0.8315 (m-80) REVERT: E 53 LYS cc_start: 0.9482 (tttm) cc_final: 0.9255 (tttm) REVERT: E 59 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8109 (pm20) REVERT: F 88 TYR cc_start: 0.9351 (m-10) cc_final: 0.9123 (m-10) REVERT: G 91 ASP cc_start: 0.8220 (t70) cc_final: 0.7461 (t70) REVERT: G 93 GLU cc_start: 0.9367 (mp0) cc_final: 0.8833 (pm20) outliers start: 19 outliers final: 12 residues processed: 202 average time/residue: 0.1022 time to fit residues: 28.9270 Evaluate side-chains 205 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 142 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.068375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.047519 restraints weight = 50083.855| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.28 r_work: 0.2744 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12629 Z= 0.138 Angle : 0.625 7.256 18303 Z= 0.365 Chirality : 0.043 0.191 2089 Planarity : 0.004 0.034 1310 Dihedral : 31.916 94.824 4071 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.43 % Allowed : 18.93 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.48 (0.30), residues: 730 helix: 3.04 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.03 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 105 TYR 0.022 0.002 TYR H 106 PHE 0.008 0.001 PHE H 93 HIS 0.003 0.001 HIS D 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (12629) covalent geometry : angle 0.62500 / 0.36 (18303) hydrogen bonds : bond 0.04361 / 3.02 ( 754) hydrogen bonds : angle 2.94696 / 2.23 ( 1895) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9475 (tttm) cc_final: 0.9231 (tttm) REVERT: A 59 GLU cc_start: 0.8478 (pt0) cc_final: 0.8180 (pm20) REVERT: A 94 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8796 (mt-10) REVERT: B 84 MET cc_start: 0.9039 (mmm) cc_final: 0.8401 (mmm) REVERT: B 88 TYR cc_start: 0.9385 (m-10) cc_final: 0.8879 (m-10) REVERT: C 65 GLU cc_start: 0.8737 (tp30) cc_final: 0.8387 (tp30) REVERT: D 91 ASP cc_start: 0.9356 (t0) cc_final: 0.9139 (t0) REVERT: D 106 TYR cc_start: 0.8526 (m-10) cc_final: 0.8318 (m-80) REVERT: E 53 LYS cc_start: 0.9462 (tttm) cc_final: 0.9234 (tttm) REVERT: E 59 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8096 (pm20) REVERT: E 81 ASP cc_start: 0.8815 (m-30) cc_final: 0.8402 (t0) REVERT: F 84 MET cc_start: 0.8787 (mmm) cc_final: 0.8384 (mmm) REVERT: F 88 TYR cc_start: 0.9113 (m-10) cc_final: 0.8536 (m-10) REVERT: G 21 LYS cc_start: 0.9471 (mmmt) cc_final: 0.9020 (tptm) REVERT: G 91 ASP cc_start: 0.8170 (t70) cc_final: 0.7258 (t70) REVERT: G 93 GLU cc_start: 0.9385 (mp0) cc_final: 0.8837 (pm20) REVERT: H 94 GLU cc_start: 0.9152 (tp30) cc_final: 0.8506 (tp30) REVERT: H 98 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8457 (mm-40) REVERT: H 106 TYR cc_start: 0.8397 (m-80) cc_final: 0.8045 (m-80) REVERT: H 128 GLU cc_start: 0.8127 (tp30) cc_final: 0.7862 (tp30) outliers start: 15 outliers final: 9 residues processed: 209 average time/residue: 0.1016 time to fit residues: 29.7625 Evaluate side-chains 207 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 72 optimal weight: 50.0000 chunk 96 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 overall best weight: 6.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 68 GLN C 83 HIS G 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.062767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.041719 restraints weight = 51320.570| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.28 r_work: 0.2584 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 12629 Z= 0.440 Angle : 0.919 10.292 18303 Z= 0.489 Chirality : 0.056 0.246 2089 Planarity : 0.006 0.043 1310 Dihedral : 32.722 89.293 4071 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.21 % Allowed : 18.28 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.30), residues: 730 helix: 2.40 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -0.58 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 30 TYR 0.031 0.003 TYR D 106 PHE 0.023 0.003 PHE D 93 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00935 / 0.44 (12629) covalent geometry : angle 0.91921 / 0.49 (18303) hydrogen bonds : bond 0.11620 / 8.15 ( 754) hydrogen bonds : angle 3.89189 / 2.88 ( 1895) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8572 (pm20) REVERT: A 73 GLU cc_start: 0.8958 (tp30) cc_final: 0.8160 (tp30) REVERT: A 81 ASP cc_start: 0.8742 (t0) cc_final: 0.8528 (t0) REVERT: B 84 MET cc_start: 0.9227 (mmm) cc_final: 0.8482 (mmm) REVERT: B 88 TYR cc_start: 0.9485 (m-10) cc_final: 0.9040 (m-10) REVERT: C 65 GLU cc_start: 0.8868 (tp30) cc_final: 0.8490 (tp30) REVERT: C 91 ASP cc_start: 0.8511 (t0) cc_final: 0.7971 (t0) REVERT: C 93 GLU cc_start: 0.9311 (mp0) cc_final: 0.8957 (pm20) REVERT: D 94 GLU cc_start: 0.9214 (tp30) cc_final: 0.8574 (tp30) REVERT: D 98 GLN cc_start: 0.9362 (mm-40) cc_final: 0.8790 (mm-40) REVERT: D 128 GLU cc_start: 0.8429 (tp30) cc_final: 0.7915 (tp30) REVERT: E 53 LYS cc_start: 0.9432 (tttm) cc_final: 0.9153 (tttm) REVERT: E 59 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8546 (pm20) REVERT: E 81 ASP cc_start: 0.8943 (m-30) cc_final: 0.8681 (t0) REVERT: G 21 LYS cc_start: 0.9446 (mmmt) cc_final: 0.9088 (tptm) REVERT: G 75 LYS cc_start: 0.9442 (mtmm) cc_final: 0.9035 (mtmm) REVERT: G 79 ILE cc_start: 0.9554 (OUTLIER) cc_final: 0.9319 (mm) REVERT: G 91 ASP cc_start: 0.8562 (t70) cc_final: 0.8186 (t0) REVERT: G 93 GLU cc_start: 0.9353 (mp0) cc_final: 0.9099 (mp0) REVERT: H 56 ASN cc_start: 0.8880 (m-40) cc_final: 0.8211 (m-40) REVERT: H 94 GLU cc_start: 0.9194 (tp30) cc_final: 0.8776 (tp30) REVERT: H 98 GLN cc_start: 0.9320 (mm-40) cc_final: 0.8836 (mm-40) REVERT: H 136 GLU cc_start: 0.9366 (mm-30) cc_final: 0.9143 (mm-30) outliers start: 26 outliers final: 14 residues processed: 186 average time/residue: 0.1273 time to fit residues: 32.2439 Evaluate side-chains 182 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 138 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 86 optimal weight: 40.0000 chunk 97 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.064779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.044079 restraints weight = 50111.858| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.25 r_work: 0.2655 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12629 Z= 0.154 Angle : 0.689 8.500 18303 Z= 0.389 Chirality : 0.046 0.211 2089 Planarity : 0.004 0.037 1310 Dihedral : 32.550 97.448 4071 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.43 % Allowed : 21.04 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.17 (0.30), residues: 730 helix: 2.89 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.37 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 122 TYR 0.022 0.002 TYR H 106 PHE 0.009 0.001 PHE B 61 HIS 0.019 0.002 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (12629) covalent geometry : angle 0.68868 / 0.39 (18303) hydrogen bonds : bond 0.05155 / 3.51 ( 754) hydrogen bonds : angle 3.19529 / 2.39 ( 1895) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8452 (pm20) REVERT: A 73 GLU cc_start: 0.8812 (tp30) cc_final: 0.8294 (tp30) REVERT: A 81 ASP cc_start: 0.8779 (t0) cc_final: 0.8494 (t0) REVERT: C 65 GLU cc_start: 0.8779 (tp30) cc_final: 0.8393 (tp30) REVERT: D 82 MET cc_start: 0.9290 (tpp) cc_final: 0.9046 (tpp) REVERT: D 94 GLU cc_start: 0.9178 (tp30) cc_final: 0.8414 (tp30) REVERT: D 98 GLN cc_start: 0.9330 (mm-40) cc_final: 0.8698 (mm-40) REVERT: D 143 LYS cc_start: 0.9656 (OUTLIER) cc_final: 0.9233 (tttm) REVERT: E 53 LYS cc_start: 0.9451 (tttm) cc_final: 0.9191 (tttm) REVERT: E 59 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8403 (pm20) REVERT: E 81 ASP cc_start: 0.8909 (m-30) cc_final: 0.8538 (t0) REVERT: F 84 MET cc_start: 0.9140 (mmm) cc_final: 0.8271 (mmm) REVERT: G 21 LYS cc_start: 0.9442 (mmmt) cc_final: 0.9057 (tptm) REVERT: G 72 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8149 (ttm110) REVERT: G 91 ASP cc_start: 0.8418 (t70) cc_final: 0.7751 (t70) REVERT: G 93 GLU cc_start: 0.9348 (mp0) cc_final: 0.8821 (pm20) REVERT: H 56 ASN cc_start: 0.8666 (m-40) cc_final: 0.8174 (m-40) REVERT: H 94 GLU cc_start: 0.9237 (tp30) cc_final: 0.8817 (tp30) REVERT: H 98 GLN cc_start: 0.9294 (mm-40) cc_final: 0.8870 (mm-40) REVERT: H 128 GLU cc_start: 0.8362 (tp30) cc_final: 0.8131 (tp30) outliers start: 15 outliers final: 5 residues processed: 207 average time/residue: 0.1116 time to fit residues: 31.8883 Evaluate side-chains 204 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 72 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 34 optimal weight: 4.9990 chunk 86 optimal weight: 50.0000 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 72 optimal weight: 50.0000 chunk 58 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.064663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.044185 restraints weight = 50770.156| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.29 r_work: 0.2662 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12629 Z= 0.174 Angle : 0.685 8.124 18303 Z= 0.387 Chirality : 0.045 0.201 2089 Planarity : 0.004 0.036 1310 Dihedral : 32.295 95.624 4071 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.62 % Allowed : 22.17 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.28 (0.30), residues: 730 helix: 2.96 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.32 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 23 TYR 0.036 0.003 TYR D 106 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (12629) covalent geometry : angle 0.68539 / 0.39 (18303) hydrogen bonds : bond 0.05410 / 3.75 ( 754) hydrogen bonds : angle 3.12160 / 2.34 ( 1895) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 199 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8419 (pm20) REVERT: A 81 ASP cc_start: 0.8782 (t0) cc_final: 0.8507 (t0) REVERT: A 94 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8781 (mt-10) REVERT: B 84 MET cc_start: 0.9012 (mmm) cc_final: 0.8532 (mmm) REVERT: B 88 TYR cc_start: 0.9353 (m-10) cc_final: 0.8900 (m-10) REVERT: C 65 GLU cc_start: 0.8784 (tp30) cc_final: 0.8371 (tp30) REVERT: C 91 ASP cc_start: 0.8257 (t0) cc_final: 0.7741 (t0) REVERT: C 93 GLU cc_start: 0.9255 (mp0) cc_final: 0.9036 (pm20) REVERT: D 82 MET cc_start: 0.9275 (tpp) cc_final: 0.9004 (tpp) REVERT: D 94 GLU cc_start: 0.9249 (tp30) cc_final: 0.8758 (tp30) REVERT: D 98 GLN cc_start: 0.9391 (mm-40) cc_final: 0.8876 (mm-40) REVERT: D 143 LYS cc_start: 0.9657 (OUTLIER) cc_final: 0.9263 (tttm) REVERT: E 53 LYS cc_start: 0.9434 (tttm) cc_final: 0.9151 (tttm) REVERT: E 59 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8395 (pm20) REVERT: E 81 ASP cc_start: 0.8937 (m-30) cc_final: 0.8642 (t0) REVERT: F 84 MET cc_start: 0.9143 (mmm) cc_final: 0.8296 (mmm) REVERT: G 21 LYS cc_start: 0.9453 (mmmt) cc_final: 0.9051 (tptm) REVERT: G 72 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8335 (ttm110) REVERT: G 91 ASP cc_start: 0.8363 (t70) cc_final: 0.7824 (t0) REVERT: G 93 GLU cc_start: 0.9349 (mp0) cc_final: 0.8823 (pm20) REVERT: H 56 ASN cc_start: 0.8781 (m-40) cc_final: 0.8412 (m-40) REVERT: H 94 GLU cc_start: 0.9257 (tp30) cc_final: 0.8744 (tp30) REVERT: H 98 GLN cc_start: 0.9326 (mm-40) cc_final: 0.8809 (mm-40) REVERT: H 128 GLU cc_start: 0.8367 (tp30) cc_final: 0.8138 (tp30) outliers start: 10 outliers final: 6 residues processed: 202 average time/residue: 0.1103 time to fit residues: 30.9077 Evaluate side-chains 202 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 121 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 74 optimal weight: 30.0000 chunk 36 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 86 optimal weight: 50.0000 chunk 47 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.065529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.045161 restraints weight = 50061.794| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.29 r_work: 0.2697 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12629 Z= 0.138 Angle : 0.660 7.934 18303 Z= 0.378 Chirality : 0.043 0.197 2089 Planarity : 0.004 0.047 1310 Dihedral : 32.113 95.510 4071 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.94 % Allowed : 22.17 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.42 (0.30), residues: 730 helix: 3.02 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -0.20 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 105 TYR 0.030 0.002 TYR D 106 PHE 0.008 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (12629) covalent geometry : angle 0.66010 / 0.38 (18303) hydrogen bonds : bond 0.04319 / 2.97 ( 754) hydrogen bonds : angle 2.96533 / 2.23 ( 1895) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 204 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8390 (pm20) REVERT: A 81 ASP cc_start: 0.8755 (t0) cc_final: 0.8499 (t0) REVERT: B 88 TYR cc_start: 0.9091 (m-10) cc_final: 0.8869 (m-10) REVERT: C 65 GLU cc_start: 0.8772 (tp30) cc_final: 0.8393 (tp30) REVERT: C 91 ASP cc_start: 0.8152 (t0) cc_final: 0.7658 (t0) REVERT: C 93 GLU cc_start: 0.9232 (mp0) cc_final: 0.8969 (pm20) REVERT: D 82 MET cc_start: 0.9236 (tpp) cc_final: 0.8975 (tpp) REVERT: D 94 GLU cc_start: 0.9238 (tp30) cc_final: 0.8736 (tp30) REVERT: D 98 GLN cc_start: 0.9364 (mm-40) cc_final: 0.8802 (mm-40) REVERT: D 106 TYR cc_start: 0.8376 (m-80) cc_final: 0.8010 (m-80) REVERT: D 143 LYS cc_start: 0.9662 (OUTLIER) cc_final: 0.9307 (tttm) REVERT: E 53 LYS cc_start: 0.9470 (tttm) cc_final: 0.9224 (tttm) REVERT: E 59 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8397 (pm20) REVERT: E 81 ASP cc_start: 0.8911 (m-30) cc_final: 0.8589 (t0) REVERT: G 21 LYS cc_start: 0.9457 (mmmt) cc_final: 0.9036 (tptm) REVERT: G 72 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8211 (ttm110) REVERT: G 79 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.8976 (mm) REVERT: G 91 ASP cc_start: 0.8213 (t70) cc_final: 0.7336 (t70) REVERT: G 93 GLU cc_start: 0.9337 (mp0) cc_final: 0.8835 (pm20) REVERT: H 56 ASN cc_start: 0.8950 (m-40) cc_final: 0.8467 (m-40) REVERT: H 94 GLU cc_start: 0.9225 (tp30) cc_final: 0.8645 (tp30) REVERT: H 98 GLN cc_start: 0.9319 (mm-40) cc_final: 0.8738 (mm-40) REVERT: H 128 GLU cc_start: 0.8319 (tp30) cc_final: 0.8076 (tp30) outliers start: 12 outliers final: 6 residues processed: 209 average time/residue: 0.1078 time to fit residues: 31.4248 Evaluate side-chains 211 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.062955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.042282 restraints weight = 50866.900| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.26 r_work: 0.2610 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 12629 Z= 0.326 Angle : 0.799 8.980 18303 Z= 0.436 Chirality : 0.050 0.219 2089 Planarity : 0.005 0.054 1310 Dihedral : 32.448 89.740 4071 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.46 % Allowed : 22.98 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.30), residues: 730 helix: 2.70 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -0.61 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 30 TYR 0.064 0.004 TYR D 106 PHE 0.014 0.002 PHE G 26 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.33 (12629) covalent geometry : angle 0.79944 / 0.44 (18303) hydrogen bonds : bond 0.08242 / 5.77 ( 754) hydrogen bonds : angle 3.54028 / 2.63 ( 1895) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 185 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8522 (pm20) REVERT: A 81 ASP cc_start: 0.8896 (t0) cc_final: 0.8626 (t0) REVERT: B 88 TYR cc_start: 0.9428 (m-10) cc_final: 0.9204 (m-10) REVERT: C 65 GLU cc_start: 0.8832 (tp30) cc_final: 0.8423 (tp30) REVERT: C 92 GLU cc_start: 0.9131 (tp30) cc_final: 0.8779 (tp30) REVERT: D 94 GLU cc_start: 0.9234 (tp30) cc_final: 0.8555 (tp30) REVERT: D 98 GLN cc_start: 0.9440 (mm-40) cc_final: 0.8740 (mm-40) REVERT: E 59 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8518 (pm20) REVERT: E 81 ASP cc_start: 0.8911 (m-30) cc_final: 0.8710 (t0) REVERT: G 21 LYS cc_start: 0.9446 (mmmt) cc_final: 0.9027 (tptm) REVERT: G 75 LYS cc_start: 0.9440 (mtmm) cc_final: 0.9034 (mtmm) REVERT: G 79 ILE cc_start: 0.9542 (OUTLIER) cc_final: 0.9308 (mm) REVERT: G 91 ASP cc_start: 0.8473 (t70) cc_final: 0.7947 (t0) REVERT: G 93 GLU cc_start: 0.9314 (mp0) cc_final: 0.8806 (pm20) REVERT: H 56 ASN cc_start: 0.8870 (m-40) cc_final: 0.8254 (m-40) REVERT: H 94 GLU cc_start: 0.9224 (tp30) cc_final: 0.8605 (tp30) REVERT: H 98 GLN cc_start: 0.9380 (mm-40) cc_final: 0.8678 (mm-40) outliers start: 9 outliers final: 5 residues processed: 188 average time/residue: 0.1111 time to fit residues: 28.9806 Evaluate side-chains 187 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 85 optimal weight: 40.0000 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN G 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.064321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.044049 restraints weight = 50436.446| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.28 r_work: 0.2668 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12629 Z= 0.147 Angle : 0.687 7.890 18303 Z= 0.388 Chirality : 0.044 0.208 2089 Planarity : 0.004 0.037 1310 Dihedral : 32.296 95.415 4071 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.94 % Allowed : 23.14 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.30), residues: 730 helix: 2.92 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -0.42 (0.41), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 122 TYR 0.035 0.002 TYR D 106 PHE 0.008 0.001 PHE A 67 HIS 0.003 0.001 HIS D 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (12629) covalent geometry : angle 0.68704 / 0.39 (18303) hydrogen bonds : bond 0.04673 / 3.21 ( 754) hydrogen bonds : angle 3.10111 / 2.32 ( 1895) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2595.82 seconds wall clock time: 44 minutes 59.94 seconds (2699.94 seconds total)