Starting phenix.real_space_refine on Mon Feb 10 23:10:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x34_32978/02_2025/7x34_32978.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x34_32978/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x34_32978/02_2025/7x34_32978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x34_32978/02_2025/7x34_32978.map" model { file = "/net/cci-nas-00/data/ceres_data/7x34_32978/02_2025/7x34_32978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x34_32978/02_2025/7x34_32978.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.31, per 1000 atoms: 1.20 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: 0.82 Conformation dependent library (CDL) restraints added in 119.3 milliseconds 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: 1.33 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: 0.85 Time building geometry restraints manager: 0.90 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: 2.000 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.450 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.150 ------------------------------------------------------------------------------- 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= 0.669 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 PHE 0.007 0.002 PHE C 368 TYR 0.014 0.002 TYR C 367 ARG 0.003 0.001 ARG C 356 *********************** 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 : 0.155 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: 0.0882 time to fit residues: 2.1110 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 : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 16 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.055634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.046617 restraints weight = 32889.834| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.87 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 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 = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3009 Z= 0.299 Angle : 0.800 9.296 4523 Z= 0.410 Chirality : 0.042 0.309 588 Planarity : 0.005 0.027 222 Dihedral : 25.969 159.351 1531 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 27.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.83), residues: 98 helix: -0.30 (0.55), residues: 73 sheet: None (None), residues: 0 loop : -1.12 (1.51), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.004 PHE C 432 TYR 0.012 0.003 TYR C 367 ARG 0.003 0.001 ARG C 359 *********************** 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 20 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.118 Fit side-chains REVERT: C 361 SER cc_start: 0.8728 (m) cc_final: 0.8444 (p) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.0774 time to fit residues: 2.0217 Evaluate side-chains 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 12 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.055314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.046095 restraints weight = 32188.835| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.40 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3009 Z= 0.276 Angle : 0.785 12.773 4523 Z= 0.406 Chirality : 0.042 0.332 588 Planarity : 0.005 0.020 222 Dihedral : 25.909 151.143 1531 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 27.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 5.19 % Allowed : 20.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.83), residues: 98 helix: -0.10 (0.56), residues: 73 sheet: None (None), residues: 0 loop : -1.25 (1.45), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.004 PHE C 432 TYR 0.012 0.004 TYR C 431 ARG 0.001 0.000 ARG C 359 *********************** 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 14 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.197 Fit side-chains REVERT: C 367 TYR cc_start: 0.8115 (m-80) cc_final: 0.7895 (m-80) REVERT: C 428 LEU cc_start: 0.9328 (mt) cc_final: 0.9098 (pp) outliers start: 4 outliers final: 2 residues processed: 12 average time/residue: 0.0940 time to fit residues: 1.8288 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 : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 ILE 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 12 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.055740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.048242 restraints weight = 32328.439| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.45 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3009 Z= 0.234 Angle : 0.742 14.260 4523 Z= 0.383 Chirality : 0.040 0.316 588 Planarity : 0.004 0.020 222 Dihedral : 25.840 148.838 1531 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 27.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.60 % Allowed : 20.78 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.85), residues: 98 helix: 0.16 (0.58), residues: 73 sheet: None (None), residues: 0 loop : -1.37 (1.41), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE C 368 TYR 0.008 0.003 TYR C 431 ARG 0.002 0.001 ARG C 359 *********************** 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 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.160 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 10 average time/residue: 0.0833 time to fit residues: 1.3275 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 : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.056561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.048985 restraints weight = 31055.490| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.16 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 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 = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3009 Z= 0.193 Angle : 0.692 12.551 4523 Z= 0.359 Chirality : 0.038 0.296 588 Planarity : 0.004 0.020 222 Dihedral : 25.800 149.640 1531 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.86), residues: 98 helix: 0.27 (0.60), residues: 73 sheet: None (None), residues: 0 loop : -1.28 (1.38), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE C 432 TYR 0.017 0.004 TYR C 367 ARG 0.001 0.000 ARG C 356 *********************** 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 : 0.154 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 11 average time/residue: 0.0739 time to fit residues: 1.2738 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 : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 ILE 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 7 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.058268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.050570 restraints weight = 31147.277| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.17 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3009 Z= 0.157 Angle : 0.636 10.334 4523 Z= 0.331 Chirality : 0.035 0.262 588 Planarity : 0.004 0.018 222 Dihedral : 25.568 150.336 1531 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.86), residues: 98 helix: 0.12 (0.58), residues: 74 sheet: None (None), residues: 0 loop : -0.65 (1.54), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE C 432 TYR 0.015 0.004 TYR C 367 ARG 0.001 0.000 ARG C 356 *********************** 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 12 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.155 Fit side-chains REVERT: C 367 TYR cc_start: 0.7761 (m-10) cc_final: 0.7550 (m-10) outliers start: 1 outliers final: 1 residues processed: 11 average time/residue: 0.0731 time to fit residues: 1.2643 Evaluate side-chains 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 overall best weight: 6.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.055777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.048346 restraints weight = 32848.318| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.99 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) = 0.041 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.041 | | 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: 0.7566 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3009 Z= 0.252 Angle : 0.760 11.455 4523 Z= 0.394 Chirality : 0.041 0.289 588 Planarity : 0.004 0.021 222 Dihedral : 25.929 138.144 1531 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 30.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.60 % Allowed : 27.27 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.89), residues: 98 helix: 0.53 (0.62), residues: 69 sheet: None (None), residues: 0 loop : -0.05 (1.43), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE C 432 TYR 0.012 0.004 TYR C 367 ARG 0.001 0.000 ARG C 356 *********************** 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: 2 poor density : 10 time to evaluate : 0.152 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 11 average time/residue: 0.0717 time to fit residues: 1.2252 Evaluate side-chains 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 13 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.056997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.049781 restraints weight = 32005.576| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.24 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4921 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= 0.204 Angle : 0.696 10.497 4523 Z= 0.365 Chirality : 0.038 0.284 588 Planarity : 0.004 0.020 222 Dihedral : 25.774 135.582 1531 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.88), residues: 98 helix: 0.24 (0.59), residues: 74 sheet: None (None), residues: 0 loop : -0.30 (1.59), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE C 432 TYR 0.009 0.003 TYR C 431 ARG 0.002 0.001 ARG C 359 *********************** 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 12 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.159 Fit side-chains REVERT: C 367 TYR cc_start: 0.7358 (m-80) cc_final: 0.7119 (m-80) outliers start: 2 outliers final: 2 residues processed: 10 average time/residue: 0.0649 time to fit residues: 1.0737 Evaluate side-chains 12 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 9 optimal weight: 0.0170 chunk 8 optimal weight: 0.0000 chunk 13 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 overall best weight: 5.4028 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.057082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.049476 restraints weight = 31685.844| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.16 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3009 Z= 0.212 Angle : 0.700 10.139 4523 Z= 0.367 Chirality : 0.038 0.287 588 Planarity : 0.004 0.020 222 Dihedral : 25.773 135.129 1531 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.90 % Allowed : 24.68 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.87), residues: 98 helix: 0.25 (0.58), residues: 74 sheet: None (None), residues: 0 loop : -0.29 (1.60), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE C 432 TYR 0.009 0.003 TYR C 431 ARG 0.000 0.000 ARG C 356 *********************** 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 13 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: C 367 TYR cc_start: 0.7115 (m-80) cc_final: 0.6856 (m-80) outliers start: 3 outliers final: 3 residues processed: 11 average time/residue: 0.0854 time to fit residues: 1.4318 Evaluate side-chains 13 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.054905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.047344 restraints weight = 33831.463| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 4.51 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3009 Z= 0.290 Angle : 0.840 11.119 4523 Z= 0.436 Chirality : 0.045 0.317 588 Planarity : 0.005 0.020 222 Dihedral : 26.158 130.384 1531 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 32.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.30 % Allowed : 27.27 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.89), residues: 98 helix: 0.43 (0.61), residues: 69 sheet: None (None), residues: 0 loop : 0.29 (1.44), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.003 PHE C 432 TYR 0.013 0.004 TYR C 367 ARG 0.004 0.002 ARG C 356 ********************** 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 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: C 367 TYR cc_start: 0.8105 (m-80) cc_final: 0.7810 (m-80) outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.0718 time to fit residues: 1.1788 Evaluate side-chains 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.055964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.046391 restraints weight = 32733.021| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.57 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3009 Z= 0.255 Angle : 0.795 15.665 4523 Z= 0.408 Chirality : 0.042 0.319 588 Planarity : 0.005 0.018 222 Dihedral : 25.993 127.022 1531 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 29.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.30 % Allowed : 28.57 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.87), residues: 98 helix: 0.39 (0.61), residues: 69 sheet: None (None), residues: 0 loop : 0.19 (1.34), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE C 432 TYR 0.011 0.003 TYR C 367 ARG 0.002 0.001 ARG C 359 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2826.82 seconds wall clock time: 50 minutes 29.14 seconds (3029.14 seconds total)