Starting phenix.real_space_refine on Thu Jul 2 19:50:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vbm_31882/07_2026/7vbm_31882.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbm_31882/07_2026/7vbm_31882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vbm_31882/07_2026/7vbm_31882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbm_31882/07_2026/7vbm_31882.map" model { file = "/net/cci-nas-00/data/ceres_data/7vbm_31882/07_2026/7vbm_31882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbm_31882/07_2026/7vbm_31882.cif" } resolution = 3.4 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= 1.000 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 251 5.49 5 S 14 5.16 5 C 5799 2.51 5 N 1944 2.21 5 O 2467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10475 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 565 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} 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: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 712 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "D" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 603 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 719 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "H" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2566 Classifications: {'DNA': 126} Link IDs: {'rna3p': 125} Chain: "J" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2597 Classifications: {'DNA': 126} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 125} Time building chain proxies: 2.35, per 1000 atoms: 0.22 Number of scatterers: 10475 At special positions: 0 Unit cell: (116.6, 94.34, 124.02, 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 14 16.00 P 251 15.00 O 2467 8.00 N 1944 7.00 C 5799 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 217.8 milliseconds 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1258 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 76.4% alpha, 3.0% beta 117 base pairs and 214 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... 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 removed outlier: 3.568A pdb=" N CYS A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.552A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.762A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.621A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.729A pdb=" N LEU C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.597A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.651A pdb=" N VAL D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.763A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.784A pdb=" N THR E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.736A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.835A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) 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 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.596A pdb=" N VAL H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.835A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.066A pdb=" N CYS 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 42 through 43 removed outlier: 7.654A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.926A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.105A pdb=" N CYS 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: 7.545A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (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 78 380 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 306 hydrogen bonds 612 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 214 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.27 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: 1717 1.33 - 1.45: 3846 1.45 - 1.57: 5084 1.57 - 1.69: 502 1.69 - 1.81: 22 Bond restraints: 11171 Sorted by residual: bond pdb=" CZ ARG C 77 " pdb=" NH2 ARG C 77 " ideal model delta sigma weight residual 1.330 1.279 0.051 1.30e-02 5.92e+03 1.55e+01 bond pdb=" C3' DC J -58 " pdb=" C2' DC J -58 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.32e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" C3' DA I 23 " pdb=" C2' DA I 23 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 ... (remaining 11166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 15145 1.79 - 3.58: 932 3.58 - 5.37: 72 5.37 - 7.16: 17 7.16 - 8.96: 3 Bond angle restraints: 16169 Sorted by residual: angle pdb=" CA CYS E 83 " pdb=" C CYS E 83 " pdb=" N PHE E 84 " ideal model delta sigma weight residual 115.55 122.08 -6.53 1.33e+00 5.65e-01 2.41e+01 angle pdb=" O5' DC I -63 " pdb=" C5' DC I -63 " pdb=" C4' DC I -63 " ideal model delta sigma weight residual 109.40 113.11 -3.71 8.00e-01 1.56e+00 2.15e+01 angle pdb=" C LEU A 61 " pdb=" N ILE A 62 " pdb=" CA ILE A 62 " ideal model delta sigma weight residual 123.14 129.14 -6.00 1.31e+00 5.83e-01 2.10e+01 angle pdb=" O4' DG J 63 " pdb=" C1' DG J 63 " pdb=" N9 DG J 63 " ideal model delta sigma weight residual 108.00 111.19 -3.19 7.00e-01 2.04e+00 2.08e+01 angle pdb=" N3 DT J -39 " pdb=" C4 DT J -39 " pdb=" O4 DT J -39 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 ... (remaining 16164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 4839 35.82 - 71.65: 1170 71.65 - 107.47: 9 107.47 - 143.29: 3 143.29 - 179.12: 3 Dihedral angle restraints: 6024 sinusoidal: 4069 harmonic: 1955 Sorted by residual: dihedral pdb=" CA LEU A 82 " pdb=" C LEU A 82 " pdb=" N CYS A 83 " pdb=" CA CYS A 83 " ideal model delta harmonic sigma weight residual 180.00 156.10 23.90 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" N GLN E 76 " pdb=" C GLN E 76 " pdb=" CA GLN E 76 " pdb=" CB GLN E 76 " ideal model delta harmonic sigma weight residual 122.80 133.49 -10.69 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" CA THR A 80 " pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta harmonic sigma weight residual -180.00 -159.06 -20.94 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 6021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1668 0.082 - 0.164: 170 0.164 - 0.245: 8 0.245 - 0.327: 2 0.327 - 0.409: 2 Chirality restraints: 1850 Sorted by residual: chirality pdb=" CA GLN E 76 " pdb=" N GLN E 76 " pdb=" C GLN E 76 " pdb=" CB GLN E 76 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA LYS E 122 " pdb=" N LYS E 122 " pdb=" C LYS E 122 " pdb=" CB LYS E 122 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ARG H 33 " pdb=" N ARG H 33 " pdb=" C ARG H 33 " pdb=" CB ARG H 33 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 1847 not shown) Planarity restraints: 1168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 78 " 0.044 2.00e-02 2.50e+03 2.81e-02 1.38e+01 pdb=" CG PHE A 78 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 78 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 78 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE A 78 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 78 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 78 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 100 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C PHE B 100 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE B 100 " -0.023 2.00e-02 2.50e+03 pdb=" N GLY B 101 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 92 " -0.281 9.50e-02 1.11e+02 1.26e-01 1.02e+01 pdb=" NE ARG H 92 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG H 92 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG H 92 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG H 92 " -0.014 2.00e-02 2.50e+03 ... (remaining 1165 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1387 2.76 - 3.29: 9078 3.29 - 3.83: 20471 3.83 - 4.36: 23963 4.36 - 4.90: 34740 Nonbonded interactions: 89639 Sorted by model distance: nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.267 3.040 nonbonded pdb=" NH1 ARG G 32 " pdb=" OP1 DG J -44 " model vdw 2.390 3.120 nonbonded pdb=" NH1 ARG C 88 " pdb=" OD1 ASN C 94 " model vdw 2.417 3.120 ... (remaining 89634 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' and resid 61 through 132) } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 106) selection = (chain 'G' and resid 16 through 106) } 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=1.00 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: 0.550 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.610 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 : 0.007 0.075 11171 Z= 0.572 Angle : 0.881 8.955 16169 Z= 0.728 Chirality : 0.052 0.409 1850 Planarity : 0.008 0.126 1168 Dihedral : 28.389 179.118 4766 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.18 % Allowed : 0.54 % Favored : 99.29 % Cbeta Deviations : 0.16 % 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 (0.32), residues: 661 helix: 1.84 (0.23), residues: 500 sheet: None (None), residues: 0 loop : -1.89 (0.40), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 92 TYR 0.023 0.002 TYR F 88 PHE 0.044 0.004 PHE A 78 HIS 0.011 0.002 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.57 (11171) covalent geometry : angle 0.88078 / 0.73 (16169) hydrogen bonds : bond 0.10167 / 6.94 ( 686) hydrogen bonds : angle 3.92453 / 2.92 ( 1743) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.304 Fit side-chains REVERT: C 61 GLU cc_start: 0.8119 (tp30) cc_final: 0.7777 (tp30) REVERT: E 79 LYS cc_start: 0.7036 (tppt) cc_final: 0.6548 (tptt) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1810 time to fit residues: 18.8121 Evaluate side-chains 70 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.168657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122245 restraints weight = 12911.266| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.06 r_work: 0.3131 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11171 Z= 0.167 Angle : 0.643 7.317 16169 Z= 0.383 Chirality : 0.046 0.296 1850 Planarity : 0.005 0.059 1168 Dihedral : 31.525 179.197 3477 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.18 % Allowed : 5.36 % Favored : 94.46 % 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 (0.32), residues: 661 helix: 2.18 (0.23), residues: 503 sheet: None (None), residues: 0 loop : -2.03 (0.41), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 92 TYR 0.018 0.001 TYR F 88 PHE 0.019 0.002 PHE G 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.17 (11171) covalent geometry : angle 0.64348 / 0.38 (16169) hydrogen bonds : bond 0.05648 / 3.73 ( 686) hydrogen bonds : angle 3.12698 / 2.31 ( 1743) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.288 Fit side-chains REVERT: C 61 GLU cc_start: 0.8426 (tp30) cc_final: 0.8141 (tp30) REVERT: F 39 ARG cc_start: 0.7471 (ttt90) cc_final: 0.7120 (mtp-110) REVERT: F 93 GLN cc_start: 0.8116 (mp10) cc_final: 0.7679 (mp10) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.1840 time to fit residues: 17.0420 Evaluate side-chains 67 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 70 optimal weight: 30.0000 chunk 84 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 1 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.179287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133840 restraints weight = 13178.915| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 0.86 r_work: 0.3101 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11171 Z= 0.157 Angle : 0.613 7.124 16169 Z= 0.364 Chirality : 0.045 0.294 1850 Planarity : 0.005 0.063 1168 Dihedral : 31.642 176.917 3477 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.54 % Allowed : 7.86 % Favored : 91.61 % 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: 2.10 (0.32), residues: 661 helix: 2.34 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.94 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.016 0.001 TYR F 88 PHE 0.018 0.002 PHE G 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.16 (11171) covalent geometry : angle 0.61305 / 0.36 (16169) hydrogen bonds : bond 0.05184 / 3.42 ( 686) hydrogen bonds : angle 2.91435 / 2.14 ( 1743) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.295 Fit side-chains REVERT: C 61 GLU cc_start: 0.8414 (tp30) cc_final: 0.8158 (tp30) REVERT: F 39 ARG cc_start: 0.7498 (ttt90) cc_final: 0.7154 (mtp-110) REVERT: F 93 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7673 (mp10) outliers start: 3 outliers final: 2 residues processed: 68 average time/residue: 0.1706 time to fit residues: 14.8882 Evaluate side-chains 68 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 76 optimal weight: 30.0000 chunk 69 optimal weight: 30.0000 chunk 47 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.180139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134794 restraints weight = 13110.075| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 0.88 r_work: 0.3134 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11171 Z= 0.157 Angle : 0.610 7.250 16169 Z= 0.360 Chirality : 0.045 0.290 1850 Planarity : 0.004 0.062 1168 Dihedral : 31.691 175.437 3477 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.07 % Allowed : 9.29 % Favored : 89.64 % 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: 2.18 (0.32), residues: 661 helix: 2.40 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.92 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.017 0.002 TYR F 88 PHE 0.021 0.002 PHE G 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 (11171) covalent geometry : angle 0.60989 / 0.36 (16169) hydrogen bonds : bond 0.05108 / 3.37 ( 686) hydrogen bonds : angle 2.85010 / 2.09 ( 1743) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.272 Fit side-chains REVERT: C 61 GLU cc_start: 0.8379 (tp30) cc_final: 0.8145 (tp30) REVERT: D 59 MET cc_start: 0.8049 (tpp) cc_final: 0.7705 (tpp) REVERT: E 125 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7136 (mp10) REVERT: F 39 ARG cc_start: 0.7556 (ttt90) cc_final: 0.7166 (mtp-110) REVERT: F 93 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7708 (mp10) outliers start: 6 outliers final: 3 residues processed: 67 average time/residue: 0.1649 time to fit residues: 14.1262 Evaluate side-chains 67 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 30.0000 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 45 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.181851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.137183 restraints weight = 13074.536| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 0.89 r_work: 0.3134 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11171 Z= 0.130 Angle : 0.571 7.026 16169 Z= 0.343 Chirality : 0.042 0.280 1850 Planarity : 0.004 0.065 1168 Dihedral : 31.612 175.148 3477 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.89 % Allowed : 11.07 % Favored : 88.04 % 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: 2.63 (0.32), residues: 661 helix: 2.72 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.81 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.014 0.001 TYR F 88 PHE 0.009 0.001 PHE G 25 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.13 (11171) covalent geometry : angle 0.57117 / 0.34 (16169) hydrogen bonds : bond 0.04537 / 2.99 ( 686) hydrogen bonds : angle 2.70792 / 1.98 ( 1743) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.277 Fit side-chains REVERT: C 61 GLU cc_start: 0.8396 (tp30) cc_final: 0.8182 (tp30) REVERT: D 46 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7881 (mmtm) REVERT: D 59 MET cc_start: 0.8041 (tpp) cc_final: 0.7664 (tpp) REVERT: E 125 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: F 39 ARG cc_start: 0.7489 (ttt90) cc_final: 0.7115 (mtp-110) REVERT: F 93 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7681 (mp10) outliers start: 5 outliers final: 2 residues processed: 70 average time/residue: 0.1753 time to fit residues: 15.6511 Evaluate side-chains 68 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 2 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.180438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.135636 restraints weight = 13126.664| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.00 r_work: 0.3103 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11171 Z= 0.139 Angle : 0.579 6.900 16169 Z= 0.344 Chirality : 0.043 0.281 1850 Planarity : 0.004 0.062 1168 Dihedral : 31.622 174.821 3477 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.61 % Allowed : 11.07 % Favored : 87.32 % 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: 2.71 (0.32), residues: 661 helix: 2.78 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.77 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.016 0.001 TYR F 88 PHE 0.014 0.001 PHE G 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (11171) covalent geometry : angle 0.57858 / 0.34 (16169) hydrogen bonds : bond 0.04620 / 3.05 ( 686) hydrogen bonds : angle 2.71176 / 1.98 ( 1743) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.307 Fit side-chains REVERT: D 46 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7920 (mmtm) REVERT: D 59 MET cc_start: 0.8102 (tpp) cc_final: 0.7720 (tpp) REVERT: E 125 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: F 39 ARG cc_start: 0.7577 (ttt90) cc_final: 0.7187 (mtp-110) REVERT: F 93 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7717 (mp10) outliers start: 9 outliers final: 4 residues processed: 72 average time/residue: 0.1804 time to fit residues: 16.5260 Evaluate side-chains 70 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 31 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 70 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.180063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.134438 restraints weight = 12993.142| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 0.92 r_work: 0.3121 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11171 Z= 0.144 Angle : 0.583 7.020 16169 Z= 0.346 Chirality : 0.043 0.279 1850 Planarity : 0.004 0.063 1168 Dihedral : 31.636 174.750 3477 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.43 % Allowed : 11.43 % Favored : 87.14 % 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: 2.67 (0.32), residues: 661 helix: 2.77 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.83 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.016 0.001 TYR F 88 PHE 0.015 0.001 PHE G 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (11171) covalent geometry : angle 0.58252 / 0.35 (16169) hydrogen bonds : bond 0.04687 / 3.09 ( 686) hydrogen bonds : angle 2.71137 / 1.98 ( 1743) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.277 Fit side-chains REVERT: D 46 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7921 (mmtm) REVERT: D 59 MET cc_start: 0.8059 (tpp) cc_final: 0.7830 (tpp) REVERT: E 125 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7114 (mp10) REVERT: F 39 ARG cc_start: 0.7540 (ttt90) cc_final: 0.7181 (mtp-110) REVERT: F 93 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7717 (mp10) REVERT: H 33 ARG cc_start: 0.5988 (mtm180) cc_final: 0.5645 (mtm180) outliers start: 8 outliers final: 4 residues processed: 71 average time/residue: 0.1664 time to fit residues: 15.1876 Evaluate side-chains 71 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 73 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 65 optimal weight: 40.0000 chunk 82 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 80 optimal weight: 20.0000 chunk 53 optimal weight: 0.0770 chunk 78 optimal weight: 30.0000 overall best weight: 3.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.176003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129055 restraints weight = 13085.003| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.02 r_work: 0.3049 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11171 Z= 0.225 Angle : 0.693 7.422 16169 Z= 0.391 Chirality : 0.049 0.298 1850 Planarity : 0.005 0.063 1168 Dihedral : 31.889 177.765 3477 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.25 % Allowed : 12.32 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.32), residues: 661 helix: 2.17 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -2.07 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 72 TYR 0.020 0.002 TYR F 88 PHE 0.032 0.003 PHE G 25 HIS 0.008 0.002 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 (11171) covalent geometry : angle 0.69256 / 0.39 (16169) hydrogen bonds : bond 0.06220 / 4.09 ( 686) hydrogen bonds : angle 3.01999 / 2.20 ( 1743) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.287 Fit side-chains REVERT: D 46 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7932 (mmtm) REVERT: D 59 MET cc_start: 0.8212 (tpp) cc_final: 0.7711 (tpp) REVERT: E 125 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7037 (mp10) REVERT: F 39 ARG cc_start: 0.7602 (ttt90) cc_final: 0.7177 (mtp-110) REVERT: F 93 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7694 (mp10) REVERT: H 33 ARG cc_start: 0.5951 (mtm180) cc_final: 0.5661 (mtm180) outliers start: 7 outliers final: 4 residues processed: 69 average time/residue: 0.1392 time to fit residues: 12.5251 Evaluate side-chains 72 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.169625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.122905 restraints weight = 12998.273| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.03 r_work: 0.3105 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11171 Z= 0.139 Angle : 0.593 7.455 16169 Z= 0.350 Chirality : 0.044 0.278 1850 Planarity : 0.004 0.067 1168 Dihedral : 31.751 175.085 3477 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.25 % Allowed : 12.50 % Favored : 86.25 % 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: 2.47 (0.32), residues: 661 helix: 2.62 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.89 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.016 0.001 TYR F 88 PHE 0.010 0.001 PHE G 25 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (11171) covalent geometry : angle 0.59289 / 0.35 (16169) hydrogen bonds : bond 0.04883 / 3.21 ( 686) hydrogen bonds : angle 2.76519 / 2.02 ( 1743) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.304 Fit side-chains REVERT: E 125 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7048 (mp10) REVERT: F 39 ARG cc_start: 0.7670 (ttt90) cc_final: 0.7191 (mtp-110) REVERT: F 93 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7750 (mp10) outliers start: 7 outliers final: 5 residues processed: 68 average time/residue: 0.1545 time to fit residues: 13.6294 Evaluate side-chains 70 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 40.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.178367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132277 restraints weight = 12956.828| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 0.99 r_work: 0.3133 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11171 Z= 0.141 Angle : 0.587 7.451 16169 Z= 0.346 Chirality : 0.043 0.277 1850 Planarity : 0.004 0.065 1168 Dihedral : 31.723 174.886 3477 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.25 % Allowed : 12.50 % Favored : 86.25 % 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: 2.66 (0.32), residues: 661 helix: 2.77 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.87 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.020 0.001 TYR F 88 PHE 0.013 0.001 PHE G 25 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (11171) covalent geometry : angle 0.58716 / 0.35 (16169) hydrogen bonds : bond 0.04772 / 3.15 ( 686) hydrogen bonds : angle 2.74610 / 2.01 ( 1743) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.222 Fit side-chains REVERT: E 125 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7109 (mp10) REVERT: F 39 ARG cc_start: 0.7556 (ttt90) cc_final: 0.7186 (mtp-110) REVERT: F 93 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7732 (mp10) outliers start: 7 outliers final: 5 residues processed: 68 average time/residue: 0.1481 time to fit residues: 13.2136 Evaluate side-chains 70 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 40.0000 chunk 14 optimal weight: 0.6980 chunk 85 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.168977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.121690 restraints weight = 13007.853| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.13 r_work: 0.3097 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11171 Z= 0.158 Angle : 0.600 7.150 16169 Z= 0.351 Chirality : 0.044 0.279 1850 Planarity : 0.004 0.067 1168 Dihedral : 31.745 175.156 3477 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.25 % Allowed : 12.50 % Favored : 86.25 % 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: 2.52 (0.32), residues: 661 helix: 2.66 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.89 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.021 0.002 TYR F 88 PHE 0.016 0.002 PHE G 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (11171) covalent geometry : angle 0.59967 / 0.35 (16169) hydrogen bonds : bond 0.04931 / 3.24 ( 686) hydrogen bonds : angle 2.77546 / 2.03 ( 1743) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1992.55 seconds wall clock time: 34 minutes 58.58 seconds (2098.58 seconds total)