Starting phenix.real_space_refine on Tue Feb 3 12:19:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k8l_62177/02_2026/9k8l_62177.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k8l_62177/02_2026/9k8l_62177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k8l_62177/02_2026/9k8l_62177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k8l_62177/02_2026/9k8l_62177.map" model { file = "/net/cci-nas-00/data/ceres_data/9k8l_62177/02_2026/9k8l_62177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k8l_62177/02_2026/9k8l_62177.cif" } resolution = 3.21 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= 0.004 sd= 0.158 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 Zn 3 6.06 5 C 837 2.51 5 N 261 2.21 5 O 273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1374 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 457 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "B" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 457 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "C" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 457 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.46, per 1000 atoms: 0.33 Number of scatterers: 1374 At special positions: 0 Unit cell: (53.865, 51.7104, 46.3239, 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) Zn 3 29.99 O 273 8.00 N 261 7.00 C 837 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: 0.30 Conformation dependent library (CDL) restraints added in 64.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 64 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS A 51 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS C 64 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 51 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS A 64 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 51 " 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 318 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 90.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing helix chain 'A' and resid 22 through 38 removed outlier: 3.539A pdb=" N ALA A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 60 removed outlier: 3.529A pdb=" N LEU A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 76 removed outlier: 3.716A pdb=" N GLU A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 41 removed outlier: 3.567A pdb=" N LYS B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS B 41 " --> pdb=" O LYS B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 60 removed outlier: 3.600A pdb=" N ARG B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 76 removed outlier: 3.788A pdb=" N ALA B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 41 removed outlier: 3.678A pdb=" N LYS C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 60 removed outlier: 3.527A pdb=" N LEU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG C 52 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 55 " --> pdb=" O HIS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 76 removed outlier: 3.784A pdb=" N LYS C 71 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) 95 hydrogen bonds defined for protein. 285 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: 0.11 Time building geometry restraints manager: 0.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.27: 261 1.27 - 1.34: 242 1.34 - 1.41: 40 1.41 - 1.48: 199 1.48 - 1.54: 635 Bond restraints: 1377 Sorted by residual: bond pdb=" CA LYS A 75 " pdb=" C LYS A 75 " ideal model delta sigma weight residual 1.523 1.452 0.071 1.34e-02 5.57e+03 2.80e+01 bond pdb=" CA ARG A 76 " pdb=" CB ARG A 76 " ideal model delta sigma weight residual 1.530 1.447 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" CA LYS A 75 " pdb=" CB LYS A 75 " ideal model delta sigma weight residual 1.530 1.472 0.058 1.69e-02 3.50e+03 1.19e+01 bond pdb=" N LYS A 75 " pdb=" CA LYS A 75 " ideal model delta sigma weight residual 1.457 1.416 0.042 1.29e-02 6.01e+03 1.04e+01 bond pdb=" CA ARG C 76 " pdb=" CB ARG C 76 " ideal model delta sigma weight residual 1.530 1.468 0.062 2.00e-02 2.50e+03 9.66e+00 ... (remaining 1372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 1788 1.82 - 3.64: 40 3.64 - 5.46: 8 5.46 - 7.28: 1 7.28 - 9.10: 2 Bond angle restraints: 1839 Sorted by residual: angle pdb=" O GLU A 74 " pdb=" C GLU A 74 " pdb=" N LYS A 75 " ideal model delta sigma weight residual 122.07 116.97 5.10 1.03e+00 9.43e-01 2.45e+01 angle pdb=" N ARG A 76 " pdb=" CA ARG A 76 " pdb=" CB ARG A 76 " ideal model delta sigma weight residual 110.50 102.22 8.28 1.70e+00 3.46e-01 2.37e+01 angle pdb=" CA GLU A 74 " pdb=" C GLU A 74 " pdb=" N LYS A 75 " ideal model delta sigma weight residual 117.07 121.80 -4.73 1.14e+00 7.69e-01 1.72e+01 angle pdb=" N GLU C 45 " pdb=" CA GLU C 45 " pdb=" C GLU C 45 " ideal model delta sigma weight residual 113.88 108.81 5.07 1.23e+00 6.61e-01 1.70e+01 angle pdb=" N GLU B 45 " pdb=" CA GLU B 45 " pdb=" C GLU B 45 " ideal model delta sigma weight residual 112.68 107.94 4.74 1.33e+00 5.65e-01 1.27e+01 ... (remaining 1834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 702 17.12 - 34.23: 125 34.23 - 51.35: 40 51.35 - 68.46: 9 68.46 - 85.58: 3 Dihedral angle restraints: 879 sinusoidal: 396 harmonic: 483 Sorted by residual: dihedral pdb=" N ARG A 76 " pdb=" C ARG A 76 " pdb=" CA ARG A 76 " pdb=" CB ARG A 76 " ideal model delta harmonic sigma weight residual 122.80 113.49 9.31 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" CA LEU C 50 " pdb=" C LEU C 50 " pdb=" N HIS C 51 " pdb=" CA HIS C 51 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" C ARG A 76 " pdb=" N ARG A 76 " pdb=" CA ARG A 76 " pdb=" CB ARG A 76 " ideal model delta harmonic sigma weight residual -122.60 -114.51 -8.09 0 2.50e+00 1.60e-01 1.05e+01 ... (remaining 876 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.022: 99 0.022 - 0.043: 65 0.043 - 0.064: 28 0.064 - 0.085: 14 0.085 - 0.106: 4 Chirality restraints: 210 Sorted by residual: chirality pdb=" CG LEU C 50 " pdb=" CB LEU C 50 " pdb=" CD1 LEU C 50 " pdb=" CD2 LEU C 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.48 -0.11 2.00e-01 2.50e+01 2.80e-01 chirality pdb=" CA LEU C 50 " pdb=" N LEU C 50 " pdb=" C LEU C 50 " pdb=" CB LEU C 50 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.55e-01 chirality pdb=" CA TYR B 38 " pdb=" N TYR B 38 " pdb=" C TYR B 38 " pdb=" CB TYR B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.12e-01 ... (remaining 207 not shown) Planarity restraints: 243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 74 " 0.014 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C GLU A 74 " -0.045 2.00e-02 2.50e+03 pdb=" O GLU A 74 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS A 75 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 75 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.50e+00 pdb=" C LYS C 75 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS C 75 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG C 76 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 44 " 0.005 2.00e-02 2.50e+03 9.42e-03 8.88e-01 pdb=" C GLU B 44 " -0.016 2.00e-02 2.50e+03 pdb=" O GLU B 44 " 0.006 2.00e-02 2.50e+03 pdb=" N GLU B 45 " 0.006 2.00e-02 2.50e+03 ... (remaining 240 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 15 2.58 - 3.16: 1116 3.16 - 3.74: 2039 3.74 - 4.32: 2814 4.32 - 4.90: 4582 Nonbonded interactions: 10566 Sorted by model distance: nonbonded pdb=" OD1 ASP C 47 " pdb="ZN ZN C 301 " model vdw 2.005 2.230 nonbonded pdb=" OD2 ASP C 47 " pdb="ZN ZN C 301 " model vdw 2.153 2.230 nonbonded pdb=" OD2 ASP C 68 " pdb="ZN ZN B 302 " model vdw 2.206 2.230 nonbonded pdb=" OD2 ASP B 47 " pdb="ZN ZN B 302 " model vdw 2.253 2.230 nonbonded pdb=" OD2 ASP A 47 " pdb="ZN ZN B 301 " model vdw 2.263 2.230 ... (remaining 10561 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 22 through 76) selection = (chain 'C' and resid 22 through 76) } 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: 0.770 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: 0.010 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.650 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 : 0.017 0.401 1383 Z= 0.623 Angle : 0.763 9.102 1839 Z= 0.487 Chirality : 0.036 0.106 210 Planarity : 0.004 0.026 243 Dihedral : 19.724 85.577 561 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.63 % Allowed : 1.26 % Favored : 98.11 % Rotamer: Outliers : 0.67 % Allowed : 33.33 % Favored : 66.00 % Cbeta Deviations : 0.63 % 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: -0.83 (0.59), residues: 159 helix: -0.23 (0.39), residues: 144 sheet: None (None), residues: 0 loop : -2.20 (1.09), residues: 15 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 76 TYR 0.008 0.002 TYR A 38 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 1377) covalent geometry : angle 0.76330 ( 1839) hydrogen bonds : bond 0.30333 ( 95) hydrogen bonds : angle 7.33551 ( 285) metal coordination : bond 0.24722 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.033 Fit side-chains REVERT: A 76 ARG cc_start: 0.6570 (mtt-85) cc_final: 0.6243 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.0535 time to fit residues: 1.3656 Evaluate side-chains 22 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.221318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.209555 restraints weight = 1097.590| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 0.63 r_work: 0.4162 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.4021 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1383 Z= 0.147 Angle : 0.486 4.878 1839 Z= 0.260 Chirality : 0.036 0.119 210 Planarity : 0.004 0.017 243 Dihedral : 3.614 13.151 186 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 6.67 % Allowed : 26.00 % Favored : 67.33 % 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: 0.73 (0.66), residues: 159 helix: 0.62 (0.42), residues: 153 sheet: None (None), residues: 0 loop : -0.08 (2.43), residues: 6 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 58 TYR 0.005 0.001 TYR A 38 HIS 0.004 0.002 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 1377) covalent geometry : angle 0.48580 ( 1839) hydrogen bonds : bond 0.05377 ( 95) hydrogen bonds : angle 4.05003 ( 285) metal coordination : bond 0.00268 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.056 Fit side-chains REVERT: A 50 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8044 (mp) outliers start: 10 outliers final: 1 residues processed: 31 average time/residue: 0.0691 time to fit residues: 2.4046 Evaluate side-chains 21 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain B residue 74 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.225703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.214440 restraints weight = 1156.375| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 0.62 r_work: 0.4155 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.4021 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1383 Z= 0.122 Angle : 0.428 4.660 1839 Z= 0.228 Chirality : 0.035 0.112 210 Planarity : 0.003 0.016 243 Dihedral : 3.371 12.319 186 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.67 % Allowed : 27.33 % Favored : 68.00 % 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: 1.03 (0.65), residues: 159 helix: 0.81 (0.41), residues: 153 sheet: None (None), residues: 0 loop : 0.07 (2.48), residues: 6 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 58 TYR 0.005 0.001 TYR A 38 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 1377) covalent geometry : angle 0.42796 ( 1839) hydrogen bonds : bond 0.04521 ( 95) hydrogen bonds : angle 3.54779 ( 285) metal coordination : bond 0.00180 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.055 Fit side-chains REVERT: A 50 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8047 (mp) REVERT: A 71 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8394 (mmtm) REVERT: B 24 ARG cc_start: 0.5553 (OUTLIER) cc_final: 0.5330 (mtt90) outliers start: 7 outliers final: 2 residues processed: 25 average time/residue: 0.0886 time to fit residues: 2.4690 Evaluate side-chains 24 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 28 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.226547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.215371 restraints weight = 1164.554| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 0.63 r_work: 0.4153 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.4021 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1383 Z= 0.117 Angle : 0.413 4.075 1839 Z= 0.219 Chirality : 0.034 0.117 210 Planarity : 0.002 0.013 243 Dihedral : 3.211 11.994 186 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.33 % Allowed : 26.00 % Favored : 68.67 % 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: 1.48 (0.63), residues: 159 helix: 1.23 (0.41), residues: 147 sheet: None (None), residues: 0 loop : -1.42 (1.36), residues: 12 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 58 TYR 0.005 0.001 TYR C 38 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 1377) covalent geometry : angle 0.41304 ( 1839) hydrogen bonds : bond 0.04205 ( 95) hydrogen bonds : angle 3.35032 ( 285) metal coordination : bond 0.00145 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.071 Fit side-chains REVERT: A 50 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7981 (mp) REVERT: A 67 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7089 (tt0) REVERT: A 71 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8530 (mmtm) outliers start: 8 outliers final: 2 residues processed: 28 average time/residue: 0.1013 time to fit residues: 3.0936 Evaluate side-chains 26 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 28 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.197194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.181637 restraints weight = 1123.928| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 0.86 r_work: 0.3911 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1383 Z= 0.119 Angle : 0.402 4.014 1839 Z= 0.214 Chirality : 0.034 0.108 210 Planarity : 0.003 0.027 243 Dihedral : 3.146 11.590 186 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.00 % Allowed : 26.00 % Favored : 68.00 % 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: 1.64 (0.63), residues: 159 helix: 1.34 (0.41), residues: 147 sheet: None (None), residues: 0 loop : -1.46 (1.33), residues: 12 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 58 TYR 0.005 0.001 TYR A 38 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 1377) covalent geometry : angle 0.40153 ( 1839) hydrogen bonds : bond 0.04178 ( 95) hydrogen bonds : angle 3.27785 ( 285) metal coordination : bond 0.00156 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.057 Fit side-chains REVERT: A 50 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7989 (mp) REVERT: A 67 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: A 71 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8555 (mmtm) REVERT: B 43 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6954 (m-30) outliers start: 9 outliers final: 3 residues processed: 28 average time/residue: 0.0658 time to fit residues: 2.0915 Evaluate side-chains 28 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 28 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.198989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.183540 restraints weight = 1115.122| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 0.86 r_work: 0.3881 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1383 Z= 0.103 Angle : 0.378 3.961 1839 Z= 0.202 Chirality : 0.034 0.111 210 Planarity : 0.002 0.016 243 Dihedral : 3.029 11.443 186 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.33 % Allowed : 27.33 % Favored : 67.33 % 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: 2.01 (0.63), residues: 159 helix: 1.57 (0.41), residues: 147 sheet: None (None), residues: 0 loop : -1.26 (1.30), residues: 12 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 58 TYR 0.004 0.001 TYR A 38 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 1377) covalent geometry : angle 0.37803 ( 1839) hydrogen bonds : bond 0.03761 ( 95) hydrogen bonds : angle 3.12256 ( 285) metal coordination : bond 0.00125 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.065 Fit side-chains REVERT: A 50 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7979 (mp) REVERT: A 67 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7101 (tt0) REVERT: A 71 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8495 (mmtm) REVERT: B 43 ASP cc_start: 0.7123 (m-30) cc_final: 0.6898 (m-30) outliers start: 8 outliers final: 1 residues processed: 26 average time/residue: 0.0694 time to fit residues: 2.0460 Evaluate side-chains 23 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain C residue 28 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.224381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.213057 restraints weight = 1111.575| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 0.61 r_work: 0.3910 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1383 Z= 0.133 Angle : 0.447 3.813 1839 Z= 0.229 Chirality : 0.035 0.111 210 Planarity : 0.003 0.019 243 Dihedral : 3.101 11.775 186 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 3.33 % Allowed : 30.67 % Favored : 66.00 % 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: 1.75 (0.63), residues: 159 helix: 1.41 (0.41), residues: 147 sheet: None (None), residues: 0 loop : -1.37 (1.28), residues: 12 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 58 TYR 0.006 0.002 TYR A 38 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 1377) covalent geometry : angle 0.44673 ( 1839) hydrogen bonds : bond 0.04315 ( 95) hydrogen bonds : angle 3.24698 ( 285) metal coordination : bond 0.00173 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.062 Fit side-chains REVERT: A 50 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7962 (mp) REVERT: A 67 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7197 (tt0) REVERT: A 71 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8560 (mmtm) REVERT: B 43 ASP cc_start: 0.7125 (m-30) cc_final: 0.6905 (m-30) outliers start: 5 outliers final: 2 residues processed: 24 average time/residue: 0.0756 time to fit residues: 2.0478 Evaluate side-chains 25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 28 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.222194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.210991 restraints weight = 1081.961| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 0.60 r_work: 0.3902 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1383 Z= 0.116 Angle : 0.421 3.930 1839 Z= 0.216 Chirality : 0.034 0.108 210 Planarity : 0.003 0.017 243 Dihedral : 3.031 11.488 186 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.00 % Allowed : 30.67 % Favored : 65.33 % 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: 1.87 (0.63), residues: 159 helix: 1.48 (0.41), residues: 147 sheet: None (None), residues: 0 loop : -1.31 (1.24), residues: 12 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 58 TYR 0.005 0.001 TYR A 38 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 1377) covalent geometry : angle 0.42127 ( 1839) hydrogen bonds : bond 0.04014 ( 95) hydrogen bonds : angle 3.15867 ( 285) metal coordination : bond 0.00140 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.060 Fit side-chains REVERT: A 50 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7446 (mp) REVERT: A 67 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7099 (tt0) REVERT: A 71 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8531 (mmtm) REVERT: B 43 ASP cc_start: 0.7095 (m-30) cc_final: 0.6862 (m-30) outliers start: 6 outliers final: 2 residues processed: 24 average time/residue: 0.0752 time to fit residues: 2.0404 Evaluate side-chains 24 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 28 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.224762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.213385 restraints weight = 1109.272| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 0.61 r_work: 0.4141 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.4010 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1383 Z= 0.128 Angle : 0.440 3.782 1839 Z= 0.226 Chirality : 0.035 0.120 210 Planarity : 0.003 0.018 243 Dihedral : 3.081 12.181 186 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 4.00 % Allowed : 32.00 % Favored : 64.00 % 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: 1.75 (0.63), residues: 159 helix: 1.41 (0.41), residues: 147 sheet: None (None), residues: 0 loop : -1.39 (1.22), residues: 12 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 58 TYR 0.006 0.001 TYR A 38 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 1377) covalent geometry : angle 0.44024 ( 1839) hydrogen bonds : bond 0.04216 ( 95) hydrogen bonds : angle 3.22900 ( 285) metal coordination : bond 0.00160 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.059 Fit side-chains REVERT: A 50 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8005 (mp) REVERT: A 67 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: A 71 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8513 (mmtm) REVERT: B 43 ASP cc_start: 0.7120 (m-30) cc_final: 0.6892 (m-30) outliers start: 6 outliers final: 2 residues processed: 25 average time/residue: 0.0715 time to fit residues: 2.0234 Evaluate side-chains 25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 28 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 2 optimal weight: 0.2980 chunk 14 optimal weight: 0.0870 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.226485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.215153 restraints weight = 1116.015| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 0.62 r_work: 0.4144 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.4009 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1383 Z= 0.090 Angle : 0.390 4.038 1839 Z= 0.201 Chirality : 0.032 0.102 210 Planarity : 0.002 0.013 243 Dihedral : 2.853 11.138 186 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.67 % Allowed : 32.00 % Favored : 65.33 % 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: 2.39 (0.63), residues: 159 helix: 1.81 (0.41), residues: 147 sheet: None (None), residues: 0 loop : -1.05 (1.25), residues: 12 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 58 TYR 0.003 0.001 TYR C 38 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 1377) covalent geometry : angle 0.39043 ( 1839) hydrogen bonds : bond 0.03353 ( 95) hydrogen bonds : angle 2.94774 ( 285) metal coordination : bond 0.00097 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 318 Ramachandran restraints generated. 159 Oldfield, 0 Emsley, 159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.035 Fit side-chains REVERT: A 50 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7396 (mp) REVERT: A 67 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: A 71 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8498 (mmtm) REVERT: B 43 ASP cc_start: 0.7099 (m-30) cc_final: 0.6884 (m-30) outliers start: 4 outliers final: 1 residues processed: 23 average time/residue: 0.0580 time to fit residues: 1.4897 Evaluate side-chains 23 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain B residue 74 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.200139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.185805 restraints weight = 1115.863| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 0.78 r_work: 0.3886 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1383 Z= 0.119 Angle : 0.416 3.450 1839 Z= 0.217 Chirality : 0.034 0.117 210 Planarity : 0.003 0.016 243 Dihedral : 2.963 11.825 186 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.67 % Allowed : 31.33 % Favored : 66.00 % 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: 2.08 (0.63), residues: 159 helix: 1.62 (0.41), residues: 147 sheet: None (None), residues: 0 loop : -1.28 (1.22), residues: 12 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 54 TYR 0.005 0.001 TYR A 38 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 1377) covalent geometry : angle 0.41636 ( 1839) hydrogen bonds : bond 0.03985 ( 95) hydrogen bonds : angle 3.09334 ( 285) metal coordination : bond 0.00143 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 575.87 seconds wall clock time: 10 minutes 37.17 seconds (637.17 seconds total)