Starting phenix.real_space_refine on Wed Jul 1 23:17:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1v_36805/07_2026/8k1v_36805.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1v_36805/07_2026/8k1v_36805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k1v_36805/07_2026/8k1v_36805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1v_36805/07_2026/8k1v_36805.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k1v_36805/07_2026/8k1v_36805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1v_36805/07_2026/8k1v_36805.map" } resolution = 3.48 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= 0.001 sd= 0.070 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 700 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: 4059 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.14, per 1000 atoms: 0.28 Number of scatterers: 4059 At special positions: 0 Unit cell: (67.1, 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 700 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: 0.27 Conformation dependent library (CDL) restraints added in 94.3 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: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 2 through 53 removed outlier: 5.615A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.718A pdb=" N ARG A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.764A 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: 5.613A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 removed outlier: 3.706A pdb=" N ARG B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.721A 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: 0.60 Time building geometry restraints manager: 0.35 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 B 118 " pdb=" N PRO B 119 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.36e-02 5.41e+03 3.25e-01 bond pdb=" C ILE A 118 " pdb=" N PRO A 119 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.36e-02 5.41e+03 3.13e-01 bond pdb=" C GLU B 70 " pdb=" N PRO B 71 " ideal model delta sigma weight residual 1.335 1.341 -0.006 1.28e-02 6.10e+03 2.24e-01 bond pdb=" N LYS A 211 " pdb=" CA LYS A 211 " ideal model delta sigma weight residual 1.457 1.463 -0.006 1.29e-02 6.01e+03 2.08e-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 2.07e-01 ... (remaining 4151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 5577 0.98 - 1.96: 48 1.96 - 2.95: 7 2.95 - 3.93: 6 3.93 - 4.91: 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 121.54 125.66 -4.12 1.91e+00 2.74e-01 4.66e+00 angle pdb=" C THR B 210 " pdb=" N LYS B 211 " pdb=" CA LYS B 211 " ideal model delta sigma weight residual 121.54 125.63 -4.09 1.91e+00 2.74e-01 4.58e+00 angle pdb=" N GLY B 117 " pdb=" CA GLY B 117 " pdb=" C GLY B 117 " ideal model delta sigma weight residual 113.18 116.68 -3.50 2.37e+00 1.78e-01 2.18e+00 angle pdb=" N GLY A 117 " pdb=" CA GLY A 117 " pdb=" C GLY A 117 " ideal model delta sigma weight residual 113.18 116.61 -3.43 2.37e+00 1.78e-01 2.09e+00 angle pdb=" CA LYS A 211 " pdb=" CB LYS A 211 " pdb=" CG LYS A 211 " ideal model delta sigma weight residual 114.10 116.55 -2.45 2.00e+00 2.50e-01 1.50e+00 ... (remaining 5639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 2406 16.01 - 32.03: 233 32.03 - 48.04: 49 48.04 - 64.06: 12 64.06 - 80.07: 12 Dihedral angle restraints: 2712 sinusoidal: 1310 harmonic: 1402 Sorted by residual: 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 -139.67 -40.33 2 1.50e+01 4.44e-03 8.94e+00 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 -139.74 -40.26 2 1.50e+01 4.44e-03 8.91e+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 79.78 -79.78 1 3.00e+01 1.11e-03 8.77e+00 ... (remaining 2709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 451 0.021 - 0.042: 82 0.042 - 0.063: 79 0.063 - 0.085: 20 0.085 - 0.106: 18 Chirality restraints: 650 Sorted by residual: chirality pdb=" CA VAL B 206 " pdb=" N VAL B 206 " pdb=" C VAL B 206 " pdb=" CB VAL B 206 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.80e-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 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 2.54 -0.10 2.00e-01 2.50e+01 2.64e-01 ... (remaining 647 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 100 " 0.011 5.00e-02 4.00e+02 1.69e-02 4.58e-01 pdb=" N PRO A 101 " -0.029 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.009 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 100 " -0.010 5.00e-02 4.00e+02 1.52e-02 3.68e-01 pdb=" N PRO B 101 " 0.026 5.00e-02 4.00e+02 pdb=" CA PRO B 101 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO B 101 " -0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 154 " 0.003 2.00e-02 2.50e+03 5.95e-03 3.54e-01 pdb=" C VAL A 154 " -0.010 2.00e-02 2.50e+03 pdb=" O VAL A 154 " 0.004 2.00e-02 2.50e+03 pdb=" N SER A 155 " 0.003 2.00e-02 2.50e+03 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 1400 2.85 - 3.43: 4457 3.43 - 4.00: 7154 4.00 - 4.57: 10305 4.57 - 5.14: 14285 Nonbonded interactions: 37601 Sorted by model distance: nonbonded pdb=" OH TYR A 96 " pdb=" OG1 THR A 196 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR A 52 " pdb=" OD2 ASP B 58 " model vdw 2.304 3.040 nonbonded pdb=" OD2 ASP A 58 " pdb=" OH TYR B 52 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR B 96 " pdb=" OG1 THR B 196 " model vdw 2.330 3.040 nonbonded pdb=" NZ LYS A 144 " pdb=" O ASP A 153 " model vdw 2.341 3.120 ... (remaining 37596 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: 0.490 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.310 Find NCS groups from input model: 0.190 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 0.011 4156 Z= 0.069 Angle : 0.315 4.911 5644 Z= 0.164 Chirality : 0.031 0.106 650 Planarity : 0.001 0.017 664 Dihedral : 13.710 80.074 1816 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 5.96 (0.37), residues: 476 helix: 4.59 (0.23), residues: 384 sheet: None (None), residues: 0 loop : 0.62 (0.73), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 47 TYR 0.010 0.001 TYR B 18 PHE 0.004 0.000 PHE B 109 TRP 0.001 0.000 TRP B 184 HIS 0.001 0.000 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00115 / 0.07 ( 4156) covalent geometry : angle 0.31478 / 0.16 ( 5644) hydrogen bonds : bond 0.09497 / 5.88 ( 333) hydrogen bonds : angle 3.99682 / 2.93 ( 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 117 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.152 Fit side-chains REVERT: A 35 MET cc_start: 0.8058 (ttp) cc_final: 0.7822 (mmm) REVERT: A 42 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7922 (tppt) REVERT: A 44 GLU cc_start: 0.8050 (tp30) cc_final: 0.7708 (tp30) REVERT: A 173 ILE cc_start: 0.7809 (mt) cc_final: 0.7532 (mt) REVERT: A 180 GLN cc_start: 0.7621 (mm110) cc_final: 0.6825 (tt0) REVERT: A 182 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7076 (mm-30) REVERT: B 35 MET cc_start: 0.8050 (ttp) cc_final: 0.7837 (mmm) REVERT: B 44 GLU cc_start: 0.8068 (tp30) cc_final: 0.7600 (tp30) REVERT: B 173 ILE cc_start: 0.7803 (mt) cc_final: 0.7526 (mt) REVERT: B 180 GLN cc_start: 0.7533 (mm110) cc_final: 0.6732 (tt0) REVERT: B 182 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7119 (mm-30) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0941 time to fit residues: 12.9911 Evaluate side-chains 95 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.178952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.128652 restraints weight = 4664.204| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.34 r_work: 0.3242 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2754 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= 0.135 Angle : 0.491 5.532 5644 Z= 0.258 Chirality : 0.037 0.117 650 Planarity : 0.003 0.020 664 Dihedral : 5.466 31.616 952 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.21 % Allowed : 8.82 % Favored : 88.97 % 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: 5.49 (0.38), residues: 476 helix: 4.03 (0.23), residues: 390 sheet: None (None), residues: 0 loop : 1.45 (0.91), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 36 TYR 0.018 0.002 TYR B 85 PHE 0.009 0.001 PHE B 223 TRP 0.003 0.001 TRP A 184 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 4156) covalent geometry : angle 0.49122 / 0.26 ( 5644) hydrogen bonds : bond 0.03608 / 2.53 ( 333) hydrogen bonds : angle 3.53761 / 2.59 ( 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 109 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.135 Fit side-chains REVERT: A 35 MET cc_start: 0.8466 (ttp) cc_final: 0.7978 (mmm) REVERT: A 36 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.7476 (mtp180) REVERT: A 42 LYS cc_start: 0.8168 (ttmm) cc_final: 0.7916 (tppt) REVERT: A 44 GLU cc_start: 0.8140 (tp30) cc_final: 0.7891 (tp30) REVERT: A 60 ARG cc_start: 0.8163 (tpp80) cc_final: 0.7899 (tpp80) REVERT: A 180 GLN cc_start: 0.7653 (mm110) cc_final: 0.6902 (tt0) REVERT: B 35 MET cc_start: 0.8516 (ttp) cc_final: 0.8084 (mmm) REVERT: B 36 ARG cc_start: 0.8371 (tpp80) cc_final: 0.7677 (mtp180) REVERT: B 44 GLU cc_start: 0.8157 (tp30) cc_final: 0.7780 (tp30) REVERT: B 180 GLN cc_start: 0.7685 (mm110) cc_final: 0.6973 (tt0) outliers start: 9 outliers final: 3 residues processed: 106 average time/residue: 0.0948 time to fit residues: 11.8728 Evaluate side-chains 101 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 134 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 HIS B 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.176115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.125506 restraints weight = 4572.433| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.30 r_work: 0.3236 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4156 Z= 0.119 Angle : 0.490 6.211 5644 Z= 0.251 Chirality : 0.035 0.106 650 Planarity : 0.002 0.015 664 Dihedral : 4.959 29.987 952 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.96 % Allowed : 10.29 % Favored : 87.75 % 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: 5.38 (0.39), residues: 476 helix: 3.90 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 1.68 (0.91), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 131 TYR 0.015 0.001 TYR B 85 PHE 0.007 0.001 PHE B 16 TRP 0.003 0.001 TRP B 78 HIS 0.001 0.000 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 4156) covalent geometry : angle 0.49009 / 0.25 ( 5644) hydrogen bonds : bond 0.03617 / 2.50 ( 333) hydrogen bonds : angle 3.41655 / 2.49 ( 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 110 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.148 Fit side-chains REVERT: A 35 MET cc_start: 0.8456 (ttp) cc_final: 0.8064 (mtt) REVERT: A 36 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.7466 (mtp180) REVERT: A 42 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7422 (tppt) REVERT: A 44 GLU cc_start: 0.8173 (tp30) cc_final: 0.7865 (tp30) REVERT: A 45 GLU cc_start: 0.7371 (pt0) cc_final: 0.6945 (pp20) REVERT: A 60 ARG cc_start: 0.8266 (tpp80) cc_final: 0.8013 (tpp80) REVERT: A 180 GLN cc_start: 0.7621 (mm110) cc_final: 0.6869 (tt0) REVERT: A 243 VAL cc_start: 0.7877 (t) cc_final: 0.7661 (t) REVERT: B 35 MET cc_start: 0.8449 (ttp) cc_final: 0.8087 (mmt) REVERT: B 36 ARG cc_start: 0.8377 (tpp80) cc_final: 0.7695 (mtp180) REVERT: B 44 GLU cc_start: 0.8175 (tp30) cc_final: 0.7788 (tp30) REVERT: B 58 ASP cc_start: 0.8284 (m-30) cc_final: 0.8017 (t0) REVERT: B 180 GLN cc_start: 0.7625 (mm110) cc_final: 0.6905 (tt0) REVERT: B 243 VAL cc_start: 0.7884 (t) cc_final: 0.7664 (t) outliers start: 8 outliers final: 6 residues processed: 107 average time/residue: 0.0847 time to fit residues: 10.7940 Evaluate side-chains 99 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 136 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.163735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115734 restraints weight = 4572.181| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.30 r_work: 0.3069 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4156 Z= 0.125 Angle : 0.488 5.766 5644 Z= 0.254 Chirality : 0.035 0.104 650 Planarity : 0.002 0.015 664 Dihedral : 4.690 35.803 952 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 3.68 % Allowed : 14.95 % Favored : 81.37 % 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: 5.22 (0.39), residues: 476 helix: 3.84 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 1.36 (0.88), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 73 TYR 0.017 0.001 TYR A 85 PHE 0.008 0.001 PHE A 16 TRP 0.002 0.001 TRP A 78 HIS 0.001 0.000 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 4156) covalent geometry : angle 0.48789 / 0.25 ( 5644) hydrogen bonds : bond 0.03905 / 2.72 ( 333) hydrogen bonds : angle 3.42316 / 2.49 ( 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 107 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.118 Fit side-chains REVERT: A 35 MET cc_start: 0.8566 (ttp) cc_final: 0.7874 (mmt) REVERT: A 42 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7854 (tppt) REVERT: A 44 GLU cc_start: 0.8104 (tp30) cc_final: 0.7761 (tp30) REVERT: A 60 ARG cc_start: 0.8407 (tpp80) cc_final: 0.8145 (tpp80) REVERT: A 180 GLN cc_start: 0.7531 (mm110) cc_final: 0.6892 (tt0) REVERT: A 243 VAL cc_start: 0.7685 (t) cc_final: 0.7469 (t) REVERT: B 35 MET cc_start: 0.8512 (ttp) cc_final: 0.7989 (mmt) REVERT: B 36 ARG cc_start: 0.8305 (tpp80) cc_final: 0.7597 (mtp180) REVERT: B 40 LYS cc_start: 0.8382 (ttmm) cc_final: 0.8170 (ttmm) REVERT: B 44 GLU cc_start: 0.8181 (tp30) cc_final: 0.7788 (tp30) REVERT: B 58 ASP cc_start: 0.8252 (m-30) cc_final: 0.7954 (t0) REVERT: B 73 ARG cc_start: 0.8330 (tpp80) cc_final: 0.8108 (mmt90) REVERT: B 180 GLN cc_start: 0.7532 (mm110) cc_final: 0.6898 (tt0) REVERT: B 243 VAL cc_start: 0.7676 (t) cc_final: 0.7458 (t) outliers start: 15 outliers final: 8 residues processed: 103 average time/residue: 0.1036 time to fit residues: 12.5298 Evaluate side-chains 94 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 7 optimal weight: 0.0470 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.163178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.115569 restraints weight = 4552.926| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.29 r_work: 0.3089 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4156 Z= 0.124 Angle : 0.522 7.245 5644 Z= 0.266 Chirality : 0.035 0.116 650 Planarity : 0.002 0.015 664 Dihedral : 4.635 38.535 952 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.96 % Allowed : 17.89 % Favored : 80.15 % 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: 5.19 (0.39), residues: 476 helix: 3.83 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 1.28 (0.87), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 73 TYR 0.013 0.001 TYR B 85 PHE 0.007 0.001 PHE A 16 TRP 0.002 0.001 TRP A 184 HIS 0.001 0.000 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 4156) covalent geometry : angle 0.52200 / 0.27 ( 5644) hydrogen bonds : bond 0.03920 / 2.72 ( 333) hydrogen bonds : angle 3.41738 / 2.48 ( 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 104 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.144 Fit side-chains REVERT: A 35 MET cc_start: 0.8598 (ttp) cc_final: 0.7864 (mmt) REVERT: A 42 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7897 (tppt) REVERT: A 44 GLU cc_start: 0.8120 (tp30) cc_final: 0.7703 (tp30) REVERT: A 60 ARG cc_start: 0.8399 (tpp80) cc_final: 0.8140 (tpp80) REVERT: A 180 GLN cc_start: 0.7441 (mm110) cc_final: 0.6900 (tt0) REVERT: A 243 VAL cc_start: 0.7658 (t) cc_final: 0.7440 (t) REVERT: B 31 SER cc_start: 0.8370 (p) cc_final: 0.8057 (m) REVERT: B 35 MET cc_start: 0.8513 (ttp) cc_final: 0.7988 (mmt) REVERT: B 36 ARG cc_start: 0.8267 (tpp80) cc_final: 0.7603 (mtp180) REVERT: B 44 GLU cc_start: 0.8149 (tp30) cc_final: 0.7756 (tp30) REVERT: B 73 ARG cc_start: 0.8351 (tpp80) cc_final: 0.8113 (mmt90) REVERT: B 180 GLN cc_start: 0.7454 (mm110) cc_final: 0.6968 (tt0) REVERT: B 243 VAL cc_start: 0.7643 (t) cc_final: 0.7412 (t) outliers start: 8 outliers final: 7 residues processed: 102 average time/residue: 0.0985 time to fit residues: 11.8393 Evaluate side-chains 95 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 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 = 0.3745 r_free = 0.3745 target = 0.158798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.112613 restraints weight = 4674.948| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.28 r_work: 0.3023 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4156 Z= 0.135 Angle : 0.514 6.258 5644 Z= 0.267 Chirality : 0.036 0.115 650 Planarity : 0.002 0.017 664 Dihedral : 4.629 40.166 952 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.70 % Allowed : 17.16 % Favored : 80.15 % 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: 5.11 (0.39), residues: 476 helix: 3.77 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 1.26 (0.87), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 73 TYR 0.012 0.001 TYR A 85 PHE 0.008 0.001 PHE A 109 TRP 0.002 0.001 TRP B 78 HIS 0.000 0.000 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 4156) covalent geometry : angle 0.51444 / 0.27 ( 5644) hydrogen bonds : bond 0.04164 / 2.90 ( 333) hydrogen bonds : angle 3.47586 / 2.52 ( 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 106 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.102 Fit side-chains REVERT: A 31 SER cc_start: 0.8376 (p) cc_final: 0.7930 (m) REVERT: A 35 MET cc_start: 0.8617 (ttp) cc_final: 0.7861 (mmt) REVERT: A 42 LYS cc_start: 0.8188 (ttmm) cc_final: 0.7482 (tppt) REVERT: A 44 GLU cc_start: 0.8115 (tp30) cc_final: 0.7738 (tp30) REVERT: A 45 GLU cc_start: 0.7640 (pt0) cc_final: 0.7128 (pp20) REVERT: A 180 GLN cc_start: 0.7451 (mm110) cc_final: 0.6910 (tt0) REVERT: A 243 VAL cc_start: 0.7699 (t) cc_final: 0.7477 (t) REVERT: B 31 SER cc_start: 0.8403 (p) cc_final: 0.7957 (m) REVERT: B 35 MET cc_start: 0.8543 (ttp) cc_final: 0.8041 (mmm) REVERT: B 36 ARG cc_start: 0.8232 (tpp80) cc_final: 0.7599 (mtp180) REVERT: B 44 GLU cc_start: 0.8167 (tp30) cc_final: 0.7783 (tp30) REVERT: B 180 GLN cc_start: 0.7495 (mm110) cc_final: 0.7011 (tt0) REVERT: B 243 VAL cc_start: 0.7699 (t) cc_final: 0.7480 (t) outliers start: 11 outliers final: 10 residues processed: 103 average time/residue: 0.1009 time to fit residues: 12.2449 Evaluate side-chains 100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 0.0040 chunk 41 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.162969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.116117 restraints weight = 4656.292| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.30 r_work: 0.3010 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4156 Z= 0.129 Angle : 0.534 7.102 5644 Z= 0.270 Chirality : 0.035 0.111 650 Planarity : 0.002 0.020 664 Dihedral : 4.611 41.699 952 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.70 % Allowed : 18.14 % Favored : 79.17 % 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: 5.07 (0.39), residues: 476 helix: 3.75 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 1.25 (0.87), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 73 TYR 0.014 0.001 TYR A 138 PHE 0.009 0.001 PHE B 109 TRP 0.003 0.001 TRP A 184 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 4156) covalent geometry : angle 0.53384 / 0.27 ( 5644) hydrogen bonds : bond 0.04125 / 2.87 ( 333) hydrogen bonds : angle 3.48453 / 2.53 ( 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 107 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.146 Fit side-chains REVERT: A 31 SER cc_start: 0.8430 (p) cc_final: 0.7884 (m) REVERT: A 35 MET cc_start: 0.8585 (ttp) cc_final: 0.7873 (mmm) REVERT: A 42 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7929 (tppt) REVERT: A 44 GLU cc_start: 0.8070 (tp30) cc_final: 0.7730 (tp30) REVERT: A 180 GLN cc_start: 0.7435 (mm110) cc_final: 0.6901 (tt0) REVERT: A 243 VAL cc_start: 0.7718 (t) cc_final: 0.7514 (t) REVERT: B 19 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7559 (mp) REVERT: B 31 SER cc_start: 0.8416 (p) cc_final: 0.7872 (m) REVERT: B 35 MET cc_start: 0.8536 (ttp) cc_final: 0.7973 (mmm) REVERT: B 36 ARG cc_start: 0.8212 (tpp80) cc_final: 0.7633 (mtp180) REVERT: B 44 GLU cc_start: 0.8200 (tp30) cc_final: 0.7862 (tp30) REVERT: B 180 GLN cc_start: 0.7454 (mm110) cc_final: 0.6988 (tt0) REVERT: B 243 VAL cc_start: 0.7702 (t) cc_final: 0.7492 (t) outliers start: 11 outliers final: 9 residues processed: 105 average time/residue: 0.0992 time to fit residues: 12.2505 Evaluate side-chains 104 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 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 = 0.3748 r_free = 0.3748 target = 0.158692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.110573 restraints weight = 4607.343| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.32 r_work: 0.3041 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4156 Z= 0.143 Angle : 0.556 7.981 5644 Z= 0.282 Chirality : 0.036 0.114 650 Planarity : 0.002 0.019 664 Dihedral : 4.716 42.590 952 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.45 % Allowed : 18.87 % Favored : 78.68 % 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: 3.68 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 1.05 (0.85), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 60 TYR 0.014 0.001 TYR B 138 PHE 0.008 0.001 PHE B 16 TRP 0.002 0.001 TRP A 78 HIS 0.000 0.000 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 4156) covalent geometry : angle 0.55630 / 0.28 ( 5644) hydrogen bonds : bond 0.04507 / 3.12 ( 333) hydrogen bonds : angle 3.53213 / 2.57 ( 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 105 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.137 Fit side-chains REVERT: A 19 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7474 (mp) REVERT: A 31 SER cc_start: 0.8476 (p) cc_final: 0.8043 (m) REVERT: A 35 MET cc_start: 0.8593 (ttp) cc_final: 0.7835 (mmt) REVERT: A 42 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7932 (tppt) REVERT: A 44 GLU cc_start: 0.8069 (tp30) cc_final: 0.7715 (tp30) REVERT: A 180 GLN cc_start: 0.7460 (mm110) cc_final: 0.6914 (tt0) REVERT: A 243 VAL cc_start: 0.7749 (t) cc_final: 0.7512 (t) REVERT: B 19 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7583 (mp) REVERT: B 31 SER cc_start: 0.8455 (p) cc_final: 0.8031 (m) REVERT: B 35 MET cc_start: 0.8557 (ttp) cc_final: 0.7995 (mmt) REVERT: B 36 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7557 (mtp180) REVERT: B 44 GLU cc_start: 0.8208 (tp30) cc_final: 0.7869 (tp30) REVERT: B 180 GLN cc_start: 0.7514 (mm110) cc_final: 0.7025 (tt0) REVERT: B 243 VAL cc_start: 0.7697 (t) cc_final: 0.7479 (t) outliers start: 10 outliers final: 8 residues processed: 103 average time/residue: 0.1039 time to fit residues: 12.5645 Evaluate side-chains 105 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.158693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.111197 restraints weight = 4689.033| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.32 r_work: 0.2988 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4156 Z= 0.135 Angle : 0.549 6.675 5644 Z= 0.278 Chirality : 0.036 0.110 650 Planarity : 0.002 0.019 664 Dihedral : 4.709 43.804 952 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.94 % Allowed : 18.87 % Favored : 78.19 % 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: 4.92 (0.38), residues: 476 helix: 3.68 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 1.01 (0.85), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 73 TYR 0.013 0.001 TYR B 138 PHE 0.009 0.001 PHE B 109 TRP 0.003 0.001 TRP A 184 HIS 0.000 0.000 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 4156) covalent geometry : angle 0.54936 / 0.28 ( 5644) hydrogen bonds : bond 0.04383 / 3.03 ( 333) hydrogen bonds : angle 3.55706 / 2.60 ( 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 108 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.136 Fit side-chains REVERT: A 19 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7497 (mp) REVERT: A 31 SER cc_start: 0.8497 (p) cc_final: 0.8055 (m) REVERT: A 35 MET cc_start: 0.8604 (ttp) cc_final: 0.7841 (mmt) REVERT: A 42 LYS cc_start: 0.8231 (ttmm) cc_final: 0.7964 (tppt) REVERT: A 44 GLU cc_start: 0.8125 (tp30) cc_final: 0.7759 (tp30) REVERT: A 180 GLN cc_start: 0.7445 (mm110) cc_final: 0.6912 (tt0) REVERT: A 243 VAL cc_start: 0.7659 (t) cc_final: 0.7425 (t) REVERT: B 19 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7597 (mp) REVERT: B 31 SER cc_start: 0.8472 (p) cc_final: 0.8050 (m) REVERT: B 35 MET cc_start: 0.8574 (ttp) cc_final: 0.7954 (mmt) REVERT: B 36 ARG cc_start: 0.8183 (tpp80) cc_final: 0.7565 (mtp180) REVERT: B 44 GLU cc_start: 0.8220 (tp30) cc_final: 0.7884 (tp30) REVERT: B 180 GLN cc_start: 0.7510 (mm110) cc_final: 0.7020 (tt0) REVERT: B 243 VAL cc_start: 0.7673 (t) cc_final: 0.7452 (t) outliers start: 12 outliers final: 10 residues processed: 106 average time/residue: 0.1107 time to fit residues: 13.7766 Evaluate side-chains 107 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.156080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110201 restraints weight = 4618.387| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.24 r_work: 0.2987 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4156 Z= 0.174 Angle : 0.600 7.752 5644 Z= 0.306 Chirality : 0.038 0.117 650 Planarity : 0.003 0.020 664 Dihedral : 4.995 43.337 952 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.94 % Allowed : 18.87 % Favored : 78.19 % 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: 4.80 (0.38), residues: 476 helix: 3.62 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.82 (0.83), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 73 TYR 0.014 0.002 TYR B 138 PHE 0.010 0.001 PHE B 16 TRP 0.003 0.001 TRP A 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 4156) covalent geometry : angle 0.59971 / 0.31 ( 5644) hydrogen bonds : bond 0.05159 / 3.54 ( 333) hydrogen bonds : angle 3.65877 / 2.68 ( 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 112 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.094 Fit side-chains REVERT: A 18 TYR cc_start: 0.8684 (t80) cc_final: 0.8392 (t80) REVERT: A 19 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7404 (mp) REVERT: A 31 SER cc_start: 0.8434 (p) cc_final: 0.8027 (m) REVERT: A 35 MET cc_start: 0.8632 (ttp) cc_final: 0.7902 (mmt) REVERT: A 42 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7961 (tppt) REVERT: A 44 GLU cc_start: 0.8129 (tp30) cc_final: 0.7751 (tp30) REVERT: A 180 GLN cc_start: 0.7550 (mm110) cc_final: 0.6967 (tt0) REVERT: A 243 VAL cc_start: 0.7752 (t) cc_final: 0.7519 (t) REVERT: B 19 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7614 (mp) REVERT: B 31 SER cc_start: 0.8475 (p) cc_final: 0.8089 (m) REVERT: B 35 MET cc_start: 0.8598 (ttp) cc_final: 0.7965 (mmt) REVERT: B 36 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7544 (mtp180) REVERT: B 44 GLU cc_start: 0.8232 (tp30) cc_final: 0.7869 (tp30) REVERT: B 180 GLN cc_start: 0.7618 (mm110) cc_final: 0.7097 (tt0) REVERT: B 243 VAL cc_start: 0.7736 (t) cc_final: 0.7528 (t) outliers start: 12 outliers final: 9 residues processed: 110 average time/residue: 0.0905 time to fit residues: 11.5768 Evaluate side-chains 106 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.157280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111137 restraints weight = 4631.113| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.28 r_work: 0.2935 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4156 Z= 0.150 Angle : 0.579 6.814 5644 Z= 0.292 Chirality : 0.036 0.108 650 Planarity : 0.003 0.019 664 Dihedral : 4.972 44.890 952 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.45 % Allowed : 19.61 % Favored : 77.94 % 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: 4.86 (0.38), residues: 476 helix: 3.66 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.83 (0.83), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 73 TYR 0.014 0.001 TYR B 138 PHE 0.010 0.001 PHE B 109 TRP 0.003 0.001 TRP A 184 HIS 0.000 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 4156) covalent geometry : angle 0.57866 / 0.29 ( 5644) hydrogen bonds : bond 0.04761 / 3.30 ( 333) hydrogen bonds : angle 3.57193 / 2.61 ( 981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1013.83 seconds wall clock time: 18 minutes 4.32 seconds (1084.32 seconds total)