Starting phenix.real_space_refine on Wed Sep 17 03:32:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x34_32978/09_2025/7x34_32978.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x34_32978/09_2025/7x34_32978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x34_32978/09_2025/7x34_32978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x34_32978/09_2025/7x34_32978.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x34_32978/09_2025/7x34_32978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x34_32978/09_2025/7x34_32978.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 215 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians P 94 5.49 5 C 1365 2.51 5 N 503 2.21 5 O 800 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2762 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 745 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "3" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 2017 Classifications: {'RNA': 94} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 54, 'rna3p_pyr': 36} Link IDs: {'rna2p': 3, 'rna3p': 90} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A 31756 " occ=0.55 ... (20 atoms not shown) pdb=" C4 A 31756 " occ=0.55 Time building chain proxies: 0.86, per 1000 atoms: 0.31 Number of scatterers: 2762 At special positions: 0 Unit cell: (141.024, 88.14, 172.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 94 15.00 O 800 8.00 N 503 7.00 C 1365 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: 0.28 Conformation dependent library (CDL) restraints added in 40.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 192 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 0 sheets defined 77.0% alpha, 0.0% beta 19 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'C' and resid 334 through 365 removed outlier: 3.869A pdb=" N ALA C 338 " --> pdb=" O ALA C 334 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 350 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS C 351 " --> pdb=" O ALA C 347 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C 355 " --> pdb=" O LYS C 351 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 362 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS C 363 " --> pdb=" O ARG C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 387 Processing helix chain 'C' and resid 389 through 403 Processing helix chain 'C' and resid 407 through 421 54 hydrogen bonds defined for protein. 162 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 0.41 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: 1.04 - 1.16: 1 1.16 - 1.27: 221 1.27 - 1.39: 849 1.39 - 1.50: 1042 1.50 - 1.62: 896 Bond restraints: 3009 Sorted by residual: bond pdb=" CG PRO C 425 " pdb=" CD PRO C 425 " ideal model delta sigma weight residual 1.503 1.043 0.460 3.40e-02 8.65e+02 1.83e+02 bond pdb=" N PRO C 425 " pdb=" CD PRO C 425 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.28e+01 bond pdb=" CA ASN C 403 " pdb=" C ASN C 403 " ideal model delta sigma weight residual 1.526 1.543 -0.017 1.08e-02 8.57e+03 2.52e+00 bond pdb=" N1 U 31708 " pdb=" C2 U 31708 " ideal model delta sigma weight residual 1.381 1.406 -0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" CB ASN C 403 " pdb=" CG ASN C 403 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.24e+00 ... (remaining 3004 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.19: 4498 5.19 - 10.38: 18 10.38 - 15.57: 4 15.57 - 20.76: 2 20.76 - 25.94: 1 Bond angle restraints: 4523 Sorted by residual: angle pdb=" N PRO C 425 " pdb=" CD PRO C 425 " pdb=" CG PRO C 425 " ideal model delta sigma weight residual 103.20 77.26 25.94 1.50e+00 4.44e-01 2.99e+02 angle pdb=" CA PRO C 425 " pdb=" CB PRO C 425 " pdb=" CG PRO C 425 " ideal model delta sigma weight residual 104.50 84.84 19.66 1.90e+00 2.77e-01 1.07e+02 angle pdb=" CA PRO C 425 " pdb=" N PRO C 425 " pdb=" CD PRO C 425 " ideal model delta sigma weight residual 112.00 100.92 11.08 1.40e+00 5.10e-01 6.27e+01 angle pdb=" CB PRO C 425 " pdb=" CG PRO C 425 " pdb=" CD PRO C 425 " ideal model delta sigma weight residual 106.10 125.98 -19.88 3.20e+00 9.77e-02 3.86e+01 angle pdb=" CA ARG C 359 " pdb=" CB ARG C 359 " pdb=" CG ARG C 359 " ideal model delta sigma weight residual 114.10 122.09 -7.99 2.00e+00 2.50e-01 1.60e+01 ... (remaining 4518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 1641 35.62 - 71.23: 237 71.23 - 106.85: 28 106.85 - 142.46: 0 142.46 - 178.08: 1 Dihedral angle restraints: 1907 sinusoidal: 1614 harmonic: 293 Sorted by residual: dihedral pdb=" O4' U 31761 " pdb=" C1' U 31761 " pdb=" N1 U 31761 " pdb=" C2 U 31761 " ideal model delta sinusoidal sigma weight residual -128.00 50.08 -178.08 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' A 31707 " pdb=" C1' A 31707 " pdb=" N9 A 31707 " pdb=" C4 A 31707 " ideal model delta sinusoidal sigma weight residual 70.00 2.44 67.56 1 2.00e+01 2.50e-03 1.48e+01 dihedral pdb=" N PRO C 425 " pdb=" CG PRO C 425 " pdb=" CD PRO C 425 " pdb=" CB PRO C 425 " ideal model delta sinusoidal sigma weight residual 30.00 77.42 -47.42 1 1.50e+01 4.44e-03 1.38e+01 ... (remaining 1904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 458 0.046 - 0.093: 89 0.093 - 0.139: 29 0.139 - 0.185: 8 0.185 - 0.231: 4 Chirality restraints: 588 Sorted by residual: chirality pdb=" CB ILE C 358 " pdb=" CA ILE C 358 " pdb=" CG1 ILE C 358 " pdb=" CG2 ILE C 358 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C1' U 31752 " pdb=" O4' U 31752 " pdb=" C2' U 31752 " pdb=" N1 U 31752 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C1' G 31760 " pdb=" O4' G 31760 " pdb=" C2' G 31760 " pdb=" N9 G 31760 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 585 not shown) Planarity restraints: 222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 31747 " 0.036 2.00e-02 2.50e+03 1.52e-02 6.96e+00 pdb=" N9 G 31747 " -0.035 2.00e-02 2.50e+03 pdb=" C8 G 31747 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G 31747 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 31747 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G 31747 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G 31747 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G 31747 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G 31747 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G 31747 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G 31747 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G 31747 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 31752 " 0.032 2.00e-02 2.50e+03 1.60e-02 5.75e+00 pdb=" N1 U 31752 " -0.031 2.00e-02 2.50e+03 pdb=" C2 U 31752 " -0.005 2.00e-02 2.50e+03 pdb=" O2 U 31752 " -0.006 2.00e-02 2.50e+03 pdb=" N3 U 31752 " 0.007 2.00e-02 2.50e+03 pdb=" C4 U 31752 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U 31752 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U 31752 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U 31752 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 31760 " 0.029 2.00e-02 2.50e+03 1.23e-02 4.57e+00 pdb=" N9 G 31760 " -0.028 2.00e-02 2.50e+03 pdb=" C8 G 31760 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G 31760 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G 31760 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G 31760 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G 31760 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G 31760 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G 31760 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G 31760 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G 31760 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G 31760 " -0.003 2.00e-02 2.50e+03 ... (remaining 219 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 823 2.83 - 3.35: 2506 3.35 - 3.87: 6051 3.87 - 4.38: 6453 4.38 - 4.90: 8054 Nonbonded interactions: 23887 Sorted by model distance: nonbonded pdb=" N2 G 31697 " pdb=" O2 U 31704 " model vdw 2.316 2.496 nonbonded pdb=" O2 U 31684 " pdb=" N2 G 31717 " model vdw 2.356 2.496 nonbonded pdb=" O2' A 31755 " pdb=" O4' A 31756 " model vdw 2.383 3.040 nonbonded pdb=" O4 U 31684 " pdb=" O6 G 31717 " model vdw 2.411 2.432 nonbonded pdb=" O GLU C 392 " pdb=" OG1 THR C 396 " model vdw 2.422 3.040 ... (remaining 23882 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=0.55 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.040 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.009 0.460 3009 Z= 0.340 Angle : 1.172 25.944 4523 Z= 0.608 Chirality : 0.047 0.231 588 Planarity : 0.007 0.070 222 Dihedral : 24.837 178.075 1715 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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 aren not related in a simple way. whole: -2.86 (0.75), residues: 98 helix: -1.82 (0.46), residues: 79 sheet: None (None), residues: 0 loop : -1.15 (1.77), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 356 TYR 0.014 0.002 TYR C 367 PHE 0.007 0.002 PHE C 368 Details of bonding type rmsd covalent geometry : bond 0.00936 ( 3009) covalent geometry : angle 1.17179 ( 4523) hydrogen bonds : bond 0.11013 ( 102) hydrogen bonds : angle 5.91121 ( 238) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.058 Fit side-chains REVERT: C 366 ASP cc_start: 0.9573 (m-30) cc_final: 0.9369 (m-30) REVERT: C 378 ASP cc_start: 0.8190 (m-30) cc_final: 0.7918 (m-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0333 time to fit residues: 0.8238 Evaluate side-chains 13 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 overall best weight: 8.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.055392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.046395 restraints weight = 33322.218| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.93 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3009 Z= 0.277 Angle : 0.811 9.425 4523 Z= 0.414 Chirality : 0.042 0.316 588 Planarity : 0.005 0.022 222 Dihedral : 25.990 159.072 1531 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 29.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.60 % Allowed : 19.48 % Favored : 77.92 % 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 aren not related in a simple way. whole: -1.00 (0.82), residues: 98 helix: -0.38 (0.54), residues: 73 sheet: None (None), residues: 0 loop : -1.08 (1.51), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 356 TYR 0.012 0.003 TYR C 367 PHE 0.011 0.003 PHE C 368 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 3009) covalent geometry : angle 0.81150 ( 4523) hydrogen bonds : bond 0.09615 ( 102) hydrogen bonds : angle 4.26527 ( 238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.054 Fit side-chains REVERT: C 361 SER cc_start: 0.8785 (m) cc_final: 0.8502 (p) REVERT: C 367 TYR cc_start: 0.7415 (m-80) cc_final: 0.6992 (m-80) REVERT: C 378 ASP cc_start: 0.8560 (m-30) cc_final: 0.8207 (m-30) outliers start: 2 outliers final: 1 residues processed: 17 average time/residue: 0.0338 time to fit residues: 0.8444 Evaluate side-chains 12 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.054532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.047489 restraints weight = 33117.932| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 4.35 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3009 Z= 0.282 Angle : 0.837 13.603 4523 Z= 0.429 Chirality : 0.045 0.345 588 Planarity : 0.005 0.021 222 Dihedral : 26.066 146.804 1531 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 33.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 5.19 % Allowed : 19.48 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.85), residues: 98 helix: -0.05 (0.60), residues: 69 sheet: None (None), residues: 0 loop : -1.01 (1.32), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 356 TYR 0.014 0.003 TYR C 367 PHE 0.013 0.004 PHE C 432 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 3009) covalent geometry : angle 0.83728 ( 4523) hydrogen bonds : bond 0.09003 ( 102) hydrogen bonds : angle 4.12976 ( 238) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.051 Fit side-chains REVERT: C 367 TYR cc_start: 0.7277 (m-80) cc_final: 0.6937 (m-80) REVERT: C 378 ASP cc_start: 0.8372 (m-30) cc_final: 0.7978 (m-30) REVERT: C 428 LEU cc_start: 0.9345 (mt) cc_final: 0.9097 (pp) outliers start: 4 outliers final: 1 residues processed: 14 average time/residue: 0.0262 time to fit residues: 0.5771 Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 0.0970 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 overall best weight: 6.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.055344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.047901 restraints weight = 32883.299| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.60 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3009 Z= 0.226 Angle : 0.755 14.598 4523 Z= 0.388 Chirality : 0.041 0.324 588 Planarity : 0.004 0.020 222 Dihedral : 25.953 143.790 1531 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 26.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.60 % Allowed : 24.68 % Favored : 72.73 % 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 aren not related in a simple way. whole: -0.47 (0.84), residues: 98 helix: 0.05 (0.57), residues: 73 sheet: None (None), residues: 0 loop : -1.07 (1.46), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 356 TYR 0.010 0.002 TYR C 367 PHE 0.010 0.003 PHE C 432 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 3009) covalent geometry : angle 0.75517 ( 4523) hydrogen bonds : bond 0.07996 ( 102) hydrogen bonds : angle 3.93032 ( 238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.037 Fit side-chains REVERT: C 367 TYR cc_start: 0.6981 (m-80) cc_final: 0.6637 (m-80) REVERT: C 378 ASP cc_start: 0.8315 (m-30) cc_final: 0.7812 (m-30) REVERT: C 428 LEU cc_start: 0.9246 (mt) cc_final: 0.9033 (pp) outliers start: 2 outliers final: 2 residues processed: 12 average time/residue: 0.0304 time to fit residues: 0.5534 Evaluate side-chains 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 429 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.055076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.047748 restraints weight = 32679.538| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.70 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3009 Z= 0.242 Angle : 0.772 12.879 4523 Z= 0.398 Chirality : 0.042 0.323 588 Planarity : 0.005 0.021 222 Dihedral : 25.986 140.380 1531 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 29.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.90 % Allowed : 23.38 % Favored : 72.73 % 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 aren not related in a simple way. whole: 0.24 (0.85), residues: 98 helix: 0.57 (0.61), residues: 69 sheet: None (None), residues: 0 loop : -0.61 (1.28), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 359 TYR 0.020 0.004 TYR C 431 PHE 0.009 0.003 PHE C 432 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 3009) covalent geometry : angle 0.77238 ( 4523) hydrogen bonds : bond 0.08496 ( 102) hydrogen bonds : angle 3.94591 ( 238) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.055 Fit side-chains REVERT: C 378 ASP cc_start: 0.8352 (m-30) cc_final: 0.8083 (m-30) outliers start: 3 outliers final: 1 residues processed: 11 average time/residue: 0.0303 time to fit residues: 0.5329 Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 14 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.056137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.048514 restraints weight = 32279.828| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.47 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3009 Z= 0.190 Angle : 0.692 10.662 4523 Z= 0.361 Chirality : 0.039 0.288 588 Planarity : 0.004 0.021 222 Dihedral : 25.873 141.492 1531 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 24.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.60 % Allowed : 23.38 % Favored : 74.03 % 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 aren not related in a simple way. whole: -0.07 (0.87), residues: 98 helix: 0.28 (0.59), residues: 74 sheet: None (None), residues: 0 loop : -0.72 (1.52), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 356 TYR 0.013 0.003 TYR C 431 PHE 0.003 0.001 PHE C 432 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3009) covalent geometry : angle 0.69244 ( 4523) hydrogen bonds : bond 0.06945 ( 102) hydrogen bonds : angle 3.76819 ( 238) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.060 Fit side-chains REVERT: C 378 ASP cc_start: 0.8304 (m-30) cc_final: 0.7985 (m-30) outliers start: 2 outliers final: 2 residues processed: 10 average time/residue: 0.0305 time to fit residues: 0.4928 Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 429 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 10 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.056191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.048698 restraints weight = 31964.070| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.22 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3009 Z= 0.186 Angle : 0.688 9.696 4523 Z= 0.360 Chirality : 0.039 0.285 588 Planarity : 0.004 0.021 222 Dihedral : 25.872 140.951 1531 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.90 % Allowed : 20.78 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.86), residues: 98 helix: 0.26 (0.57), residues: 74 sheet: None (None), residues: 0 loop : -0.54 (1.55), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 359 TYR 0.031 0.006 TYR C 367 PHE 0.008 0.002 PHE C 432 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 3009) covalent geometry : angle 0.68836 ( 4523) hydrogen bonds : bond 0.07016 ( 102) hydrogen bonds : angle 3.69697 ( 238) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.056 Fit side-chains REVERT: C 367 TYR cc_start: 0.8070 (m-10) cc_final: 0.7861 (m-10) REVERT: C 378 ASP cc_start: 0.8421 (m-30) cc_final: 0.7995 (m-30) outliers start: 3 outliers final: 3 residues processed: 11 average time/residue: 0.0325 time to fit residues: 0.5581 Evaluate side-chains 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 8 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 429 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.055974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.048359 restraints weight = 33136.182| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.84 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3009 Z= 0.231 Angle : 0.711 9.059 4523 Z= 0.371 Chirality : 0.041 0.291 588 Planarity : 0.004 0.020 222 Dihedral : 25.859 140.089 1531 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 25.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.90 % Allowed : 22.08 % Favored : 74.03 % 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 aren not related in a simple way. whole: -0.15 (0.84), residues: 98 helix: 0.16 (0.56), residues: 74 sheet: None (None), residues: 0 loop : -0.51 (1.55), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 356 TYR 0.020 0.004 TYR C 367 PHE 0.009 0.002 PHE C 432 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 3009) covalent geometry : angle 0.71122 ( 4523) hydrogen bonds : bond 0.07204 ( 102) hydrogen bonds : angle 3.74493 ( 238) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 8 time to evaluate : 0.044 Fit side-chains REVERT: C 378 ASP cc_start: 0.8287 (m-30) cc_final: 0.7856 (m-30) outliers start: 3 outliers final: 3 residues processed: 10 average time/residue: 0.0314 time to fit residues: 0.4737 Evaluate side-chains 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 8 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 429 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.056984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.047394 restraints weight = 32286.300| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.35 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3009 Z= 0.166 Angle : 0.664 8.812 4523 Z= 0.349 Chirality : 0.038 0.261 588 Planarity : 0.004 0.024 222 Dihedral : 25.795 140.997 1531 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.60 % Allowed : 23.38 % Favored : 74.03 % 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 aren not related in a simple way. whole: 0.04 (0.86), residues: 98 helix: 0.22 (0.56), residues: 74 sheet: None (None), residues: 0 loop : -0.13 (1.65), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 356 TYR 0.017 0.004 TYR C 367 PHE 0.003 0.001 PHE C 432 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3009) covalent geometry : angle 0.66438 ( 4523) hydrogen bonds : bond 0.06546 ( 102) hydrogen bonds : angle 3.67550 ( 238) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.054 Fit side-chains REVERT: C 378 ASP cc_start: 0.8659 (m-30) cc_final: 0.8329 (m-30) outliers start: 2 outliers final: 1 residues processed: 10 average time/residue: 0.0259 time to fit residues: 0.4299 Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.056583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.049201 restraints weight = 32425.408| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.35 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3009 Z= 0.199 Angle : 0.692 9.423 4523 Z= 0.362 Chirality : 0.039 0.273 588 Planarity : 0.004 0.019 222 Dihedral : 25.781 139.076 1531 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 26.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.30 % Allowed : 23.38 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.86), residues: 98 helix: 0.15 (0.56), residues: 74 sheet: None (None), residues: 0 loop : -0.23 (1.62), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 359 TYR 0.007 0.003 TYR C 431 PHE 0.007 0.001 PHE C 432 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 3009) covalent geometry : angle 0.69191 ( 4523) hydrogen bonds : bond 0.07004 ( 102) hydrogen bonds : angle 3.63517 ( 238) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.057 Fit side-chains REVERT: C 367 TYR cc_start: 0.6792 (m-80) cc_final: 0.6405 (m-80) REVERT: C 378 ASP cc_start: 0.8251 (m-30) cc_final: 0.7690 (m-30) outliers start: 1 outliers final: 1 residues processed: 9 average time/residue: 0.0300 time to fit residues: 0.4215 Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 13 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.057987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.048326 restraints weight = 31203.438| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.65 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3009 Z= 0.141 Angle : 0.642 9.097 4523 Z= 0.335 Chirality : 0.036 0.257 588 Planarity : 0.004 0.029 222 Dihedral : 25.675 142.408 1531 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.30 % Allowed : 23.38 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.85), residues: 98 helix: 0.15 (0.58), residues: 74 sheet: None (None), residues: 0 loop : -0.27 (1.53), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG C 356 TYR 0.005 0.002 TYR C 431 PHE 0.003 0.001 PHE C 432 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3009) covalent geometry : angle 0.64168 ( 4523) hydrogen bonds : bond 0.05877 ( 102) hydrogen bonds : angle 3.64662 ( 238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.29 seconds wall clock time: 27 minutes 15.73 seconds (1635.73 seconds total)