Starting phenix.real_space_refine on Thu Sep 10 20:39:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x34_32978/09_2026/7x34_32978.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x34_32978/09_2026/7x34_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_32978/09_2026/7x34_32978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x34_32978/09_2026/7x34_32978.map" model { file = "/net/cci-nas-00/data/ceres_data/7x34_32978/09_2026/7x34_32978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x34_32978/09_2026/7x34_32978.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7x34_32978/09_2026/7x34_32978.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x34_32978/09_2026/7x34_32978.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 215 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians P 94 5.49 5 C 1365 2.51 5 N 503 2.21 5 O 800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2762 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 745 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "3" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 2017 Classifications: {'RNAv2': 94} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 54, 'rna3p_pyr': 36} Link IDs: {'rna2p': 3, 'rna3p': 90} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A 31756 " occ=0.55 ... (20 atoms not shown) pdb=" C4 A 31756 " occ=0.55 Time building chain proxies: 0.86, per 1000 atoms: 0.31 Number of scatterers: 2762 At special positions: 0 Unit cell: (141.024, 88.14, 172.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 94 15.00 O 800 8.00 N 503 7.00 C 1365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 37.0 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: 0.58 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: 0.49 Time building geometry restraints manager: 0.34 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: 4496 5.19 - 10.38: 20 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 - 17.52: 1259 17.52 - 35.05: 161 35.05 - 52.57: 127 52.57 - 70.09: 52 70.09 - 87.61: 6 Dihedral angle restraints: 1605 sinusoidal: 1312 harmonic: 293 Sorted by residual: dihedral pdb=" C4' C 31700 " pdb=" C3' C 31700 " pdb=" C2' C 31700 " pdb=" C1' C 31700 " ideal model delta sinusoidal sigma weight residual 36.34 -40.40 76.74 1 3.10e+00 1.04e-01 7.70e+02 dihedral pdb=" C4' A 31765 " pdb=" C3' A 31765 " pdb=" C2' A 31765 " pdb=" C1' A 31765 " ideal model delta sinusoidal sigma weight residual 36.35 -34.13 70.48 1 3.10e+00 1.04e-01 6.65e+02 dihedral pdb=" C4' U 31761 " pdb=" C3' U 31761 " pdb=" C2' U 31761 " pdb=" C1' U 31761 " ideal model delta sinusoidal sigma weight residual 36.35 -33.47 69.82 1 3.10e+00 1.04e-01 6.54e+02 ... (remaining 1602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 411 0.068 - 0.135: 63 0.135 - 0.202: 24 0.202 - 0.270: 81 0.270 - 0.337: 9 Chirality restraints: 588 Sorted by residual: chirality pdb=" C3' C 31700 " pdb=" C4' C 31700 " pdb=" O3' C 31700 " pdb=" C2' C 31700 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" P C 31703 " pdb=" OP1 C 31703 " pdb=" OP2 C 31703 " pdb=" O5' C 31703 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" P A 31689 " pdb=" OP1 A 31689 " pdb=" OP2 A 31689 " pdb=" O5' A 31689 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.29 2.00e-01 2.50e+01 2.16e+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: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.070 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 0.010 0.460 3009 Z= 0.342 Angle : 1.332 25.944 4523 Z= 0.608 Chirality : 0.107 0.337 588 Planarity : 0.007 0.070 222 Dihedral : 20.966 87.615 1413 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.75), residues: 98 helix: -1.82 (0.46), residues: 79 sheet: None (None), residues: 0 loop : -1.15 (1.77), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 356 TYR 0.014 0.002 TYR C 367 PHE 0.007 0.002 PHE C 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00953 / 0.34 ( 3009) covalent geometry : angle 1.33217 / 0.61 ( 4523) hydrogen bonds : bond 0.11013 / 7.95 ( 102) hydrogen bonds : angle 5.91121 / 4.38 ( 238) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.035 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: 0.0271 time to fit residues: 0.6914 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 : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.055983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.046868 restraints weight = 33732.419| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.75 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 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 = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 3009 Z= 0.295 Angle : 1.245 12.126 4523 Z= 0.501 Chirality : 0.082 0.484 588 Planarity : 0.005 0.027 222 Dihedral : 19.746 139.687 1229 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 28.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.60 % Allowed : 16.88 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.83), residues: 98 helix: -0.30 (0.55), residues: 73 sheet: None (None), residues: 0 loop : -1.08 (1.50), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 359 TYR 0.013 0.003 TYR C 367 PHE 0.009 0.003 PHE C 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.29 ( 3009) covalent geometry : angle 1.24490 / 0.50 ( 4523) hydrogen bonds : bond 0.09167 / 5.76 ( 102) hydrogen bonds : angle 4.25615 / 2.94 ( 238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.053 Fit side-chains REVERT: C 361 SER cc_start: 0.8659 (m) cc_final: 0.8366 (p) REVERT: C 366 ASP cc_start: 0.9553 (m-30) cc_final: 0.9338 (m-30) REVERT: C 367 TYR cc_start: 0.7167 (m-80) cc_final: 0.6735 (m-80) REVERT: C 378 ASP cc_start: 0.8560 (m-30) cc_final: 0.8205 (m-30) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.0297 time to fit residues: 0.8000 Evaluate side-chains 14 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.055120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.046105 restraints weight = 34329.031| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.74 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3009 Z= 0.292 Angle : 1.254 11.946 4523 Z= 0.508 Chirality : 0.083 0.555 588 Planarity : 0.005 0.018 222 Dihedral : 19.753 143.389 1229 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 28.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.90 % Allowed : 18.18 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.83), residues: 98 helix: -0.28 (0.56), residues: 73 sheet: None (None), residues: 0 loop : -1.13 (1.49), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 359 TYR 0.014 0.004 TYR C 367 PHE 0.012 0.004 PHE C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.29 ( 3009) covalent geometry : angle 1.25438 / 0.51 ( 4523) hydrogen bonds : bond 0.08444 / 5.28 ( 102) hydrogen bonds : angle 4.01083 / 2.75 ( 238) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.060 Fit side-chains REVERT: C 367 TYR cc_start: 0.7471 (m-80) cc_final: 0.7211 (m-80) REVERT: C 378 ASP cc_start: 0.8508 (m-30) cc_final: 0.8210 (m-30) REVERT: C 428 LEU cc_start: 0.9344 (mt) cc_final: 0.9129 (pp) outliers start: 3 outliers final: 1 residues processed: 14 average time/residue: 0.0233 time to fit residues: 0.4948 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 : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 0.0670 chunk 9 optimal weight: 0.0060 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 overall best weight: 4.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.048079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.041310 restraints weight = 39227.517| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 4.09 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3930 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= 0.198 Angle : 1.128 13.481 4523 Z= 0.454 Chirality : 0.079 0.629 588 Planarity : 0.004 0.019 222 Dihedral : 19.462 140.982 1229 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 22.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.84), residues: 98 helix: 0.13 (0.58), residues: 73 sheet: None (None), residues: 0 loop : -1.27 (1.41), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 359 TYR 0.009 0.003 TYR C 367 PHE 0.009 0.003 PHE C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.20 ( 3009) covalent geometry : angle 1.12790 / 0.45 ( 4523) hydrogen bonds : bond 0.06754 / 3.99 ( 102) hydrogen bonds : angle 3.89925 / 2.67 ( 238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.031 Fit side-chains REVERT: C 367 TYR cc_start: 0.7142 (m-80) cc_final: 0.6875 (m-80) REVERT: C 378 ASP cc_start: 0.8396 (m-30) cc_final: 0.7970 (m-30) outliers start: 2 outliers final: 1 residues processed: 11 average time/residue: 0.0280 time to fit residues: 0.4987 Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 8 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.056133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.047139 restraints weight = 33251.049| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.71 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 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 = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4008 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= 0.245 Angle : 1.169 12.090 4523 Z= 0.469 Chirality : 0.080 0.680 588 Planarity : 0.004 0.020 222 Dihedral : 19.478 141.478 1229 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 24.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.30 % Allowed : 23.38 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.84), residues: 98 helix: -0.02 (0.57), residues: 79 sheet: None (None), residues: 0 loop : -0.45 (1.63), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 359 TYR 0.009 0.003 TYR C 367 PHE 0.006 0.002 PHE C 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.24 ( 3009) covalent geometry : angle 1.16946 / 0.47 ( 4523) hydrogen bonds : bond 0.07359 / 4.42 ( 102) hydrogen bonds : angle 3.79469 / 2.59 ( 238) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.066 Fit side-chains REVERT: C 367 TYR cc_start: 0.7393 (m-80) cc_final: 0.7084 (m-80) REVERT: C 378 ASP cc_start: 0.8647 (m-30) cc_final: 0.8282 (m-30) outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.0297 time to fit residues: 0.5008 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 : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 389 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 14 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.047587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.040859 restraints weight = 39451.870| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 4.24 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4037 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= 0.230 Angle : 1.174 16.638 4523 Z= 0.468 Chirality : 0.080 0.689 588 Planarity : 0.004 0.020 222 Dihedral : 19.453 141.307 1229 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 25.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.86), residues: 98 helix: 0.05 (0.58), residues: 79 sheet: None (None), residues: 0 loop : -0.32 (1.65), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 359 TYR 0.010 0.003 TYR C 367 PHE 0.006 0.002 PHE C 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.23 ( 3009) covalent geometry : angle 1.17414 / 0.47 ( 4523) hydrogen bonds : bond 0.07407 / 4.44 ( 102) hydrogen bonds : angle 3.87606 / 2.67 ( 238) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.057 Fit side-chains REVERT: C 367 TYR cc_start: 0.7255 (m-80) cc_final: 0.6898 (m-80) REVERT: C 378 ASP cc_start: 0.8415 (m-30) cc_final: 0.7950 (m-30) outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.0310 time to fit residues: 0.5012 Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 10 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.047880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.041191 restraints weight = 39129.524| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 4.28 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3009 Z= 0.215 Angle : 1.163 14.363 4523 Z= 0.465 Chirality : 0.080 0.712 588 Planarity : 0.005 0.020 222 Dihedral : 19.430 141.340 1229 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.30 % Allowed : 24.68 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.87), residues: 98 helix: 0.08 (0.58), residues: 79 sheet: None (None), residues: 0 loop : 0.25 (1.73), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 359 TYR 0.018 0.004 TYR C 431 PHE 0.020 0.005 PHE C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.22 ( 3009) covalent geometry : angle 1.16256 / 0.47 ( 4523) hydrogen bonds : bond 0.07262 / 4.33 ( 102) hydrogen bonds : angle 3.83952 / 2.64 ( 238) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.030 Fit side-chains REVERT: C 367 TYR cc_start: 0.7260 (m-80) cc_final: 0.6860 (m-80) REVERT: C 378 ASP cc_start: 0.8375 (m-30) cc_final: 0.7890 (m-30) outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.0181 time to fit residues: 0.2956 Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.049 ------------------------------------------------------------------------------- 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 3 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.047841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.041108 restraints weight = 40290.141| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 4.38 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 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 = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3009 Z= 0.219 Angle : 1.160 13.216 4523 Z= 0.464 Chirality : 0.080 0.722 588 Planarity : 0.005 0.020 222 Dihedral : 19.432 141.376 1229 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 25.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.30 % Allowed : 24.68 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.86), residues: 98 helix: 0.05 (0.57), residues: 79 sheet: None (None), residues: 0 loop : 0.33 (1.75), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 359 TYR 0.010 0.002 TYR C 367 PHE 0.016 0.004 PHE C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.22 ( 3009) covalent geometry : angle 1.15950 / 0.46 ( 4523) hydrogen bonds : bond 0.07279 / 4.38 ( 102) hydrogen bonds : angle 3.82918 / 2.61 ( 238) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.064 Fit side-chains REVERT: C 367 TYR cc_start: 0.7272 (m-80) cc_final: 0.6867 (m-80) REVERT: C 378 ASP cc_start: 0.8386 (m-30) cc_final: 0.7899 (m-30) outliers start: 1 outliers final: 1 residues processed: 9 average time/residue: 0.0304 time to fit residues: 0.4616 Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 8 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.057840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.048848 restraints weight = 33499.063| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.55 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 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 = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3009 Z= 0.175 Angle : 1.120 12.903 4523 Z= 0.449 Chirality : 0.081 0.757 588 Planarity : 0.004 0.020 222 Dihedral : 19.335 141.356 1229 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.30 % Allowed : 24.68 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.88), residues: 98 helix: 0.13 (0.59), residues: 79 sheet: None (None), residues: 0 loop : 0.67 (1.75), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG C 356 TYR 0.014 0.003 TYR C 431 PHE 0.008 0.002 PHE C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 ( 3009) covalent geometry : angle 1.12042 / 0.45 ( 4523) hydrogen bonds : bond 0.06587 / 3.86 ( 102) hydrogen bonds : angle 3.68215 / 2.52 ( 238) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.033 Fit side-chains REVERT: C 367 TYR cc_start: 0.7444 (m-80) cc_final: 0.7094 (m-80) REVERT: C 378 ASP cc_start: 0.8528 (m-30) cc_final: 0.8079 (m-30) outliers start: 1 outliers final: 1 residues processed: 9 average time/residue: 0.0385 time to fit residues: 0.5423 Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.063 ------------------------------------------------------------------------------- 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 7 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 3 optimal weight: 0.0010 chunk 14 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.049264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.042590 restraints weight = 39283.040| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 4.30 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 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 = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3009 Z= 0.162 Angle : 1.107 12.383 4523 Z= 0.441 Chirality : 0.080 0.763 588 Planarity : 0.004 0.021 222 Dihedral : 19.336 141.808 1229 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.00 % Allowed : 25.97 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.87), residues: 98 helix: 0.13 (0.58), residues: 79 sheet: None (None), residues: 0 loop : 0.54 (1.72), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 359 TYR 0.008 0.002 TYR C 367 PHE 0.006 0.001 PHE C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 ( 3009) covalent geometry : angle 1.10729 / 0.44 ( 4523) hydrogen bonds : bond 0.06403 / 3.73 ( 102) hydrogen bonds : angle 3.71785 / 2.56 ( 238) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 196 Ramachandran restraints generated. 98 Oldfield, 0 Emsley, 98 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.043 Fit side-chains REVERT: C 367 TYR cc_start: 0.7463 (m-80) cc_final: 0.7108 (m-80) REVERT: C 378 ASP cc_start: 0.8473 (m-30) cc_final: 0.8005 (m-30) outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0259 time to fit residues: 0.4325 Evaluate side-chains 10 residues out of total 77 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 0.2980 chunk 17 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.057808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.048743 restraints weight = 32696.822| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.62 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 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 = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4217 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= 0.202 Angle : 1.124 12.523 4523 Z= 0.449 Chirality : 0.080 0.802 588 Planarity : 0.004 0.021 222 Dihedral : 19.318 141.572 1229 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.00 % Allowed : 27.27 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.88), residues: 98 helix: 0.17 (0.59), residues: 79 sheet: None (None), residues: 0 loop : 0.45 (1.71), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 356 TYR 0.009 0.002 TYR C 431 PHE 0.005 0.002 PHE C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 ( 3009) covalent geometry : angle 1.12364 / 0.45 ( 4523) hydrogen bonds : bond 0.06464 / 3.83 ( 102) hydrogen bonds : angle 3.74754 / 2.58 ( 238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1502.59 seconds wall clock time: 26 minutes 20.79 seconds (1580.79 seconds total)