Starting phenix.real_space_refine on Tue Feb 3 12:25:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k8d_62169/02_2026/9k8d_62169.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k8d_62169/02_2026/9k8d_62169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k8d_62169/02_2026/9k8d_62169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k8d_62169/02_2026/9k8d_62169.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k8d_62169/02_2026/9k8d_62169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k8d_62169/02_2026/9k8d_62169.map" } resolution = 3.06 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= 0.003 sd= 0.224 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: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 3 5.16 5 C 1286 2.51 5 N 328 2.21 5 O 379 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 1999 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 660 Classifications: {'peptide': 85} Link IDs: {'TRANS': 84} Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 668 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "C" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 668 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "A" 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: 0.62, per 1000 atoms: 0.31 Number of scatterers: 1999 At special positions: 0 Unit cell: (52.7877, 60.3288, 58.1742, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 3 16.00 O 379 8.00 N 328 7.00 C 1286 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: 0.12 Conformation dependent library (CDL) restraints added in 89.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 58 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS C 15 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS B 58 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 15 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 58 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS B 15 " 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 84.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 8 through 24 removed outlier: 3.988A pdb=" N ILE A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 43 Processing helix chain 'A' and resid 50 through 65 Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'B' and resid 10 through 26 removed outlier: 4.083A pdb=" N GLU B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 26 " --> pdb=" O TYR B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 43 removed outlier: 3.587A pdb=" N ALA B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 68 removed outlier: 4.121A pdb=" N ARG B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 88 Processing helix chain 'C' and resid 9 through 26 removed outlier: 3.746A pdb=" N GLU C 25 " --> pdb=" O LYS C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 42 removed outlier: 3.760A pdb=" N ALA C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 66 Processing helix chain 'C' and resid 69 through 89 removed outlier: 3.559A pdb=" N ALA C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) 158 hydrogen bonds defined for protein. 474 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: 0.34 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 638 1.34 - 1.46: 208 1.46 - 1.57: 1156 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 2008 Sorted by residual: bond pdb=" N ASP B 47 " pdb=" CA ASP B 47 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.50e+00 bond pdb=" CA LEU C 64 " pdb=" C LEU C 64 " ideal model delta sigma weight residual 1.522 1.532 -0.010 1.34e-02 5.57e+03 5.13e-01 bond pdb=" CA ILE C 61 " pdb=" C ILE C 61 " ideal model delta sigma weight residual 1.524 1.515 0.009 1.22e-02 6.72e+03 5.01e-01 bond pdb=" N LEU A 64 " pdb=" CA LEU A 64 " ideal model delta sigma weight residual 1.460 1.451 0.009 1.27e-02 6.20e+03 4.76e-01 bond pdb=" N LEU C 64 " pdb=" CA LEU C 64 " ideal model delta sigma weight residual 1.456 1.464 -0.009 1.35e-02 5.49e+03 4.00e-01 ... (remaining 2003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 2507 1.17 - 2.34: 137 2.34 - 3.51: 25 3.51 - 4.67: 4 4.67 - 5.84: 5 Bond angle restraints: 2678 Sorted by residual: angle pdb=" N MET B 6 " pdb=" CA MET B 6 " pdb=" C MET B 6 " ideal model delta sigma weight residual 112.58 107.00 5.58 1.22e+00 6.72e-01 2.09e+01 angle pdb=" N LYS B 27 " pdb=" CA LYS B 27 " pdb=" C LYS B 27 " ideal model delta sigma weight residual 107.98 113.32 -5.34 1.88e+00 2.83e-01 8.05e+00 angle pdb=" N MET A 6 " pdb=" CA MET A 6 " pdb=" C MET A 6 " ideal model delta sigma weight residual 113.97 110.55 3.42 1.28e+00 6.10e-01 7.12e+00 angle pdb=" C GLU C 7 " pdb=" N LYS C 8 " pdb=" CA LYS C 8 " ideal model delta sigma weight residual 121.54 126.36 -4.82 1.91e+00 2.74e-01 6.37e+00 angle pdb=" N ALA A 49 " pdb=" CA ALA A 49 " pdb=" C ALA A 49 " ideal model delta sigma weight residual 114.39 110.76 3.63 1.45e+00 4.76e-01 6.27e+00 ... (remaining 2673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 1051 18.00 - 35.99: 147 35.99 - 53.99: 59 53.99 - 71.99: 11 71.99 - 89.98: 2 Dihedral angle restraints: 1270 sinusoidal: 519 harmonic: 751 Sorted by residual: dihedral pdb=" CA GLY B 26 " pdb=" C GLY B 26 " pdb=" N LYS B 27 " pdb=" CA LYS B 27 " ideal model delta harmonic sigma weight residual -180.00 -161.91 -18.09 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CB GLU C 44 " pdb=" CG GLU C 44 " pdb=" CD GLU C 44 " pdb=" OE1 GLU C 44 " ideal model delta sinusoidal sigma weight residual 0.00 -89.98 89.98 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU A 85 " pdb=" CG GLU A 85 " pdb=" CD GLU A 85 " pdb=" OE1 GLU A 85 " ideal model delta sinusoidal sigma weight residual 0.00 -89.01 89.01 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 1267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 228 0.034 - 0.068: 82 0.068 - 0.102: 10 0.102 - 0.136: 3 0.136 - 0.170: 1 Chirality restraints: 324 Sorted by residual: chirality pdb=" CG LEU C 64 " pdb=" CB LEU C 64 " pdb=" CD1 LEU C 64 " pdb=" CD2 LEU C 64 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA LEU C 64 " pdb=" N LEU C 64 " pdb=" C LEU C 64 " pdb=" CB LEU C 64 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA ILE B 61 " pdb=" N ILE B 61 " pdb=" C ILE B 61 " pdb=" CB ILE B 61 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.99e-01 ... (remaining 321 not shown) Planarity restraints: 325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 62 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.78e+00 pdb=" C ASP C 62 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP C 62 " 0.009 2.00e-02 2.50e+03 pdb=" N THR C 63 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 61 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C ILE C 61 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE C 61 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP C 62 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 46 " -0.005 2.00e-02 2.50e+03 1.09e-02 1.18e+00 pdb=" C GLY B 46 " 0.019 2.00e-02 2.50e+03 pdb=" O GLY B 46 " -0.007 2.00e-02 2.50e+03 pdb=" N ASP B 47 " -0.006 2.00e-02 2.50e+03 ... (remaining 322 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 13 2.54 - 3.13: 1459 3.13 - 3.72: 3099 3.72 - 4.31: 4077 4.31 - 4.90: 7228 Nonbonded interactions: 15876 Sorted by model distance: nonbonded pdb=" OD2 ASP C 37 " pdb="ZN ZN A 301 " model vdw 1.952 2.230 nonbonded pdb=" OD2 ASP A 37 " pdb="ZN ZN A 302 " model vdw 1.999 2.230 nonbonded pdb=" OD1 ASP A 32 " pdb="ZN ZN A 301 " model vdw 2.053 2.230 nonbonded pdb=" OD2 ASP B 37 " pdb="ZN ZN C 301 " model vdw 2.060 2.230 nonbonded pdb=" OD1 ASP B 32 " pdb="ZN ZN A 302 " model vdw 2.078 2.230 ... (remaining 15871 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' and resid 5 through 89) selection = (chain 'B' and resid 5 through 89) selection = (chain 'C' and resid 5 through 89) } 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: 0.900 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.010 Find NCS groups from input model: 0.040 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:1.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 6.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 : 0.012 0.286 2014 Z= 0.399 Angle : 0.643 5.843 2678 Z= 0.415 Chirality : 0.035 0.170 324 Planarity : 0.002 0.013 325 Dihedral : 19.723 89.982 784 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.79 % Allowed : 3.95 % Favored : 95.26 % Rotamer: Outliers : 0.49 % Allowed : 26.47 % Favored : 73.04 % 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: 0.52 (0.52), residues: 253 helix: 1.22 (0.36), residues: 203 sheet: None (None), residues: 0 loop : -3.37 (0.61), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 66 TYR 0.004 0.001 TYR C 83 HIS 0.001 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 2008) covalent geometry : angle 0.64286 ( 2678) hydrogen bonds : bond 0.14487 ( 158) hydrogen bonds : angle 5.31910 ( 474) metal coordination : bond 0.20707 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.084 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 10 average time/residue: 0.0428 time to fit residues: 0.6083 Evaluate side-chains 10 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.185148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.164591 restraints weight = 1666.996| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.51 r_work: 0.3733 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2014 Z= 0.148 Angle : 0.583 10.514 2678 Z= 0.298 Chirality : 0.033 0.106 324 Planarity : 0.002 0.017 325 Dihedral : 4.682 19.496 268 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.53 % Favored : 94.07 % Rotamer: Outliers : 1.96 % Allowed : 26.47 % Favored : 71.57 % 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: 0.61 (0.51), residues: 253 helix: 1.07 (0.35), residues: 213 sheet: None (None), residues: 0 loop : -3.11 (0.71), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.002 0.001 TYR C 79 HIS 0.003 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 2008) covalent geometry : angle 0.58255 ( 2678) hydrogen bonds : bond 0.04298 ( 158) hydrogen bonds : angle 4.27080 ( 474) metal coordination : bond 0.00707 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 6 time to evaluate : 0.087 Fit side-chains REVERT: B 6 MET cc_start: 0.5333 (ttt) cc_final: 0.4829 (tpt) REVERT: C 53 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7819 (tt) outliers start: 4 outliers final: 2 residues processed: 9 average time/residue: 0.0647 time to fit residues: 0.7650 Evaluate side-chains 9 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain C residue 53 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 4 optimal weight: 0.0370 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.186711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.166125 restraints weight = 1657.238| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.51 r_work: 0.3761 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2014 Z= 0.116 Angle : 0.513 10.075 2678 Z= 0.263 Chirality : 0.032 0.095 324 Planarity : 0.002 0.016 325 Dihedral : 4.444 19.307 268 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.74 % Favored : 94.86 % Rotamer: Outliers : 1.96 % Allowed : 26.96 % Favored : 71.08 % 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: 0.96 (0.52), residues: 253 helix: 1.40 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -3.11 (0.64), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 66 TYR 0.002 0.000 TYR A 79 HIS 0.002 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 2008) covalent geometry : angle 0.51296 ( 2678) hydrogen bonds : bond 0.03743 ( 158) hydrogen bonds : angle 4.07145 ( 474) metal coordination : bond 0.00507 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.075 Fit side-chains REVERT: B 6 MET cc_start: 0.5324 (ttt) cc_final: 0.4709 (tpt) outliers start: 4 outliers final: 1 residues processed: 11 average time/residue: 0.0962 time to fit residues: 1.2816 Evaluate side-chains 7 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.182638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.162774 restraints weight = 1633.452| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.44 r_work: 0.3722 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2014 Z= 0.142 Angle : 0.545 10.552 2678 Z= 0.277 Chirality : 0.033 0.102 324 Planarity : 0.002 0.017 325 Dihedral : 4.518 19.463 268 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.14 % Favored : 94.47 % Rotamer: Outliers : 4.41 % Allowed : 24.51 % Favored : 71.08 % 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: 0.95 (0.52), residues: 253 helix: 1.30 (0.35), residues: 213 sheet: None (None), residues: 0 loop : -3.03 (0.71), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.002 0.001 TYR A 79 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 2008) covalent geometry : angle 0.54502 ( 2678) hydrogen bonds : bond 0.04206 ( 158) hydrogen bonds : angle 4.11020 ( 474) metal coordination : bond 0.00575 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 7 time to evaluate : 0.062 Fit side-chains REVERT: B 6 MET cc_start: 0.5625 (ttt) cc_final: 0.5351 (ttt) REVERT: B 71 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6493 (mm-30) outliers start: 9 outliers final: 2 residues processed: 16 average time/residue: 0.0396 time to fit residues: 0.7925 Evaluate side-chains 10 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 71 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 0.0030 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.183443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.163351 restraints weight = 1644.642| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.46 r_work: 0.3726 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2014 Z= 0.129 Angle : 0.519 10.554 2678 Z= 0.264 Chirality : 0.032 0.100 324 Planarity : 0.002 0.016 325 Dihedral : 4.416 19.280 268 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.53 % Favored : 94.07 % Rotamer: Outliers : 3.92 % Allowed : 25.98 % Favored : 70.10 % 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: 1.10 (0.52), residues: 253 helix: 1.42 (0.35), residues: 213 sheet: None (None), residues: 0 loop : -3.07 (0.69), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.001 0.000 TYR A 79 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 2008) covalent geometry : angle 0.51932 ( 2678) hydrogen bonds : bond 0.03926 ( 158) hydrogen bonds : angle 4.02404 ( 474) metal coordination : bond 0.00523 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 9 time to evaluate : 0.044 Fit side-chains REVERT: B 6 MET cc_start: 0.5563 (ttt) cc_final: 0.5289 (ttt) REVERT: B 43 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.6672 (mtmt) REVERT: B 71 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6456 (mm-30) outliers start: 8 outliers final: 4 residues processed: 17 average time/residue: 0.0391 time to fit residues: 0.8241 Evaluate side-chains 15 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 9 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 71 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.185632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.165556 restraints weight = 1649.851| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.46 r_work: 0.3754 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2014 Z= 0.110 Angle : 0.485 10.239 2678 Z= 0.247 Chirality : 0.032 0.095 324 Planarity : 0.002 0.016 325 Dihedral : 4.374 18.804 268 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.90 % Allowed : 25.49 % Favored : 69.61 % 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: 1.51 (0.51), residues: 253 helix: 1.84 (0.35), residues: 207 sheet: None (None), residues: 0 loop : -3.08 (0.59), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 66 TYR 0.001 0.000 TYR B 83 HIS 0.002 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 2008) covalent geometry : angle 0.48459 ( 2678) hydrogen bonds : bond 0.03503 ( 158) hydrogen bonds : angle 3.88926 ( 474) metal coordination : bond 0.00432 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 12 time to evaluate : 0.045 Fit side-chains REVERT: A 53 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7286 (tt) REVERT: B 6 MET cc_start: 0.5493 (ttt) cc_final: 0.4789 (tpt) REVERT: B 43 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.6584 (mtmt) REVERT: B 71 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6484 (mm-30) outliers start: 10 outliers final: 5 residues processed: 22 average time/residue: 0.0398 time to fit residues: 1.0610 Evaluate side-chains 18 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 10 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 61 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.181427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.161460 restraints weight = 1623.016| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.43 r_work: 0.3723 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2014 Z= 0.135 Angle : 0.525 10.608 2678 Z= 0.264 Chirality : 0.033 0.103 324 Planarity : 0.002 0.016 325 Dihedral : 4.407 18.819 268 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.90 % Allowed : 25.00 % Favored : 70.10 % 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: 1.36 (0.51), residues: 253 helix: 1.64 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -3.02 (0.63), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.002 0.001 TYR A 79 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 2008) covalent geometry : angle 0.52542 ( 2678) hydrogen bonds : bond 0.04026 ( 158) hydrogen bonds : angle 3.99286 ( 474) metal coordination : bond 0.00525 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 10 time to evaluate : 0.045 Fit side-chains REVERT: B 6 MET cc_start: 0.5540 (ttt) cc_final: 0.4838 (tpt) REVERT: B 43 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.6701 (mtmt) REVERT: B 71 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6496 (mm-30) outliers start: 10 outliers final: 6 residues processed: 20 average time/residue: 0.0356 time to fit residues: 0.8887 Evaluate side-chains 18 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 10 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 9 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 chunk 18 optimal weight: 0.0050 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.187152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.167627 restraints weight = 1674.213| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 1.41 r_work: 0.3770 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2014 Z= 0.106 Angle : 0.481 10.299 2678 Z= 0.242 Chirality : 0.032 0.095 324 Planarity : 0.002 0.015 325 Dihedral : 4.226 18.007 268 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.92 % Allowed : 25.49 % Favored : 70.59 % 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: 1.63 (0.52), residues: 253 helix: 1.84 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -3.02 (0.61), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 66 TYR 0.002 0.000 TYR A 79 HIS 0.002 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 2008) covalent geometry : angle 0.48129 ( 2678) hydrogen bonds : bond 0.03426 ( 158) hydrogen bonds : angle 3.86416 ( 474) metal coordination : bond 0.00408 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 10 time to evaluate : 0.045 Fit side-chains REVERT: A 53 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7261 (tt) REVERT: B 6 MET cc_start: 0.5463 (ttt) cc_final: 0.4802 (tpt) REVERT: B 43 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.6531 (mtmt) REVERT: B 71 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6427 (mm-30) outliers start: 8 outliers final: 4 residues processed: 18 average time/residue: 0.0380 time to fit residues: 0.8482 Evaluate side-chains 17 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 10 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 71 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.183515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.163899 restraints weight = 1610.633| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.41 r_work: 0.3735 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2014 Z= 0.131 Angle : 0.516 10.505 2678 Z= 0.258 Chirality : 0.033 0.102 324 Planarity : 0.002 0.016 325 Dihedral : 4.314 18.101 268 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.41 % Allowed : 25.00 % Favored : 70.59 % 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: 1.51 (0.51), residues: 253 helix: 1.74 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -2.95 (0.61), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.002 0.001 TYR A 79 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 2008) covalent geometry : angle 0.51560 ( 2678) hydrogen bonds : bond 0.03931 ( 158) hydrogen bonds : angle 3.95333 ( 474) metal coordination : bond 0.00515 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 9 time to evaluate : 0.047 Fit side-chains REVERT: B 6 MET cc_start: 0.5496 (ttt) cc_final: 0.4875 (tpt) REVERT: B 43 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.6692 (mtmt) REVERT: B 71 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6478 (mm-30) outliers start: 9 outliers final: 5 residues processed: 18 average time/residue: 0.0376 time to fit residues: 0.8425 Evaluate side-chains 16 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.182068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.161987 restraints weight = 1676.721| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.46 r_work: 0.3705 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2014 Z= 0.148 Angle : 0.541 10.683 2678 Z= 0.270 Chirality : 0.034 0.106 324 Planarity : 0.002 0.017 325 Dihedral : 4.404 18.293 268 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.41 % Allowed : 25.00 % Favored : 70.59 % 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: 1.34 (0.51), residues: 253 helix: 1.61 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -2.95 (0.61), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.003 0.001 TYR A 79 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 2008) covalent geometry : angle 0.54086 ( 2678) hydrogen bonds : bond 0.04242 ( 158) hydrogen bonds : angle 4.04337 ( 474) metal coordination : bond 0.00572 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 13 time to evaluate : 0.075 Fit side-chains REVERT: A 27 LYS cc_start: 0.7337 (mptt) cc_final: 0.7060 (mptt) REVERT: B 6 MET cc_start: 0.5580 (ttt) cc_final: 0.4902 (tpt) REVERT: B 43 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.6723 (mtmt) REVERT: B 71 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6473 (mm-30) outliers start: 9 outliers final: 6 residues processed: 22 average time/residue: 0.0578 time to fit residues: 1.4996 Evaluate side-chains 21 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 13 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.181685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.162454 restraints weight = 1670.948| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.38 r_work: 0.3687 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2014 Z= 0.156 Angle : 0.550 10.735 2678 Z= 0.275 Chirality : 0.034 0.108 324 Planarity : 0.002 0.017 325 Dihedral : 4.445 18.419 268 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.43 % Allowed : 26.47 % Favored : 70.10 % 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: 1.25 (0.51), residues: 253 helix: 1.55 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -2.99 (0.61), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.003 0.001 TYR A 79 HIS 0.003 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 2008) covalent geometry : angle 0.54969 ( 2678) hydrogen bonds : bond 0.04357 ( 158) hydrogen bonds : angle 4.07875 ( 474) metal coordination : bond 0.00587 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 481.66 seconds wall clock time: 8 minutes 52.84 seconds (532.84 seconds total)