Starting phenix.real_space_refine on Fri Sep 11 15:09:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vbm_31882/09_2026/7vbm_31882.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbm_31882/09_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_31882/09_2026/7vbm_31882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbm_31882/09_2026/7vbm_31882.map" model { file = "/net/cci-nas-00/data/ceres_data/7vbm_31882/09_2026/7vbm_31882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbm_31882/09_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-2.2.1-6174/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: 2.46, per 1000 atoms: 0.23 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: 0.81 Conformation dependent library (CDL) restraints added in 216.8 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: 1.53 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: 1.99 Time building geometry restraints manager: 1.04 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: 15138 1.79 - 3.58: 939 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.560 Find NCS groups from input model: 0.120 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- 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 : 0.887 8.955 16169 Z= 0.734 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 0.88721 / 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 : 0.280 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: 0.1606 time to fit residues: 16.6836 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 : 0.262 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.168573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121719 restraints weight = 12896.312| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.05 r_work: 0.3090 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11171 Z= 0.166 Angle : 0.661 7.365 16169 Z= 0.387 Chirality : 0.047 0.320 1850 Planarity : 0.005 0.059 1168 Dihedral : 31.491 179.366 3477 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.18 % Allowed : 5.89 % Favored : 93.93 % 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: 1.87 (0.32), residues: 661 helix: 2.18 (0.23), residues: 503 sheet: None (None), residues: 0 loop : -2.02 (0.41), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 92 TYR 0.018 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 0.00304 / 0.17 (11171) covalent geometry : angle 0.66108 / 0.39 (16169) hydrogen bonds : bond 0.05573 / 3.68 ( 686) hydrogen bonds : angle 3.10216 / 2.29 ( 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 76 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.279 Fit side-chains REVERT: C 61 GLU cc_start: 0.8425 (tp30) cc_final: 0.8139 (tp30) REVERT: F 39 ARG cc_start: 0.7493 (ttt90) cc_final: 0.7105 (mtp-110) REVERT: F 93 GLN cc_start: 0.8120 (mp10) cc_final: 0.7696 (mp10) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.1797 time to fit residues: 16.8543 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 : 0.255 ------------------------------------------------------------------------------- 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: 4.9990 chunk 88 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.169170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.122013 restraints weight = 12886.757| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.09 r_work: 0.3144 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11171 Z= 0.149 Angle : 0.611 6.972 16169 Z= 0.362 Chirality : 0.045 0.311 1850 Planarity : 0.005 0.062 1168 Dihedral : 31.570 176.775 3477 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.71 % Allowed : 7.86 % Favored : 91.43 % 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: 2.21 (0.32), residues: 661 helix: 2.41 (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 0.007 0.000 ARG A 116 TYR 0.017 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 0.00259 / 0.15 (11171) covalent geometry : angle 0.61084 / 0.36 (16169) hydrogen bonds : bond 0.04996 / 3.30 ( 686) hydrogen bonds : angle 2.86318 / 2.10 ( 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 73 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.251 Fit side-chains REVERT: C 61 GLU cc_start: 0.8442 (tp30) cc_final: 0.8194 (tp30) REVERT: E 125 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: F 39 ARG cc_start: 0.7537 (ttt90) cc_final: 0.7090 (mtp-110) REVERT: F 93 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7684 (mp10) outliers start: 4 outliers final: 1 residues processed: 72 average time/residue: 0.1492 time to fit residues: 13.8013 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 : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 125 GLN 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: 20.0000 chunk 69 optimal weight: 30.0000 chunk 47 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 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 = 0.3903 r_free = 0.3903 target = 0.168726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.120584 restraints weight = 12868.405| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.13 r_work: 0.3071 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1029 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 : 0.622 7.110 16169 Z= 0.362 Chirality : 0.045 0.310 1850 Planarity : 0.004 0.062 1168 Dihedral : 31.622 176.088 3477 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.54 % Allowed : 9.82 % 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: 2.22 (0.32), residues: 661 helix: 2.43 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.95 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.017 0.001 TYR D 121 PHE 0.017 0.002 PHE G 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 (11171) covalent geometry : angle 0.62227 / 0.36 (16169) hydrogen bonds : bond 0.05073 / 3.34 ( 686) hydrogen bonds : angle 2.83801 / 2.08 ( 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 68 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.305 Fit side-chains REVERT: C 61 GLU cc_start: 0.8381 (tp30) cc_final: 0.8154 (tp30) REVERT: F 39 ARG cc_start: 0.7542 (ttt90) cc_final: 0.7149 (mtp-110) REVERT: F 93 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: H 33 ARG cc_start: 0.5832 (mtm180) cc_final: 0.5461 (mtt180) outliers start: 3 outliers final: 2 residues processed: 67 average time/residue: 0.1670 time to fit residues: 14.1853 Evaluate side-chains 67 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR 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: 5.9990 chunk 69 optimal weight: 30.0000 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 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: 6.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.180737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135747 restraints weight = 13087.198| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 0.85 r_work: 0.3130 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11171 Z= 0.133 Angle : 0.590 6.932 16169 Z= 0.349 Chirality : 0.043 0.300 1850 Planarity : 0.004 0.062 1168 Dihedral : 31.554 175.133 3477 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.07 % Allowed : 11.07 % Favored : 87.86 % 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: 2.55 (0.32), residues: 661 helix: 2.67 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.86 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.019 0.001 TYR D 121 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 0.00210 / 0.13 (11171) covalent geometry : angle 0.58986 / 0.35 (16169) hydrogen bonds : bond 0.04602 / 3.03 ( 686) hydrogen bonds : angle 2.71429 / 1.99 ( 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 75 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.276 Fit side-chains REVERT: C 61 GLU cc_start: 0.8398 (tp30) cc_final: 0.8182 (tp30) REVERT: D 46 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7885 (mmtm) REVERT: D 59 MET cc_start: 0.8031 (tpp) cc_final: 0.7747 (tpp) REVERT: E 125 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7135 (mp10) REVERT: F 39 ARG cc_start: 0.7486 (ttt90) cc_final: 0.7099 (mtp-110) REVERT: F 93 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7666 (mp10) outliers start: 6 outliers final: 1 residues processed: 74 average time/residue: 0.1568 time to fit residues: 14.7414 Evaluate side-chains 69 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 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: 30.0000 chunk 55 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.180595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.135436 restraints weight = 13129.787| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 0.89 r_work: 0.3113 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1190 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= 0.155 Angle : 0.611 6.889 16169 Z= 0.356 Chirality : 0.044 0.304 1850 Planarity : 0.004 0.062 1168 Dihedral : 31.603 175.406 3477 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.05 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: 2.47 (0.32), residues: 661 helix: 2.61 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.85 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.018 0.001 TYR D 121 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 0.00290 / 0.15 (11171) covalent geometry : angle 0.61079 / 0.36 (16169) hydrogen bonds : bond 0.04943 / 3.26 ( 686) hydrogen bonds : angle 2.78174 / 2.04 ( 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 73 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.238 Fit side-chains REVERT: C 61 GLU cc_start: 0.8423 (tp30) cc_final: 0.8207 (tp30) REVERT: D 46 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7910 (mmtm) REVERT: D 59 MET cc_start: 0.8108 (tpp) cc_final: 0.7903 (tpp) REVERT: E 125 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7155 (mp10) REVERT: F 39 ARG cc_start: 0.7546 (ttt90) cc_final: 0.7174 (mtp-110) REVERT: F 93 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7720 (mp10) outliers start: 9 outliers final: 4 residues processed: 71 average time/residue: 0.1508 time to fit residues: 13.7201 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 : 0.242 ------------------------------------------------------------------------------- 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: 4.9990 chunk 61 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 70 optimal weight: 30.0000 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.178018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132710 restraints weight = 13011.347| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 0.99 r_work: 0.3094 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11171 Z= 0.138 Angle : 0.596 7.001 16169 Z= 0.350 Chirality : 0.044 0.299 1850 Planarity : 0.004 0.062 1168 Dihedral : 31.585 175.340 3477 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.61 % Allowed : 11.79 % Favored : 86.61 % 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: 2.61 (0.32), residues: 661 helix: 2.72 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.84 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.018 0.001 TYR D 121 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 0.00234 / 0.14 (11171) covalent geometry : angle 0.59603 / 0.35 (16169) hydrogen bonds : bond 0.04718 / 3.10 ( 686) hydrogen bonds : angle 2.73399 / 2.00 ( 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 72 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.286 Fit side-chains REVERT: C 61 GLU cc_start: 0.8495 (tp30) cc_final: 0.8288 (tp30) REVERT: D 46 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7910 (mmtm) REVERT: D 59 MET cc_start: 0.8132 (tpp) cc_final: 0.7699 (tpp) REVERT: E 125 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7170 (mp10) REVERT: F 39 ARG cc_start: 0.7548 (ttt90) cc_final: 0.7183 (mtp-110) REVERT: F 93 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: H 33 ARG cc_start: 0.5998 (mtm180) cc_final: 0.5653 (mtm180) outliers start: 9 outliers final: 5 residues processed: 70 average time/residue: 0.1649 time to fit residues: 14.7356 Evaluate side-chains 71 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 93 LEU 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: 2.9990 chunk 86 optimal weight: 20.0000 chunk 65 optimal weight: 50.0000 chunk 82 optimal weight: 20.0000 chunk 50 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 80 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 78 optimal weight: 30.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.167329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.119458 restraints weight = 12999.761| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.04 r_work: 0.2956 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11171 Z= 0.214 Angle : 0.684 7.253 16169 Z= 0.385 Chirality : 0.049 0.315 1850 Planarity : 0.005 0.063 1168 Dihedral : 31.769 177.545 3477 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.43 % Allowed : 12.50 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.32), residues: 661 helix: 2.27 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -2.03 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 32 TYR 0.020 0.002 TYR D 121 PHE 0.029 0.002 PHE G 25 HIS 0.007 0.002 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (11171) covalent geometry : angle 0.68409 / 0.39 (16169) hydrogen bonds : bond 0.05898 / 3.88 ( 686) hydrogen bonds : angle 2.96441 / 2.17 ( 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 73 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.268 Fit side-chains REVERT: C 61 GLU cc_start: 0.8470 (tp30) cc_final: 0.8255 (tp30) REVERT: D 46 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7925 (mmtm) REVERT: D 59 MET cc_start: 0.8157 (tpp) cc_final: 0.7945 (tpp) REVERT: E 125 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.6988 (mp10) REVERT: F 39 ARG cc_start: 0.7595 (ttt90) cc_final: 0.7147 (mtp-110) REVERT: F 93 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: H 33 ARG cc_start: 0.5898 (mtm180) cc_final: 0.5599 (mtm180) outliers start: 8 outliers final: 5 residues processed: 70 average time/residue: 0.1542 time to fit residues: 13.8633 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 : 0.261 ------------------------------------------------------------------------------- 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 93 LEU 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: 1.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.0570 chunk 9 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.0040 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.4510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.180053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134383 restraints weight = 13052.669| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 0.88 r_work: 0.3113 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11171 Z= 0.128 Angle : 0.582 7.443 16169 Z= 0.345 Chirality : 0.042 0.294 1850 Planarity : 0.004 0.068 1168 Dihedral : 31.568 175.707 3477 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.07 % Allowed : 12.68 % 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: 2.71 (0.32), residues: 661 helix: 2.80 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.84 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.017 0.001 TYR D 121 PHE 0.009 0.001 PHE B 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.13 (11171) covalent geometry : angle 0.58188 / 0.34 (16169) hydrogen bonds : bond 0.04467 / 2.94 ( 686) hydrogen bonds : angle 2.68877 / 1.97 ( 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 76 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.271 Fit side-chains REVERT: E 125 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7114 (mp10) REVERT: F 39 ARG cc_start: 0.7492 (ttt90) cc_final: 0.7132 (mtp-110) REVERT: F 93 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7730 (mp10) outliers start: 6 outliers final: 2 residues processed: 74 average time/residue: 0.1572 time to fit residues: 14.8518 Evaluate side-chains 71 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 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: 0.9990 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 50.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.180700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135141 restraints weight = 12929.718| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 0.87 r_work: 0.3111 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11171 Z= 0.135 Angle : 0.586 7.289 16169 Z= 0.344 Chirality : 0.043 0.293 1850 Planarity : 0.004 0.065 1168 Dihedral : 31.581 176.085 3477 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.71 % Allowed : 12.86 % 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: 2.83 (0.32), residues: 661 helix: 2.90 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.84 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.019 0.001 TYR D 121 PHE 0.012 0.001 PHE G 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.13 (11171) covalent geometry : angle 0.58579 / 0.34 (16169) hydrogen bonds : bond 0.04529 / 2.99 ( 686) hydrogen bonds : angle 2.69220 / 1.97 ( 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 69 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.289 Fit side-chains REVERT: E 125 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: F 39 ARG cc_start: 0.7488 (ttt90) cc_final: 0.7142 (mtp-110) REVERT: F 93 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7709 (mp10) outliers start: 4 outliers final: 2 residues processed: 67 average time/residue: 0.1579 time to fit residues: 13.5861 Evaluate side-chains 69 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 40.0000 chunk 14 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.178886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133170 restraints weight = 13122.091| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 0.99 r_work: 0.3145 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11171 Z= 0.147 Angle : 0.597 7.194 16169 Z= 0.347 Chirality : 0.044 0.296 1850 Planarity : 0.004 0.067 1168 Dihedral : 31.604 176.399 3477 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.89 % Allowed : 12.68 % 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: 2.72 (0.32), residues: 661 helix: 2.81 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.86 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.021 0.001 TYR D 121 PHE 0.015 0.001 PHE G 25 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (11171) covalent geometry : angle 0.59652 / 0.35 (16169) hydrogen bonds : bond 0.04678 / 3.08 ( 686) hydrogen bonds : angle 2.72286 / 2.00 ( 1743) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2007.43 seconds wall clock time: 35 minutes 10.27 seconds (2110.27 seconds total)