Starting phenix.real_space_refine on Tue Aug 4 12:22:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vdg_43149/08_2026/8vdg_43149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vdg_43149/08_2026/8vdg_43149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vdg_43149/08_2026/8vdg_43149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vdg_43149/08_2026/8vdg_43149.map" model { file = "/net/cci-nas-00/data/ceres_data/8vdg_43149/08_2026/8vdg_43149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vdg_43149/08_2026/8vdg_43149.cif" } resolution = 3.35 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 1653 2.51 5 N 427 2.21 5 O 489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2583 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 811 Classifications: {'peptide': 93} Link IDs: {'TRANS': 92} Chain breaks: 4 Chain: "H" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "K" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Time building chain proxies: 0.83, per 1000 atoms: 0.32 Number of scatterers: 2583 At special positions: 0 Unit cell: (55.1, 59.45, 94.975, 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) S 14 16.00 O 489 8.00 N 427 7.00 C 1653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 715 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 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: 0.19 Conformation dependent library (CDL) restraints added in 90.7 milliseconds 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 606 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 7 sheets defined 29.7% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 579 through 598 Processing helix chain 'A' and resid 617 through 636 Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 660 through 668 removed outlier: 3.590A pdb=" N VAL A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 699 through 714 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.517A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.780A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR H 87 " --> pdb=" O ASP H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.963A pdb=" N PHE K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.561A pdb=" N ALA H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER H 110 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.561A pdb=" N ALA H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER H 110 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.540A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.869A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 19 through 20 111 hydrogen bonds defined for protein. 291 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.38 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 803 1.34 - 1.46: 654 1.46 - 1.58: 1162 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 2639 Sorted by residual: bond pdb=" N SER K 7 " pdb=" CA SER K 7 " ideal model delta sigma weight residual 1.461 1.490 -0.028 9.20e-03 1.18e+04 9.53e+00 bond pdb=" N VAL K 3 " pdb=" CA VAL K 3 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.27e-02 6.20e+03 8.42e+00 bond pdb=" N GLU K 17 " pdb=" CA GLU K 17 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.16e-02 7.43e+03 7.63e+00 bond pdb=" N ASP K 18 " pdb=" CA ASP K 18 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.33e-02 5.65e+03 6.85e+00 bond pdb=" N LEU K 13 " pdb=" CA LEU K 13 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.27e-02 6.20e+03 6.67e+00 ... (remaining 2634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 3439 1.96 - 3.92: 106 3.92 - 5.88: 12 5.88 - 7.83: 4 7.83 - 9.79: 1 Bond angle restraints: 3562 Sorted by residual: angle pdb=" N ILE H 53 " pdb=" CA ILE H 53 " pdb=" C ILE H 53 " ideal model delta sigma weight residual 109.34 102.26 7.08 2.08e+00 2.31e-01 1.16e+01 angle pdb=" CB MET A 665 " pdb=" CG MET A 665 " pdb=" SD MET A 665 " ideal model delta sigma weight residual 112.70 122.49 -9.79 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C ASP K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" CA THR K 5 " pdb=" CB THR K 5 " pdb=" OG1 THR K 5 " ideal model delta sigma weight residual 109.60 104.99 4.61 1.50e+00 4.44e-01 9.43e+00 angle pdb=" CA GLN K 6 " pdb=" C GLN K 6 " pdb=" O GLN K 6 " ideal model delta sigma weight residual 121.58 118.26 3.32 1.12e+00 7.97e-01 8.80e+00 ... (remaining 3557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 1408 15.66 - 31.32: 107 31.32 - 46.97: 41 46.97 - 62.63: 9 62.63 - 78.29: 3 Dihedral angle restraints: 1568 sinusoidal: 634 harmonic: 934 Sorted by residual: dihedral pdb=" CA MET A 665 " pdb=" C MET A 665 " pdb=" N LYS A 666 " pdb=" CA LYS A 666 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB MET H 34 " pdb=" CG MET H 34 " pdb=" SD MET H 34 " pdb=" CE MET H 34 " ideal model delta sinusoidal sigma weight residual 60.00 119.05 -59.05 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN K 6 " pdb=" CA GLN K 6 " pdb=" CB GLN K 6 " pdb=" CG GLN K 6 " ideal model delta sinusoidal sigma weight residual -60.00 -116.32 56.32 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 1565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 273 0.045 - 0.090: 83 0.090 - 0.134: 25 0.134 - 0.179: 7 0.179 - 0.224: 3 Chirality restraints: 391 Sorted by residual: chirality pdb=" CA ILE H 53 " pdb=" N ILE H 53 " pdb=" C ILE H 53 " pdb=" CB ILE H 53 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE K 48 " pdb=" N ILE K 48 " pdb=" C ILE K 48 " pdb=" CB ILE K 48 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CA ILE K 2 " pdb=" N ILE K 2 " pdb=" C ILE K 2 " pdb=" CB ILE K 2 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.58e-01 ... (remaining 388 not shown) Planarity restraints: 442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 67 " 0.001 2.00e-02 2.50e+03 1.97e-02 6.82e+00 pdb=" CG PHE H 67 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE H 67 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE H 67 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE H 67 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE H 67 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE H 67 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 96 " -0.010 2.00e-02 2.50e+03 1.09e-02 2.99e+00 pdb=" CG TRP K 96 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP K 96 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP K 96 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP K 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP K 96 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 96 " -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 96 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP K 96 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 96 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO H 97 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO H 97 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 97 " -0.023 5.00e-02 4.00e+02 ... (remaining 439 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 645 2.80 - 3.32: 2132 3.32 - 3.85: 4378 3.85 - 4.37: 4955 4.37 - 4.90: 9045 Nonbonded interactions: 21155 Sorted by model distance: nonbonded pdb=" OE1 GLU H 33 " pdb=" OH TYR H 50 " model vdw 2.274 3.040 nonbonded pdb=" O TYR K 49 " pdb=" OH TYR K 91 " model vdw 2.304 3.040 nonbonded pdb=" OE1 GLU A 680 " pdb=" OH TYR A 707 " model vdw 2.310 3.040 nonbonded pdb=" O ASP K 82 " pdb=" OH TYR K 86 " model vdw 2.332 3.040 nonbonded pdb=" NH1 ARG K 54 " pdb=" O ILE K 58 " model vdw 2.379 3.120 ... (remaining 21150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.660 Find NCS groups from input model: 0.010 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.006 0.058 2642 Z= 0.311 Angle : 0.821 9.793 3568 Z= 0.473 Chirality : 0.051 0.224 391 Planarity : 0.006 0.042 442 Dihedral : 13.860 78.288 953 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.35 % Allowed : 1.41 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.56 (0.45), residues: 309 helix: -0.56 (0.43), residues: 75 sheet: -1.18 (0.59), residues: 92 loop : -1.05 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 61 TYR 0.017 0.003 TYR A 586 PHE 0.034 0.003 PHE H 67 TRP 0.024 0.002 TRP K 96 HIS 0.004 0.002 HIS A 663 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.31 ( 2639) covalent geometry : angle 0.82083 / 0.47 ( 3562) SS BOND : bond 0.00295 / 0.14 ( 3) SS BOND : angle 1.08332 / 0.82 ( 6) hydrogen bonds : bond 0.18643 / 12.54 ( 106) hydrogen bonds : angle 8.00241 / 5.66 ( 291) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.098 Fit side-chains REVERT: A 658 GLU cc_start: 0.8161 (tt0) cc_final: 0.6991 (mp0) REVERT: A 665 MET cc_start: 0.7804 (mmp) cc_final: 0.7381 (mmp) REVERT: K 52 SER cc_start: 0.8176 (p) cc_final: 0.7849 (m) REVERT: K 61 ARG cc_start: 0.7068 (ptt90) cc_final: 0.6518 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.0930 time to fit residues: 3.7431 Evaluate side-chains 29 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.176049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.157371 restraints weight = 2955.644| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.81 r_work: 0.3603 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2642 Z= 0.171 Angle : 0.595 12.493 3568 Z= 0.301 Chirality : 0.041 0.146 391 Planarity : 0.004 0.029 442 Dihedral : 4.169 14.007 343 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.35 % Allowed : 7.39 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.48), residues: 309 helix: 1.79 (0.51), residues: 77 sheet: -1.18 (0.52), residues: 102 loop : -0.27 (0.55), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 71 TYR 0.015 0.002 TYR K 49 PHE 0.013 0.002 PHE A 662 TRP 0.014 0.002 TRP H 79 HIS 0.004 0.002 HIS A 663 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 2639) covalent geometry : angle 0.59496 / 0.30 ( 3562) SS BOND : bond 0.00592 / 0.29 ( 3) SS BOND : angle 0.84525 / 0.60 ( 6) hydrogen bonds : bond 0.03601 / 2.02 ( 106) hydrogen bonds : angle 5.18498 / 3.57 ( 291) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: A 658 GLU cc_start: 0.8418 (tt0) cc_final: 0.7212 (mp0) REVERT: A 665 MET cc_start: 0.8084 (mmp) cc_final: 0.7682 (mmp) REVERT: H 85 GLU cc_start: 0.7735 (pm20) cc_final: 0.7523 (pm20) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.0657 time to fit residues: 2.4155 Evaluate side-chains 30 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 10 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.7737 > 50:) chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.0770 chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.172757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.153974 restraints weight = 2990.427| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.81 r_work: 0.3581 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2642 Z= 0.149 Angle : 0.525 9.420 3568 Z= 0.266 Chirality : 0.040 0.147 391 Planarity : 0.003 0.031 442 Dihedral : 4.080 13.127 343 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.06 % Allowed : 9.51 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.29 (0.49), residues: 309 helix: 2.68 (0.51), residues: 77 sheet: -1.07 (0.52), residues: 107 loop : -0.07 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 71 TYR 0.015 0.002 TYR K 91 PHE 0.010 0.001 PHE A 662 TRP 0.012 0.001 TRP H 79 HIS 0.004 0.002 HIS A 663 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 2639) covalent geometry : angle 0.52477 / 0.27 ( 3562) SS BOND : bond 0.00286 / 0.14 ( 3) SS BOND : angle 0.70219 / 0.49 ( 6) hydrogen bonds : bond 0.03059 / 1.79 ( 106) hydrogen bonds : angle 4.92555 / 3.37 ( 291) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.067 Fit side-chains REVERT: A 665 MET cc_start: 0.8053 (mmp) cc_final: 0.7570 (mmp) outliers start: 3 outliers final: 3 residues processed: 31 average time/residue: 0.0494 time to fit residues: 1.8222 Evaluate side-chains 31 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 56 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 0.0050 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 627 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.157078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.139207 restraints weight = 2948.413| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.76 r_work: 0.3466 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 2642 Z= 0.151 Angle : 0.524 9.163 3568 Z= 0.263 Chirality : 0.040 0.143 391 Planarity : 0.003 0.029 442 Dihedral : 4.030 13.325 343 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.41 % Allowed : 11.27 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.48 (0.49), residues: 309 helix: 3.08 (0.50), residues: 77 sheet: -0.97 (0.52), residues: 107 loop : -0.13 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 100B TYR 0.014 0.002 TYR K 91 PHE 0.009 0.001 PHE A 662 TRP 0.011 0.001 TRP H 79 HIS 0.004 0.002 HIS A 663 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 ( 2639) covalent geometry : angle 0.52415 / 0.26 ( 3562) SS BOND : bond 0.00215 / 0.11 ( 3) SS BOND : angle 0.59239 / 0.42 ( 6) hydrogen bonds : bond 0.02767 / 1.62 ( 106) hydrogen bonds : angle 4.75162 / 3.26 ( 291) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.055 Fit side-chains REVERT: A 665 MET cc_start: 0.7993 (mmp) cc_final: 0.7533 (mmp) outliers start: 4 outliers final: 4 residues processed: 28 average time/residue: 0.0413 time to fit residues: 1.4197 Evaluate side-chains 30 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 75 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 2 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.0270 chunk 19 optimal weight: 0.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.160335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.142295 restraints weight = 2865.630| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.75 r_work: 0.3466 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2642 Z= 0.110 Angle : 0.467 7.854 3568 Z= 0.237 Chirality : 0.038 0.143 391 Planarity : 0.003 0.029 442 Dihedral : 3.797 12.834 343 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.76 % Allowed : 11.27 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.76 (0.50), residues: 309 helix: 3.47 (0.51), residues: 77 sheet: -0.79 (0.53), residues: 107 loop : -0.08 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 71 TYR 0.012 0.001 TYR K 91 PHE 0.007 0.001 PHE A 662 TRP 0.009 0.001 TRP H 79 HIS 0.003 0.001 HIS A 663 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 2639) covalent geometry : angle 0.46737 / 0.24 ( 3562) SS BOND : bond 0.00106 / 0.05 ( 3) SS BOND : angle 0.43861 / 0.31 ( 6) hydrogen bonds : bond 0.02554 / 1.51 ( 106) hydrogen bonds : angle 4.50572 / 3.10 ( 291) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.117 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 29 average time/residue: 0.0634 time to fit residues: 2.2762 Evaluate side-chains 28 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.0270 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.151559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.133795 restraints weight = 2928.469| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.74 r_work: 0.3401 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 2642 Z= 0.208 Angle : 0.567 9.787 3568 Z= 0.289 Chirality : 0.042 0.144 391 Planarity : 0.003 0.029 442 Dihedral : 4.274 15.223 343 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.41 % Allowed : 13.03 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.49 (0.49), residues: 309 helix: 3.17 (0.50), residues: 77 sheet: -0.86 (0.53), residues: 107 loop : -0.30 (0.54), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 108 TYR 0.013 0.002 TYR K 49 PHE 0.011 0.002 PHE A 662 TRP 0.011 0.001 TRP K 96 HIS 0.005 0.002 HIS A 663 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 ( 2639) covalent geometry : angle 0.56618 / 0.29 ( 3562) SS BOND : bond 0.00324 / 0.16 ( 3) SS BOND : angle 0.86195 / 0.63 ( 6) hydrogen bonds : bond 0.02864 / 1.68 ( 106) hydrogen bonds : angle 4.86512 / 3.35 ( 291) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.095 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 27 average time/residue: 0.0865 time to fit residues: 2.7641 Evaluate side-chains 27 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.153077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.135180 restraints weight = 2913.955| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.76 r_work: 0.3434 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2642 Z= 0.139 Angle : 0.501 8.127 3568 Z= 0.253 Chirality : 0.039 0.143 391 Planarity : 0.003 0.026 442 Dihedral : 3.957 14.308 343 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.11 % Allowed : 13.03 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.71 (0.50), residues: 309 helix: 3.46 (0.51), residues: 77 sheet: -0.70 (0.55), residues: 107 loop : -0.28 (0.55), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 24 TYR 0.012 0.002 TYR K 91 PHE 0.007 0.001 PHE A 662 TRP 0.009 0.001 TRP H 79 HIS 0.003 0.002 HIS A 663 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 2639) covalent geometry : angle 0.50156 / 0.25 ( 3562) SS BOND : bond 0.00163 / 0.08 ( 3) SS BOND : angle 0.43416 / 0.33 ( 6) hydrogen bonds : bond 0.02591 / 1.54 ( 106) hydrogen bonds : angle 4.56609 / 3.15 ( 291) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.092 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 32 average time/residue: 0.0587 time to fit residues: 2.2923 Evaluate side-chains 30 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.152513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135068 restraints weight = 2996.679| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.75 r_work: 0.3432 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2642 Z= 0.135 Angle : 0.486 7.288 3568 Z= 0.248 Chirality : 0.039 0.142 391 Planarity : 0.003 0.026 442 Dihedral : 3.846 13.519 343 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.41 % Allowed : 13.73 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.80 (0.50), residues: 309 helix: 3.62 (0.51), residues: 77 sheet: -0.70 (0.55), residues: 107 loop : -0.23 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 71 TYR 0.012 0.002 TYR K 91 PHE 0.009 0.001 PHE A 662 TRP 0.009 0.001 TRP H 79 HIS 0.003 0.002 HIS A 663 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 2639) covalent geometry : angle 0.48556 / 0.25 ( 3562) SS BOND : bond 0.00181 / 0.09 ( 3) SS BOND : angle 0.48392 / 0.36 ( 6) hydrogen bonds : bond 0.02521 / 1.49 ( 106) hydrogen bonds : angle 4.50494 / 3.12 ( 291) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.104 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.0626 time to fit residues: 2.3182 Evaluate side-chains 29 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 overall best weight: 0.2996 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.156881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.139241 restraints weight = 2960.791| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.70 r_work: 0.3463 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2642 Z= 0.100 Angle : 0.450 5.669 3568 Z= 0.232 Chirality : 0.037 0.144 391 Planarity : 0.003 0.026 442 Dihedral : 3.603 12.458 343 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.41 % Allowed : 14.08 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.95 (0.52), residues: 309 helix: 3.94 (0.51), residues: 76 sheet: -0.63 (0.57), residues: 107 loop : -0.23 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 71 TYR 0.012 0.001 TYR K 91 PHE 0.007 0.001 PHE A 662 TRP 0.008 0.001 TRP H 79 HIS 0.002 0.001 HIS A 663 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 2639) covalent geometry : angle 0.45008 / 0.23 ( 3562) SS BOND : bond 0.00093 / 0.05 ( 3) SS BOND : angle 0.26158 / 0.18 ( 6) hydrogen bonds : bond 0.02348 / 1.39 ( 106) hydrogen bonds : angle 4.24488 / 2.95 ( 291) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.091 Fit side-chains REVERT: H 53 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7138 (mm) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.0672 time to fit residues: 1.9500 Evaluate side-chains 24 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.155310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.137498 restraints weight = 2958.834| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.73 r_work: 0.3440 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2642 Z= 0.135 Angle : 0.481 6.879 3568 Z= 0.247 Chirality : 0.039 0.145 391 Planarity : 0.003 0.025 442 Dihedral : 3.711 13.177 343 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.41 % Allowed : 14.44 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.93 (0.51), residues: 309 helix: 3.74 (0.51), residues: 77 sheet: -0.68 (0.56), residues: 107 loop : -0.09 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 24 TYR 0.011 0.002 TYR K 91 PHE 0.009 0.001 PHE A 662 TRP 0.009 0.001 TRP K 96 HIS 0.004 0.002 HIS A 663 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 2639) covalent geometry : angle 0.48088 / 0.25 ( 3562) SS BOND : bond 0.00168 / 0.08 ( 3) SS BOND : angle 0.50053 / 0.37 ( 6) hydrogen bonds : bond 0.02457 / 1.45 ( 106) hydrogen bonds : angle 4.34366 / 3.02 ( 291) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 618 Ramachandran restraints generated. 309 Oldfield, 0 Emsley, 309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.093 Fit side-chains REVERT: K 105 GLU cc_start: 0.7560 (pt0) cc_final: 0.7338 (pt0) outliers start: 4 outliers final: 4 residues processed: 26 average time/residue: 0.0780 time to fit residues: 2.3751 Evaluate side-chains 25 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.154982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.138165 restraints weight = 2965.213| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.67 r_work: 0.3434 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2642 Z= 0.178 Angle : 0.529 7.835 3568 Z= 0.272 Chirality : 0.040 0.144 391 Planarity : 0.004 0.041 442 Dihedral : 3.935 14.507 343 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.11 % Allowed : 13.38 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.78 (0.50), residues: 309 helix: 3.59 (0.51), residues: 77 sheet: -0.73 (0.55), residues: 107 loop : -0.21 (0.55), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 24 TYR 0.012 0.002 TYR K 91 PHE 0.010 0.001 PHE A 662 TRP 0.010 0.001 TRP K 96 HIS 0.005 0.002 HIS A 663 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 2639) covalent geometry : angle 0.52835 / 0.27 ( 3562) SS BOND : bond 0.00227 / 0.11 ( 3) SS BOND : angle 0.65201 / 0.49 ( 6) hydrogen bonds : bond 0.02669 / 1.58 ( 106) hydrogen bonds : angle 4.54634 / 3.18 ( 291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 846.06 seconds wall clock time: 15 minutes 8.57 seconds (908.57 seconds total)