Starting phenix.real_space_refine on Thu Jul 2 05:49:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfp_61435/07_2026/9jfp_61435.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfp_61435/07_2026/9jfp_61435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jfp_61435/07_2026/9jfp_61435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfp_61435/07_2026/9jfp_61435.map" model { file = "/net/cci-nas-00/data/ceres_data/9jfp_61435/07_2026/9jfp_61435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfp_61435/07_2026/9jfp_61435.cif" } resolution = 2.96 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= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 164 5.49 5 S 15 5.16 5 C 3743 2.51 5 N 1273 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 6921 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 329 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "F" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2875 Classifications: {'RNA': 134} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 67, 'rna3p_pyr': 52} Link IDs: {'rna2p': 15, 'rna3p': 118} Chain breaks: 2 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3432 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 24, 'TRANS': 406} Chain breaks: 1 Time building chain proxies: 1.73, per 1000 atoms: 0.25 Number of scatterers: 6921 At special positions: 0 Unit cell: (103.726, 94.4496, 118.062, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 164 15.00 O 1726 8.00 N 1273 7.00 C 3743 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: 0.60 Conformation dependent library (CDL) restraints added in 289.0 milliseconds 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 822 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 45.5% alpha, 10.9% beta 57 base pairs and 91 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 26 through 51 Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.607A pdb=" N ARG A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.664A pdb=" N LYS A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.897A pdb=" N ASP A 276 " --> pdb=" O GLN A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 339 through 375 removed outlier: 3.666A pdb=" N ILE A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 402 through 415 removed outlier: 3.928A pdb=" N PHE A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 147 removed outlier: 4.244A pdb=" N THR A 206 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS A 174 " --> pdb=" O TYR A 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 253 removed outlier: 7.331A pdb=" N TYR A 268 " --> pdb=" O ILE A 259 " (cutoff:3.500A) 158 hydrogen bonds defined for protein. 450 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 147 hydrogen bonds 278 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 91 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1377 1.33 - 1.45: 2499 1.45 - 1.57: 3180 1.57 - 1.69: 322 1.69 - 1.81: 26 Bond restraints: 7404 Sorted by residual: bond pdb=" O3' C F 21 " pdb=" P A F 22 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.50e-02 4.44e+03 1.02e+01 bond pdb=" C3' DT C 17 " pdb=" C2' DT C 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.07e+00 bond pdb=" C3' DC D 10 " pdb=" C2' DC D 10 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.29e+00 bond pdb=" C3' DT D 6 " pdb=" C2' DT D 6 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.49e+00 bond pdb=" C3' DT D 7 " pdb=" C2' DT D 7 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 4.98e+00 ... (remaining 7399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 10510 1.77 - 3.53: 247 3.53 - 5.30: 22 5.30 - 7.06: 3 7.06 - 8.83: 3 Bond angle restraints: 10785 Sorted by residual: angle pdb=" C4' G F 77 " pdb=" C3' G F 77 " pdb=" O3' G F 77 " ideal model delta sigma weight residual 109.40 118.23 -8.83 1.50e+00 4.44e-01 3.46e+01 angle pdb=" O3' C F 76 " pdb=" C3' C F 76 " pdb=" C2' C F 76 " ideal model delta sigma weight residual 109.50 118.06 -8.56 1.50e+00 4.44e-01 3.25e+01 angle pdb=" O4' DC C 28 " pdb=" C4' DC C 28 " pdb=" C3' DC C 28 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.49e+01 angle pdb=" O4' U F 23 " pdb=" C1' U F 23 " pdb=" C2' U F 23 " ideal model delta sigma weight residual 105.80 110.08 -4.28 1.00e+00 1.00e+00 1.83e+01 angle pdb=" N3 DT C 17 " pdb=" C4 DT C 17 " pdb=" O4 DT C 17 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 ... (remaining 10780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 3992 35.53 - 71.07: 514 71.07 - 106.60: 49 106.60 - 142.14: 3 142.14 - 177.67: 4 Dihedral angle restraints: 4562 sinusoidal: 3297 harmonic: 1265 Sorted by residual: dihedral pdb=" O4' C F 88 " pdb=" C1' C F 88 " pdb=" N1 C F 88 " pdb=" C2 C F 88 " ideal model delta sinusoidal sigma weight residual -128.00 49.67 -177.67 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U F 23 " pdb=" C2' U F 23 " pdb=" C1' U F 23 " pdb=" C3' U F 23 " ideal model delta sinusoidal sigma weight residual -35.00 2.87 -37.87 1 8.00e+00 1.56e-02 3.16e+01 dihedral pdb=" C4' U F 23 " pdb=" C3' U F 23 " pdb=" C2' U F 23 " pdb=" C1' U F 23 " ideal model delta sinusoidal sigma weight residual -35.00 2.17 -37.17 1 8.00e+00 1.56e-02 3.05e+01 ... (remaining 4559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1231 0.083 - 0.166: 59 0.166 - 0.249: 6 0.249 - 0.332: 1 0.332 - 0.415: 1 Chirality restraints: 1298 Sorted by residual: chirality pdb=" C3' G F 77 " pdb=" C4' G F 77 " pdb=" O3' G F 77 " pdb=" C2' G F 77 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" C3' C F 76 " pdb=" C4' C F 76 " pdb=" O3' C F 76 " pdb=" C2' C F 76 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" P G F 24 " pdb=" OP1 G F 24 " pdb=" OP2 G F 24 " pdb=" O5' G F 24 " both_signs ideal model delta sigma weight residual True 2.41 -2.62 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1295 not shown) Planarity restraints: 779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G F 77 " -0.024 2.00e-02 2.50e+03 1.19e-02 4.25e+00 pdb=" N9 G F 77 " 0.024 2.00e-02 2.50e+03 pdb=" C8 G F 77 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G F 77 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G F 77 " 0.008 2.00e-02 2.50e+03 pdb=" C6 G F 77 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G F 77 " -0.015 2.00e-02 2.50e+03 pdb=" N1 G F 77 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G F 77 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G F 77 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G F 77 " -0.010 2.00e-02 2.50e+03 pdb=" C4 G F 77 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 23 " -0.025 2.00e-02 2.50e+03 1.23e-02 3.43e+00 pdb=" N1 U F 23 " 0.021 2.00e-02 2.50e+03 pdb=" C2 U F 23 " 0.008 2.00e-02 2.50e+03 pdb=" O2 U F 23 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U F 23 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U F 23 " -0.009 2.00e-02 2.50e+03 pdb=" O4 U F 23 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U F 23 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U F 23 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 84 " -0.020 2.00e-02 2.50e+03 1.18e-02 3.15e+00 pdb=" N1 U F 84 " 0.029 2.00e-02 2.50e+03 pdb=" C2 U F 84 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U F 84 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U F 84 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U F 84 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U F 84 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U F 84 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U F 84 " 0.000 2.00e-02 2.50e+03 ... (remaining 776 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1382 2.78 - 3.31: 6260 3.31 - 3.84: 13367 3.84 - 4.37: 15153 4.37 - 4.90: 21883 Nonbonded interactions: 58045 Sorted by model distance: nonbonded pdb=" O2' U F 87 " pdb=" O2' U F 90 " model vdw 2.249 3.040 nonbonded pdb=" O ALA A 97 " pdb=" OG1 THR A 101 " model vdw 2.258 3.040 nonbonded pdb=" NE2 GLN A 32 " pdb=" O LYS A 168 " model vdw 2.311 3.120 nonbonded pdb=" OP2 U F 158 " pdb=" OG SER A 26 " model vdw 2.337 3.040 nonbonded pdb=" O2' G F 5 " pdb=" OP1 G F 6 " model vdw 2.346 3.040 ... (remaining 58040 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.590 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.450 Find NCS groups from input model: 0.030 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 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 : 0.003 0.048 7404 Z= 0.283 Angle : 0.620 8.829 10785 Z= 0.511 Chirality : 0.039 0.415 1298 Planarity : 0.004 0.040 779 Dihedral : 24.317 177.673 3740 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -0.17 (0.42), residues: 427 helix: 1.16 (0.42), residues: 176 sheet: -0.53 (0.61), residues: 75 loop : -1.21 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 141 TYR 0.014 0.001 TYR A 412 PHE 0.017 0.001 PHE A 143 TRP 0.005 0.001 TRP A 292 HIS 0.006 0.001 HIS A 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.28 ( 7404) covalent geometry : angle 0.62003 / 0.51 (10785) hydrogen bonds : bond 0.12640 / 15.19 ( 305) hydrogen bonds : angle 4.98066 / 6.21 ( 728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.107 Fit side-chains REVERT: A 388 MET cc_start: 0.3144 (ptp) cc_final: 0.2794 (mmp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.5426 time to fit residues: 41.6534 Evaluate side-chains 42 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN A 190 HIS A 365 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.255410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.210722 restraints weight = 7503.351| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 1.27 r_work: 0.3842 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7404 Z= 0.137 Angle : 0.574 9.347 10785 Z= 0.328 Chirality : 0.038 0.243 1298 Planarity : 0.005 0.040 779 Dihedral : 25.971 178.289 2862 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.65 % Allowed : 14.60 % Favored : 83.75 % 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: -0.04 (0.42), residues: 427 helix: 1.31 (0.42), residues: 179 sheet: -0.39 (0.62), residues: 75 loop : -1.27 (0.44), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.031 0.002 TYR A 412 PHE 0.022 0.001 PHE A 143 TRP 0.006 0.001 TRP A 183 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 ( 7404) covalent geometry : angle 0.57410 / 0.33 (10785) hydrogen bonds : bond 0.05222 / 5.84 ( 305) hydrogen bonds : angle 3.80435 / 5.23 ( 728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.117 Fit side-chains REVERT: A 75 MET cc_start: 0.7056 (mtm) cc_final: 0.6359 (mtt) REVERT: A 182 ILE cc_start: 0.6089 (pp) cc_final: 0.5810 (mp) REVERT: A 268 TYR cc_start: 0.6399 (m-80) cc_final: 0.5579 (m-80) REVERT: A 286 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7792 (mtm180) REVERT: A 388 MET cc_start: 0.3483 (ptp) cc_final: 0.3238 (mmp) outliers start: 6 outliers final: 2 residues processed: 49 average time/residue: 0.4549 time to fit residues: 23.6634 Evaluate side-chains 41 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 39 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.251390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.208388 restraints weight = 7334.590| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 1.92 r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7404 Z= 0.154 Angle : 0.558 8.788 10785 Z= 0.319 Chirality : 0.037 0.285 1298 Planarity : 0.005 0.037 779 Dihedral : 25.815 178.171 2862 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.41 % Allowed : 14.88 % Favored : 80.72 % 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: 0.01 (0.42), residues: 427 helix: 1.35 (0.42), residues: 179 sheet: -0.63 (0.62), residues: 76 loop : -1.10 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 358 TYR 0.031 0.002 TYR A 412 PHE 0.024 0.002 PHE A 143 TRP 0.017 0.003 TRP A 183 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 7404) covalent geometry : angle 0.55815 / 0.32 (10785) hydrogen bonds : bond 0.05022 / 5.71 ( 305) hydrogen bonds : angle 3.65621 / 5.09 ( 728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 132 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6435 (tpt170) REVERT: A 268 TYR cc_start: 0.6671 (m-80) cc_final: 0.6340 (m-80) REVERT: A 353 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.5994 (tt0) outliers start: 16 outliers final: 7 residues processed: 53 average time/residue: 0.5676 time to fit residues: 31.6824 Evaluate side-chains 46 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 56 optimal weight: 0.0020 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.252991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.208306 restraints weight = 7467.652| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 2.08 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7404 Z= 0.141 Angle : 0.553 9.377 10785 Z= 0.312 Chirality : 0.037 0.257 1298 Planarity : 0.004 0.037 779 Dihedral : 25.774 177.623 2862 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.75 % Allowed : 16.53 % Favored : 80.72 % 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: 0.09 (0.42), residues: 427 helix: 1.53 (0.43), residues: 176 sheet: -0.49 (0.60), residues: 75 loop : -1.20 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.025 0.002 TYR A 412 PHE 0.020 0.002 PHE A 143 TRP 0.009 0.002 TRP A 183 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 7404) covalent geometry : angle 0.55274 / 0.31 (10785) hydrogen bonds : bond 0.04601 / 5.14 ( 305) hydrogen bonds : angle 3.55273 / 5.03 ( 728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7258 (mtm) cc_final: 0.6710 (mtt) REVERT: A 132 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6388 (tpt-90) REVERT: A 268 TYR cc_start: 0.6690 (m-80) cc_final: 0.6345 (m-80) REVERT: A 353 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.5991 (tt0) outliers start: 10 outliers final: 6 residues processed: 44 average time/residue: 0.5037 time to fit residues: 23.4770 Evaluate side-chains 43 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 46 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 50.0000 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.250563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.198893 restraints weight = 7478.322| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 1.51 r_work: 0.3664 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7404 Z= 0.149 Angle : 0.556 9.243 10785 Z= 0.315 Chirality : 0.038 0.287 1298 Planarity : 0.005 0.037 779 Dihedral : 25.726 177.496 2862 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.86 % Allowed : 19.56 % Favored : 76.58 % 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: 0.06 (0.42), residues: 427 helix: 1.42 (0.42), residues: 177 sheet: -0.36 (0.61), residues: 75 loop : -1.21 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.026 0.002 TYR A 412 PHE 0.023 0.002 PHE A 143 TRP 0.007 0.002 TRP A 235 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 7404) covalent geometry : angle 0.55554 / 0.31 (10785) hydrogen bonds : bond 0.04721 / 5.32 ( 305) hydrogen bonds : angle 3.54567 / 5.03 ( 728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 268 TYR cc_start: 0.6257 (m-80) cc_final: 0.5213 (m-80) REVERT: A 353 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6104 (tt0) outliers start: 14 outliers final: 5 residues processed: 44 average time/residue: 0.5450 time to fit residues: 25.3971 Evaluate side-chains 39 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.0050 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 50.0000 chunk 4 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- 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 = 0.4674 r_free = 0.4674 target = 0.248396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.194840 restraints weight = 7490.001| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 1.50 r_work: 0.3679 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7404 Z= 0.164 Angle : 0.579 9.333 10785 Z= 0.326 Chirality : 0.038 0.290 1298 Planarity : 0.005 0.037 779 Dihedral : 25.743 177.177 2862 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.48 % Allowed : 22.04 % Favored : 75.48 % 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: 0.05 (0.41), residues: 427 helix: 1.38 (0.42), residues: 176 sheet: -0.37 (0.61), residues: 75 loop : -1.16 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 358 TYR 0.024 0.002 TYR A 412 PHE 0.025 0.002 PHE A 143 TRP 0.007 0.001 TRP A 80 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 7404) covalent geometry : angle 0.57898 / 0.33 (10785) hydrogen bonds : bond 0.04641 / 5.23 ( 305) hydrogen bonds : angle 3.63039 / 5.18 ( 728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 268 TYR cc_start: 0.6424 (m-80) cc_final: 0.5347 (m-80) REVERT: A 353 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6038 (tt0) REVERT: A 388 MET cc_start: 0.4135 (mmp) cc_final: 0.2912 (ptp) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 0.5270 time to fit residues: 23.9976 Evaluate side-chains 39 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 50.0000 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 50.0000 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.249135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.195361 restraints weight = 7439.454| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 1.39 r_work: 0.3696 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7404 Z= 0.147 Angle : 0.557 9.465 10785 Z= 0.314 Chirality : 0.037 0.275 1298 Planarity : 0.005 0.037 779 Dihedral : 25.713 177.411 2862 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.20 % Allowed : 21.49 % Favored : 76.31 % 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: 0.01 (0.42), residues: 427 helix: 1.39 (0.42), residues: 176 sheet: -0.54 (0.60), residues: 75 loop : -1.15 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 291 TYR 0.021 0.002 TYR A 412 PHE 0.021 0.002 PHE A 143 TRP 0.006 0.001 TRP A 80 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 ( 7404) covalent geometry : angle 0.55727 / 0.31 (10785) hydrogen bonds : bond 0.04409 / 4.95 ( 305) hydrogen bonds : angle 3.56283 / 5.12 ( 728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 268 TYR cc_start: 0.6491 (m-80) cc_final: 0.5402 (m-80) REVERT: A 353 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6057 (tt0) REVERT: A 388 MET cc_start: 0.4235 (mmp) cc_final: 0.3000 (ptp) outliers start: 8 outliers final: 4 residues processed: 42 average time/residue: 0.5077 time to fit residues: 22.6256 Evaluate side-chains 39 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 50.0000 chunk 47 optimal weight: 0.0470 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 50.0000 overall best weight: 1.3484 ------------------------------------------------------------------------------- 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 = 0.4655 r_free = 0.4655 target = 0.246414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.199150 restraints weight = 7419.453| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.24 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7404 Z= 0.192 Angle : 0.607 9.432 10785 Z= 0.342 Chirality : 0.040 0.327 1298 Planarity : 0.005 0.039 779 Dihedral : 25.715 177.158 2862 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.38 % Allowed : 22.31 % Favored : 76.31 % 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: -0.21 (0.41), residues: 427 helix: 1.19 (0.41), residues: 176 sheet: -0.64 (0.60), residues: 75 loop : -1.24 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 358 TYR 0.028 0.002 TYR A 412 PHE 0.028 0.003 PHE A 143 TRP 0.008 0.002 TRP A 80 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 ( 7404) covalent geometry : angle 0.60703 / 0.34 (10785) hydrogen bonds : bond 0.04895 / 5.60 ( 305) hydrogen bonds : angle 3.73849 / 5.31 ( 728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: A 268 TYR cc_start: 0.6849 (m-80) cc_final: 0.6381 (m-80) REVERT: A 353 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6072 (tt0) REVERT: A 388 MET cc_start: 0.3178 (mmp) cc_final: 0.2771 (ptp) outliers start: 5 outliers final: 4 residues processed: 36 average time/residue: 0.5133 time to fit residues: 19.6545 Evaluate side-chains 36 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 50.0000 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.4686 r_free = 0.4686 target = 0.249803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.196934 restraints weight = 7467.676| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 1.39 r_work: 0.3674 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7404 Z= 0.133 Angle : 0.559 9.666 10785 Z= 0.314 Chirality : 0.037 0.256 1298 Planarity : 0.004 0.037 779 Dihedral : 25.678 177.546 2862 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 1.65 % Allowed : 22.59 % Favored : 75.76 % 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: -0.09 (0.41), residues: 427 helix: 1.32 (0.41), residues: 176 sheet: -0.62 (0.61), residues: 75 loop : -1.20 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 291 TYR 0.017 0.002 TYR A 412 PHE 0.018 0.002 PHE A 143 TRP 0.010 0.002 TRP A 235 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 7404) covalent geometry : angle 0.55907 / 0.31 (10785) hydrogen bonds : bond 0.04226 / 4.72 ( 305) hydrogen bonds : angle 3.55417 / 5.07 ( 728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 91 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7260 (mt) REVERT: A 268 TYR cc_start: 0.6546 (m-80) cc_final: 0.5402 (m-80) REVERT: A 353 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6066 (tt0) outliers start: 6 outliers final: 4 residues processed: 38 average time/residue: 0.4414 time to fit residues: 18.0080 Evaluate side-chains 40 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 50.0000 chunk 5 optimal weight: 50.0000 chunk 35 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.250613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.199344 restraints weight = 7444.274| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 1.54 r_work: 0.3698 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7404 Z= 0.129 Angle : 0.550 9.761 10785 Z= 0.308 Chirality : 0.036 0.249 1298 Planarity : 0.004 0.037 779 Dihedral : 25.622 177.812 2862 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.93 % Allowed : 22.59 % Favored : 75.48 % 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: -0.05 (0.41), residues: 427 helix: 1.37 (0.41), residues: 176 sheet: -0.56 (0.61), residues: 75 loop : -1.23 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 291 TYR 0.022 0.002 TYR A 302 PHE 0.018 0.001 PHE A 143 TRP 0.021 0.002 TRP A 235 HIS 0.008 0.002 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 ( 7404) covalent geometry : angle 0.54974 / 0.31 (10785) hydrogen bonds : bond 0.04090 / 4.58 ( 305) hydrogen bonds : angle 3.46412 / 4.94 ( 728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 268 TYR cc_start: 0.6647 (m-80) cc_final: 0.5500 (m-80) REVERT: A 353 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6069 (tt0) outliers start: 7 outliers final: 3 residues processed: 35 average time/residue: 0.5148 time to fit residues: 19.2408 Evaluate side-chains 33 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 0.0170 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 50.0000 overall best weight: 0.6820 ------------------------------------------------------------------------------- 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 = 0.4689 r_free = 0.4689 target = 0.250039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.198315 restraints weight = 7454.493| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 1.47 r_work: 0.3693 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7404 Z= 0.136 Angle : 0.556 9.842 10785 Z= 0.312 Chirality : 0.036 0.263 1298 Planarity : 0.004 0.036 779 Dihedral : 25.588 177.763 2862 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.93 % Allowed : 23.42 % Favored : 74.66 % 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: -0.08 (0.41), residues: 427 helix: 1.33 (0.41), residues: 176 sheet: -0.59 (0.62), residues: 75 loop : -1.21 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 358 TYR 0.020 0.002 TYR A 302 PHE 0.019 0.002 PHE A 143 TRP 0.015 0.002 TRP A 235 HIS 0.007 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 7404) covalent geometry : angle 0.55572 / 0.31 (10785) hydrogen bonds : bond 0.04144 / 4.65 ( 305) hydrogen bonds : angle 3.48212 / 4.96 ( 728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.73 seconds wall clock time: 31 minutes 26.26 seconds (1886.26 seconds total)