Starting phenix.real_space_refine on Wed Mar 5 18:11:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x34_32978/03_2025/7x34_32978.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x34_32978/03_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_32978/03_2025/7x34_32978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x34_32978/03_2025/7x34_32978.map" model { file = "/net/cci-nas-00/data/ceres_data/7x34_32978/03_2025/7x34_32978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x34_32978/03_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-5624/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: 3.27, per 1000 atoms: 1.18 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: 1.98 Conformation dependent library (CDL) restraints added in 434.9 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: 2.30 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: 0.91 Time building geometry restraints manager: 0.91 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: 2.840 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.540 Find NCS groups from input model: 0.020 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.520 ------------------------------------------------------------------------------- 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 : 0.212 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: 0.0871 time to fit residues: 2.1050 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 : 0.157 ------------------------------------------------------------------------------- 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 = 63)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.046625 restraints weight = 32890.091| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.92 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 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 = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.158 Fit side-chains REVERT: C 361 SER cc_start: 0.8779 (m) cc_final: 0.8498 (p) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.0796 time to fit residues: 2.0535 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 : 0.150 ------------------------------------------------------------------------------- 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: 4.9990 chunk 16 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.055801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.046620 restraints weight = 31925.789| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.53 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 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 = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3420 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= 0.249 Angle : 0.755 12.475 4523 Z= 0.390 Chirality : 0.041 0.326 588 Planarity : 0.004 0.020 222 Dihedral : 25.844 153.127 1531 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 25.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.19 % Allowed : 18.18 % 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: -0.62 (0.83), residues: 98 helix: -0.05 (0.56), residues: 73 sheet: None (None), residues: 0 loop : -1.15 (1.45), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.004 PHE C 432 TYR 0.013 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 : 0.157 Fit side-chains REVERT: C 367 TYR cc_start: 0.7961 (m-80) cc_final: 0.7727 (m-80) outliers start: 4 outliers final: 2 residues processed: 12 average time/residue: 0.0753 time to fit residues: 1.3990 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.055753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.046494 restraints weight = 32305.716| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.66 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3009 Z= 0.234 Angle : 0.743 14.217 4523 Z= 0.383 Chirality : 0.040 0.321 588 Planarity : 0.004 0.019 222 Dihedral : 25.815 150.855 1531 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.60 % Allowed : 18.18 % Favored : 79.22 % 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: -0.51 (0.84), residues: 98 helix: 0.10 (0.58), residues: 73 sheet: None (None), residues: 0 loop : -1.35 (1.41), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.003 PHE C 432 TYR 0.011 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 : 0.164 Fit side-chains REVERT: C 367 TYR cc_start: 0.8094 (m-80) cc_final: 0.7868 (m-80) REVERT: C 378 ASP cc_start: 0.8632 (m-30) cc_final: 0.8403 (m-30) outliers start: 2 outliers final: 2 residues processed: 10 average time/residue: 0.0790 time to fit residues: 1.2506 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 : 0.165 ------------------------------------------------------------------------------- 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: 20.0000 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.055120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.047392 restraints weight = 31754.212| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.43 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) = 0.040 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.040 | | 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: 0.7569 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3009 Z= 0.290 Angle : 0.778 13.297 4523 Z= 0.400 Chirality : 0.042 0.327 588 Planarity : 0.004 0.021 222 Dihedral : 25.843 147.411 1531 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 32.93 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 (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: 0.06 (0.83), residues: 98 helix: 0.51 (0.59), residues: 69 sheet: None (None), residues: 0 loop : -0.91 (1.25), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.003 PHE C 368 TYR 0.011 0.003 TYR C 431 ARG 0.002 0.000 ARG C 359 *********************** 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 13 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.158 Fit side-chains REVERT: C 367 TYR cc_start: 0.7600 (m-80) cc_final: 0.7359 (m-80) REVERT: C 378 ASP cc_start: 0.8461 (m-30) cc_final: 0.8172 (m-30) outliers start: 3 outliers final: 2 residues processed: 12 average time/residue: 0.0771 time to fit residues: 1.4277 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 : 0.156 ------------------------------------------------------------------------------- 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: 4.9990 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: 6.9990 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 overall best weight: 4.8588 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.056431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.049401 restraints weight = 31953.249| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.35 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3009 Z= 0.203 Angle : 0.710 15.434 4523 Z= 0.361 Chirality : 0.038 0.298 588 Planarity : 0.004 0.019 222 Dihedral : 25.788 148.953 1531 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 24.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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 (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: -0.11 (0.85), residues: 98 helix: 0.36 (0.59), residues: 73 sheet: None (None), residues: 0 loop : -1.09 (1.42), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE C 432 TYR 0.007 0.003 TYR C 431 ARG 0.001 0.001 ARG C 359 *********************** 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 13 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.157 Fit side-chains REVERT: C 367 TYR cc_start: 0.8138 (m-80) cc_final: 0.7857 (m-80) REVERT: C 378 ASP cc_start: 0.8695 (m-30) cc_final: 0.8359 (m-30) outliers start: 2 outliers final: 2 residues processed: 12 average time/residue: 0.0762 time to fit residues: 1.3951 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 : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 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: 7.9990 chunk 10 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.054856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.047186 restraints weight = 33389.505| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.30 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 0.005 0.032 3009 Z= 0.298 Angle : 0.816 14.854 4523 Z= 0.417 Chirality : 0.044 0.305 588 Planarity : 0.005 0.021 222 Dihedral : 26.026 137.870 1531 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 33.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.19 % Allowed : 24.68 % 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: -0.23 (0.85), residues: 98 helix: 0.01 (0.59), residues: 75 sheet: None (None), residues: 0 loop : -0.21 (1.47), residues: 23 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE C 432 TYR 0.005 0.002 TYR C 431 ARG 0.002 0.001 ARG C 359 *********************** 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 13 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 9 time to evaluate : 0.164 Fit side-chains REVERT: C 367 TYR cc_start: 0.7731 (m-80) cc_final: 0.7467 (m-10) REVERT: C 378 ASP cc_start: 0.8212 (m-30) cc_final: 0.7949 (m-30) outliers start: 4 outliers final: 3 residues processed: 11 average time/residue: 0.0785 time to fit residues: 1.3708 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 : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 377 ILE 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: 6.9990 chunk 14 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.055813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.048226 restraints weight = 32226.698| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.67 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) = 0.041 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4661 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= 0.236 Angle : 0.744 13.818 4523 Z= 0.383 Chirality : 0.040 0.278 588 Planarity : 0.004 0.020 222 Dihedral : 25.946 135.769 1531 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % 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: -0.44 (0.85), residues: 98 helix: -0.12 (0.56), residues: 79 sheet: None (None), residues: 0 loop : -0.32 (1.74), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE C 432 TYR 0.013 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 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.164 Fit side-chains REVERT: C 378 ASP cc_start: 0.8418 (m-30) cc_final: 0.8135 (m-30) outliers start: 2 outliers final: 2 residues processed: 10 average time/residue: 0.0765 time to fit residues: 1.2285 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 : 0.156 ------------------------------------------------------------------------------- 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: 0.0970 chunk 8 optimal weight: 0.0030 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: 7.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 overall best weight: 4.8194 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.056340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.048912 restraints weight = 31997.732| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.84 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 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 = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4741 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= 0.201 Angle : 0.725 13.260 4523 Z= 0.374 Chirality : 0.040 0.280 588 Planarity : 0.004 0.023 222 Dihedral : 25.883 135.285 1531 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 25.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.60 % Allowed : 28.57 % Favored : 68.83 % 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: 0.10 (0.87), residues: 98 helix: 0.33 (0.57), residues: 73 sheet: None (None), residues: 0 loop : -0.33 (1.62), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE C 432 TYR 0.013 0.004 TYR C 367 ARG 0.002 0.001 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 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.149 Fit side-chains REVERT: C 378 ASP cc_start: 0.8295 (m-30) cc_final: 0.7955 (m-30) outliers start: 2 outliers final: 2 residues processed: 10 average time/residue: 0.0720 time to fit residues: 1.1540 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 : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.056339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.048682 restraints weight = 32219.626| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 4.47 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 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 = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3009 Z= 0.217 Angle : 0.727 13.097 4523 Z= 0.377 Chirality : 0.040 0.277 588 Planarity : 0.005 0.021 222 Dihedral : 25.874 134.720 1531 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.90 % Allowed : 27.27 % Favored : 68.83 % 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: 0.14 (0.88), residues: 98 helix: 0.29 (0.58), residues: 73 sheet: None (None), residues: 0 loop : -0.11 (1.63), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.002 PHE C 432 TYR 0.037 0.007 TYR C 367 ARG 0.001 0.000 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 12 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.162 Fit side-chains REVERT: C 378 ASP cc_start: 0.8299 (m-30) cc_final: 0.8005 (m-30) outliers start: 3 outliers final: 2 residues processed: 10 average time/residue: 0.0772 time to fit residues: 1.2367 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 : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.056204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.048610 restraints weight = 32067.545| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 4.47 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4754 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= 0.233 Angle : 0.727 12.999 4523 Z= 0.377 Chirality : 0.040 0.279 588 Planarity : 0.004 0.021 222 Dihedral : 25.871 134.559 1531 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 26.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.90 % Allowed : 27.27 % Favored : 68.83 % 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: 0.14 (0.88), residues: 98 helix: 0.29 (0.58), residues: 73 sheet: None (None), residues: 0 loop : -0.10 (1.63), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE C 432 TYR 0.031 0.006 TYR C 367 ARG 0.002 0.001 ARG C 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2928.45 seconds wall clock time: 50 minutes 49.40 seconds (3049.40 seconds total)