Starting phenix.real_space_refine on Wed Jul 1 23:17:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1j_36793/07_2026/8k1j_36793.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1j_36793/07_2026/8k1j_36793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1j_36793/07_2026/8k1j_36793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1j_36793/07_2026/8k1j_36793.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1j_36793/07_2026/8k1j_36793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1j_36793/07_2026/8k1j_36793.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.100 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 K 5 8.98 5 S 32 5.16 5 C 2706 2.51 5 N 616 2.21 5 O 710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 4069 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1921 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "B" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1921 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 105 Ad-hoc single atom residues: {' K': 5} Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 5 Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 1.13, per 1000 atoms: 0.28 Number of scatterers: 4069 At special positions: 0 Unit cell: (69.3, 71.5, 90.2, 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) K 5 19.00 S 32 16.00 O 710 8.00 N 616 7.00 C 2706 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: 0.22 Conformation dependent library (CDL) restraints added in 105.0 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 896 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 2 through 53 removed outlier: 5.638A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.764A pdb=" N ARG A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 147 Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 183 Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 243 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'B' and resid 3 through 53 removed outlier: 5.634A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 removed outlier: 3.901A pdb=" N ARG B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 147 Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 183 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 243 Processing helix chain 'B' and resid 244 through 247 333 hydrogen bonds defined for protein. 981 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.46 Time building geometry restraints manager: 0.31 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: 664 1.33 - 1.45: 1092 1.45 - 1.57: 2352 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4156 Sorted by residual: bond pdb=" C ILE A 118 " pdb=" N PRO A 119 " ideal model delta sigma weight residual 1.335 1.343 -0.007 1.36e-02 5.41e+03 2.94e-01 bond pdb=" N LYS A 211 " pdb=" CA LYS A 211 " ideal model delta sigma weight residual 1.457 1.464 -0.007 1.29e-02 6.01e+03 2.64e-01 bond pdb=" C ILE B 118 " pdb=" N PRO B 119 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.36e-02 5.41e+03 2.43e-01 bond pdb=" C GLU A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.36e-02 5.41e+03 2.42e-01 bond pdb=" CA LYS B 211 " pdb=" CB LYS B 211 " ideal model delta sigma weight residual 1.530 1.538 -0.008 1.69e-02 3.50e+03 2.33e-01 ... (remaining 4151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 5548 1.00 - 2.00: 75 2.00 - 3.00: 9 3.00 - 4.00: 6 4.00 - 5.00: 6 Bond angle restraints: 5644 Sorted by residual: angle pdb=" C THR A 210 " pdb=" N LYS A 211 " pdb=" CA LYS A 211 " ideal model delta sigma weight residual 121.54 125.68 -4.14 1.91e+00 2.74e-01 4.70e+00 angle pdb=" C THR B 210 " pdb=" N LYS B 211 " pdb=" CA LYS B 211 " ideal model delta sigma weight residual 121.54 125.66 -4.12 1.91e+00 2.74e-01 4.66e+00 angle pdb=" N GLY A 117 " pdb=" CA GLY A 117 " pdb=" C GLY A 117 " ideal model delta sigma weight residual 113.18 116.98 -3.80 2.37e+00 1.78e-01 2.57e+00 angle pdb=" N GLY B 117 " pdb=" CA GLY B 117 " pdb=" C GLY B 117 " ideal model delta sigma weight residual 113.18 116.93 -3.75 2.37e+00 1.78e-01 2.51e+00 angle pdb=" CA TYR A 18 " pdb=" CB TYR A 18 " pdb=" CG TYR A 18 " ideal model delta sigma weight residual 113.90 116.71 -2.81 1.80e+00 3.09e-01 2.44e+00 ... (remaining 5639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 2433 16.20 - 32.39: 211 32.39 - 48.59: 36 48.59 - 64.79: 20 64.79 - 80.99: 12 Dihedral angle restraints: 2712 sinusoidal: 1310 harmonic: 1402 Sorted by residual: dihedral pdb=" CG ARG B 3 " pdb=" CD ARG B 3 " pdb=" NE ARG B 3 " pdb=" CZ ARG B 3 " ideal model delta sinusoidal sigma weight residual 180.00 -139.84 -40.16 2 1.50e+01 4.44e-03 8.87e+00 dihedral pdb=" CG ARG A 3 " pdb=" CD ARG A 3 " pdb=" NE ARG A 3 " pdb=" CZ ARG A 3 " ideal model delta sinusoidal sigma weight residual -180.00 -139.85 -40.15 2 1.50e+01 4.44e-03 8.87e+00 dihedral pdb=" CB GLU B 130 " pdb=" CG GLU B 130 " pdb=" CD GLU B 130 " pdb=" OE1 GLU B 130 " ideal model delta sinusoidal sigma weight residual 0.00 80.30 -80.30 1 3.00e+01 1.11e-03 8.87e+00 ... (remaining 2709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 437 0.021 - 0.043: 96 0.043 - 0.064: 82 0.064 - 0.086: 20 0.086 - 0.107: 15 Chirality restraints: 650 Sorted by residual: chirality pdb=" CA VAL B 76 " pdb=" N VAL B 76 " pdb=" C VAL B 76 " pdb=" CB VAL B 76 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.86e-01 chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.85e-01 chirality pdb=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.10 2.00e-01 2.50e+01 2.73e-01 ... (remaining 647 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 18 " -0.009 2.00e-02 2.50e+03 6.07e-03 7.38e-01 pdb=" CG TYR B 18 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR B 18 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 18 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 18 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 18 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 18 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 18 " -0.009 2.00e-02 2.50e+03 5.99e-03 7.17e-01 pdb=" CG TYR A 18 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 18 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 18 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 18 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 18 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 18 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 113 " 0.006 2.00e-02 2.50e+03 4.21e-03 3.54e-01 pdb=" CG TYR A 113 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 113 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 113 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 113 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 113 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 113 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 113 " 0.002 2.00e-02 2.50e+03 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.86: 1426 2.86 - 3.43: 4548 3.43 - 4.00: 7182 4.00 - 4.57: 10541 4.57 - 5.14: 14505 Nonbonded interactions: 38202 Sorted by model distance: nonbonded pdb=" OH TYR A 52 " pdb=" OD2 ASP B 58 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A 96 " pdb=" OG1 THR A 196 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR B 96 " pdb=" OG1 THR B 196 " model vdw 2.301 3.040 nonbonded pdb=" O TYR A 113 " pdb=" OH TYR B 18 " model vdw 2.323 3.040 nonbonded pdb=" OH TYR A 18 " pdb=" O TYR B 113 " model vdw 2.324 3.040 ... (remaining 38197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 303) selection = chain 'B' } 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: 0.610 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.760 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 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:5.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.001 0.012 4156 Z= 0.075 Angle : 0.341 4.999 5644 Z= 0.179 Chirality : 0.031 0.107 650 Planarity : 0.002 0.015 664 Dihedral : 13.842 80.987 1816 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 5.90 (0.38), residues: 476 helix: 4.48 (0.22), residues: 384 sheet: None (None), residues: 0 loop : 0.94 (0.85), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 47 TYR 0.014 0.001 TYR B 18 PHE 0.004 0.000 PHE A 135 TRP 0.002 0.000 TRP A 184 HIS 0.002 0.000 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00124 / 0.08 ( 4156) covalent geometry : angle 0.34094 / 0.18 ( 5644) hydrogen bonds : bond 0.09170 / 5.55 ( 333) hydrogen bonds : angle 4.06201 / 2.96 ( 981) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.7254 (tt) cc_final: 0.6627 (tp) REVERT: B 244 LEU cc_start: 0.7241 (tt) cc_final: 0.6615 (tp) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.6744 time to fit residues: 39.4623 Evaluate side-chains 51 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.191247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.142408 restraints weight = 4228.435| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.05 r_work: 0.3576 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4156 Z= 0.171 Angle : 0.526 5.579 5644 Z= 0.290 Chirality : 0.039 0.145 650 Planarity : 0.003 0.015 664 Dihedral : 6.534 46.785 952 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.47 % Allowed : 11.27 % Favored : 87.25 % 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: 5.21 (0.37), residues: 476 helix: 3.91 (0.23), residues: 390 sheet: None (None), residues: 0 loop : 0.88 (0.83), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 137 TYR 0.029 0.002 TYR A 85 PHE 0.012 0.002 PHE B 223 TRP 0.011 0.002 TRP A 184 HIS 0.002 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 4156) covalent geometry : angle 0.52629 / 0.29 ( 5644) hydrogen bonds : bond 0.04753 / 3.31 ( 333) hydrogen bonds : angle 3.47275 / 2.52 ( 981) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.139 Fit side-chains REVERT: A 180 GLN cc_start: 0.7661 (tp40) cc_final: 0.7273 (mp10) REVERT: A 190 TYR cc_start: 0.8781 (t80) cc_final: 0.8417 (t80) REVERT: A 244 LEU cc_start: 0.7110 (tt) cc_final: 0.6716 (tp) REVERT: B 180 GLN cc_start: 0.7658 (tp40) cc_final: 0.7274 (mp10) REVERT: B 190 TYR cc_start: 0.8774 (t80) cc_final: 0.8400 (t80) REVERT: B 244 LEU cc_start: 0.7106 (tt) cc_final: 0.6706 (tp) outliers start: 6 outliers final: 5 residues processed: 60 average time/residue: 0.6920 time to fit residues: 42.5997 Evaluate side-chains 60 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 245 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN B 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.188436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138680 restraints weight = 4141.968| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.02 r_work: 0.3533 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4156 Z= 0.141 Angle : 0.464 5.229 5644 Z= 0.254 Chirality : 0.036 0.125 650 Planarity : 0.003 0.020 664 Dihedral : 5.855 40.947 952 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.21 % Allowed : 11.52 % Favored : 86.27 % 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: 5.20 (0.38), residues: 476 helix: 3.91 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.88 (0.82), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.023 0.002 TYR B 85 PHE 0.011 0.001 PHE B 135 TRP 0.003 0.001 TRP B 78 HIS 0.002 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4156) covalent geometry : angle 0.46425 / 0.25 ( 5644) hydrogen bonds : bond 0.04626 / 3.20 ( 333) hydrogen bonds : angle 3.39592 / 2.48 ( 981) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.145 Fit side-chains REVERT: A 140 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6901 (mm) REVERT: A 180 GLN cc_start: 0.7782 (tp40) cc_final: 0.7394 (mp10) REVERT: A 190 TYR cc_start: 0.8858 (t80) cc_final: 0.8448 (t80) REVERT: B 140 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6930 (mm) REVERT: B 180 GLN cc_start: 0.7757 (tp40) cc_final: 0.7363 (mp10) REVERT: B 190 TYR cc_start: 0.8849 (t80) cc_final: 0.8429 (t80) outliers start: 9 outliers final: 2 residues processed: 56 average time/residue: 0.7961 time to fit residues: 45.7210 Evaluate side-chains 57 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.0060 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.0020 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN B 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.188271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138873 restraints weight = 4148.587| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.02 r_work: 0.3540 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4156 Z= 0.119 Angle : 0.431 4.801 5644 Z= 0.237 Chirality : 0.035 0.125 650 Planarity : 0.003 0.025 664 Dihedral : 5.424 35.368 952 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.47 % Allowed : 12.75 % Favored : 85.78 % 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: 5.15 (0.38), residues: 476 helix: 3.87 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.90 (0.84), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 137 TYR 0.017 0.001 TYR B 85 PHE 0.007 0.001 PHE A 109 TRP 0.002 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 4156) covalent geometry : angle 0.43120 / 0.24 ( 5644) hydrogen bonds : bond 0.04359 / 3.03 ( 333) hydrogen bonds : angle 3.32743 / 2.43 ( 981) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.130 Fit side-chains REVERT: A 39 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7231 (pt0) REVERT: A 140 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6935 (mm) REVERT: A 180 GLN cc_start: 0.7731 (tp40) cc_final: 0.7321 (mp10) REVERT: A 190 TYR cc_start: 0.8841 (t80) cc_final: 0.8482 (t80) REVERT: B 39 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7236 (pt0) REVERT: B 140 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6958 (mm) REVERT: B 180 GLN cc_start: 0.7736 (tp40) cc_final: 0.7337 (mp10) REVERT: B 190 TYR cc_start: 0.8840 (t80) cc_final: 0.8473 (t80) outliers start: 6 outliers final: 2 residues processed: 62 average time/residue: 0.8929 time to fit residues: 56.5846 Evaluate side-chains 66 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.183496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134139 restraints weight = 4158.663| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.96 r_work: 0.3487 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4156 Z= 0.148 Angle : 0.485 6.702 5644 Z= 0.265 Chirality : 0.036 0.150 650 Planarity : 0.003 0.028 664 Dihedral : 5.174 33.260 952 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.47 % Allowed : 13.73 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.94 (0.38), residues: 476 helix: 3.75 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.69 (0.81), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 137 TYR 0.022 0.002 TYR B 85 PHE 0.009 0.001 PHE A 135 TRP 0.005 0.001 TRP A 184 HIS 0.002 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 4156) covalent geometry : angle 0.48540 / 0.27 ( 5644) hydrogen bonds : bond 0.04981 / 3.43 ( 333) hydrogen bonds : angle 3.43316 / 2.50 ( 981) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.088 Fit side-chains REVERT: A 39 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7493 (pt0) REVERT: A 140 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6917 (mm) REVERT: A 180 GLN cc_start: 0.7795 (tp40) cc_final: 0.7412 (mp10) REVERT: A 190 TYR cc_start: 0.8936 (t80) cc_final: 0.8555 (t80) REVERT: B 39 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7474 (pt0) REVERT: B 140 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6930 (mm) REVERT: B 180 GLN cc_start: 0.7772 (tp40) cc_final: 0.7379 (mp10) REVERT: B 190 TYR cc_start: 0.8926 (t80) cc_final: 0.8537 (t80) outliers start: 6 outliers final: 2 residues processed: 68 average time/residue: 0.8403 time to fit residues: 58.4340 Evaluate side-chains 69 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.0060 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.0370 chunk 43 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5274 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.185540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.136544 restraints weight = 4254.591| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.02 r_work: 0.3512 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4156 Z= 0.122 Angle : 0.451 7.601 5644 Z= 0.247 Chirality : 0.035 0.171 650 Planarity : 0.003 0.025 664 Dihedral : 4.923 34.205 952 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.47 % Allowed : 14.46 % Favored : 84.07 % 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: 4.97 (0.38), residues: 476 helix: 3.78 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.62 (0.79), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 137 TYR 0.015 0.001 TYR B 85 PHE 0.008 0.001 PHE A 109 TRP 0.003 0.001 TRP B 184 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 4156) covalent geometry : angle 0.45130 / 0.25 ( 5644) hydrogen bonds : bond 0.04470 / 3.10 ( 333) hydrogen bonds : angle 3.30216 / 2.40 ( 981) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.147 Fit side-chains REVERT: A 39 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7407 (pt0) REVERT: A 135 PHE cc_start: 0.7917 (t80) cc_final: 0.7635 (t80) REVERT: A 140 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6964 (mm) REVERT: A 156 MET cc_start: 0.5850 (tpp) cc_final: 0.5605 (tpt) REVERT: A 180 GLN cc_start: 0.7707 (tp40) cc_final: 0.7316 (mp10) REVERT: A 190 TYR cc_start: 0.8904 (t80) cc_final: 0.8522 (t80) REVERT: B 39 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7390 (pt0) REVERT: B 156 MET cc_start: 0.6078 (tpp) cc_final: 0.5852 (tpt) REVERT: B 180 GLN cc_start: 0.7695 (tp40) cc_final: 0.7303 (mp10) REVERT: B 190 TYR cc_start: 0.8900 (t80) cc_final: 0.8517 (t80) outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 0.7736 time to fit residues: 54.6280 Evaluate side-chains 70 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.181731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.132186 restraints weight = 4266.046| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.98 r_work: 0.3465 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4156 Z= 0.148 Angle : 0.498 8.198 5644 Z= 0.272 Chirality : 0.037 0.175 650 Planarity : 0.003 0.027 664 Dihedral : 4.863 36.925 952 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.72 % Allowed : 15.44 % Favored : 82.84 % 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: 4.84 (0.38), residues: 476 helix: 3.70 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.52 (0.78), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 137 TYR 0.017 0.002 TYR B 85 PHE 0.008 0.001 PHE B 109 TRP 0.002 0.001 TRP B 184 HIS 0.002 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 4156) covalent geometry : angle 0.49833 / 0.27 ( 5644) hydrogen bonds : bond 0.05117 / 3.52 ( 333) hydrogen bonds : angle 3.42265 / 2.49 ( 981) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.153 Fit side-chains REVERT: A 39 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7466 (pt0) REVERT: A 140 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6890 (mm) REVERT: A 180 GLN cc_start: 0.7718 (tp40) cc_final: 0.7229 (mp10) REVERT: A 190 TYR cc_start: 0.8957 (t80) cc_final: 0.8562 (t80) REVERT: B 39 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7472 (pt0) REVERT: B 135 PHE cc_start: 0.7840 (t80) cc_final: 0.7560 (t80) REVERT: B 180 GLN cc_start: 0.7720 (tp40) cc_final: 0.7240 (mp10) REVERT: B 190 TYR cc_start: 0.8944 (t80) cc_final: 0.8543 (t80) outliers start: 7 outliers final: 4 residues processed: 66 average time/residue: 0.8459 time to fit residues: 57.1675 Evaluate side-chains 68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.181783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132299 restraints weight = 4166.713| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.99 r_work: 0.3473 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4156 Z= 0.148 Angle : 0.495 8.352 5644 Z= 0.269 Chirality : 0.036 0.176 650 Planarity : 0.003 0.029 664 Dihedral : 4.854 37.865 952 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.96 % Allowed : 15.44 % Favored : 82.60 % 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: 4.81 (0.38), residues: 476 helix: 3.68 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.51 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.015 0.001 TYR B 85 PHE 0.008 0.001 PHE B 109 TRP 0.002 0.001 TRP B 184 HIS 0.002 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 4156) covalent geometry : angle 0.49527 / 0.27 ( 5644) hydrogen bonds : bond 0.05110 / 3.52 ( 333) hydrogen bonds : angle 3.45048 / 2.52 ( 981) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.141 Fit side-chains REVERT: A 39 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7480 (pt0) REVERT: A 140 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6962 (mm) REVERT: A 180 GLN cc_start: 0.7715 (tp40) cc_final: 0.7219 (mp10) REVERT: A 190 TYR cc_start: 0.8957 (t80) cc_final: 0.8543 (t80) REVERT: B 39 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7481 (pt0) REVERT: B 135 PHE cc_start: 0.7889 (t80) cc_final: 0.7595 (t80) REVERT: B 180 GLN cc_start: 0.7715 (tp40) cc_final: 0.7220 (mp10) REVERT: B 190 TYR cc_start: 0.8951 (t80) cc_final: 0.8535 (t80) outliers start: 8 outliers final: 4 residues processed: 69 average time/residue: 0.8220 time to fit residues: 58.0287 Evaluate side-chains 68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.182631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.133173 restraints weight = 4223.635| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.00 r_work: 0.3475 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4156 Z= 0.141 Angle : 0.497 8.933 5644 Z= 0.270 Chirality : 0.036 0.178 650 Planarity : 0.003 0.029 664 Dihedral : 4.806 38.783 952 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.23 % Allowed : 16.67 % Favored : 82.11 % 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: 4.83 (0.38), residues: 476 helix: 3.71 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.47 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.013 0.001 TYR B 85 PHE 0.008 0.001 PHE B 109 TRP 0.003 0.001 TRP A 184 HIS 0.002 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4156) covalent geometry : angle 0.49659 / 0.27 ( 5644) hydrogen bonds : bond 0.04989 / 3.44 ( 333) hydrogen bonds : angle 3.43500 / 2.52 ( 981) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.145 Fit side-chains REVERT: A 39 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7540 (pt0) REVERT: A 140 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6954 (mm) REVERT: A 180 GLN cc_start: 0.7716 (tp40) cc_final: 0.7224 (mp10) REVERT: A 190 TYR cc_start: 0.8951 (t80) cc_final: 0.8535 (t80) REVERT: B 39 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7471 (pt0) REVERT: B 135 PHE cc_start: 0.7924 (t80) cc_final: 0.7642 (t80) REVERT: B 180 GLN cc_start: 0.7715 (tp40) cc_final: 0.7226 (mp10) REVERT: B 190 TYR cc_start: 0.8953 (t80) cc_final: 0.8537 (t80) outliers start: 5 outliers final: 4 residues processed: 66 average time/residue: 0.8488 time to fit residues: 57.3042 Evaluate side-chains 69 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.180968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.131742 restraints weight = 4165.705| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.94 r_work: 0.3461 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4156 Z= 0.156 Angle : 0.511 8.879 5644 Z= 0.278 Chirality : 0.037 0.186 650 Planarity : 0.003 0.030 664 Dihedral : 4.850 40.514 952 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.23 % Allowed : 16.91 % Favored : 81.86 % 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: 4.76 (0.38), residues: 476 helix: 3.66 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.43 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 137 TYR 0.014 0.002 TYR B 85 PHE 0.008 0.001 PHE B 109 TRP 0.002 0.001 TRP B 184 HIS 0.002 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 4156) covalent geometry : angle 0.51135 / 0.28 ( 5644) hydrogen bonds : bond 0.05288 / 3.64 ( 333) hydrogen bonds : angle 3.46330 / 2.53 ( 981) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.150 Fit side-chains REVERT: A 39 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7530 (pt0) REVERT: A 140 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6928 (mm) REVERT: A 180 GLN cc_start: 0.7690 (tp40) cc_final: 0.7190 (mp10) REVERT: B 39 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7466 (pt0) REVERT: B 180 GLN cc_start: 0.7696 (tp40) cc_final: 0.7195 (mp10) REVERT: B 190 TYR cc_start: 0.8944 (t80) cc_final: 0.8520 (t80) outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.8638 time to fit residues: 53.8441 Evaluate side-chains 63 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.181926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.133173 restraints weight = 4222.334| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.97 r_work: 0.3453 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4156 Z= 0.158 Angle : 0.515 8.821 5644 Z= 0.281 Chirality : 0.037 0.182 650 Planarity : 0.003 0.030 664 Dihedral : 4.885 41.476 952 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.23 % Allowed : 17.16 % Favored : 81.62 % 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: 4.76 (0.38), residues: 476 helix: 3.66 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.46 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.014 0.002 TYR B 85 PHE 0.007 0.001 PHE A 16 TRP 0.002 0.001 TRP A 184 HIS 0.002 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 4156) covalent geometry : angle 0.51457 / 0.28 ( 5644) hydrogen bonds : bond 0.05359 / 3.69 ( 333) hydrogen bonds : angle 3.47778 / 2.54 ( 981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1659.09 seconds wall clock time: 28 minutes 59.24 seconds (1739.24 seconds total)