Starting phenix.real_space_refine on Wed Sep 17 02:59:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3t_38898/09_2025/8y3t_38898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3t_38898/09_2025/8y3t_38898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3t_38898/09_2025/8y3t_38898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3t_38898/09_2025/8y3t_38898.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3t_38898/09_2025/8y3t_38898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3t_38898/09_2025/8y3t_38898.cif" } resolution = 2.61 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= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1126 2.51 5 N 308 2.21 5 O 350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1790 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 895 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 0.49, per 1000 atoms: 0.27 Number of scatterers: 1790 At special positions: 0 Unit cell: (62.7, 47.5, 60.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 350 8.00 N 308 7.00 C 1126 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: 0.08 Conformation dependent library (CDL) restraints added in 41.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 448 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 21.0% alpha, 35.3% 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 97 through 112 removed outlier: 3.525A pdb=" N LEU A 112 " --> pdb=" O MET A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 Processing helix chain 'B' and resid 97 through 112 removed outlier: 3.525A pdb=" N LEU B 112 " --> pdb=" O MET B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 5.457A pdb=" N VAL A 8 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 20 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU A 31 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 25 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ARG A 83 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ARG B 83 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE B 25 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU B 31 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL B 20 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL B 8 " --> pdb=" O VAL B 20 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 270 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: 0.14 Time building geometry restraints manager: 0.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 590 1.34 - 1.45: 278 1.45 - 1.57: 942 1.57 - 1.68: 0 1.68 - 1.80: 10 Bond restraints: 1820 Sorted by residual: bond pdb=" CB THR A 45 " pdb=" CG2 THR A 45 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" CB THR B 45 " pdb=" CG2 THR B 45 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 bond pdb=" CB ARG A 56 " pdb=" CG ARG A 56 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" CB ARG B 56 " pdb=" CG ARG B 56 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" C VAL B 20 " pdb=" N ALA B 21 " ideal model delta sigma weight residual 1.331 1.313 0.018 1.59e-02 3.96e+03 1.32e+00 ... (remaining 1815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 2260 1.17 - 2.34: 182 2.34 - 3.50: 24 3.50 - 4.67: 6 4.67 - 5.84: 4 Bond angle restraints: 2476 Sorted by residual: angle pdb=" N ASN A 55 " pdb=" CA ASN A 55 " pdb=" C ASN A 55 " ideal model delta sigma weight residual 109.24 112.99 -3.75 1.67e+00 3.59e-01 5.04e+00 angle pdb=" N ASN B 55 " pdb=" CA ASN B 55 " pdb=" C ASN B 55 " ideal model delta sigma weight residual 109.24 112.94 -3.70 1.67e+00 3.59e-01 4.92e+00 angle pdb=" C ALA A 124 " pdb=" N ASN A 125 " pdb=" CA ASN A 125 " ideal model delta sigma weight residual 121.54 125.69 -4.15 1.91e+00 2.74e-01 4.72e+00 angle pdb=" C ALA B 124 " pdb=" N ASN B 125 " pdb=" CA ASN B 125 " ideal model delta sigma weight residual 121.54 125.69 -4.15 1.91e+00 2.74e-01 4.72e+00 angle pdb=" N PRO B 117 " pdb=" CA PRO B 117 " pdb=" C PRO B 117 " ideal model delta sigma weight residual 112.47 116.08 -3.61 2.06e+00 2.36e-01 3.08e+00 ... (remaining 2471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 1016 16.84 - 33.68: 64 33.68 - 50.52: 10 50.52 - 67.36: 2 67.36 - 84.20: 2 Dihedral angle restraints: 1094 sinusoidal: 404 harmonic: 690 Sorted by residual: dihedral pdb=" CA ASN B 55 " pdb=" C ASN B 55 " pdb=" N ARG B 56 " pdb=" CA ARG B 56 " ideal model delta harmonic sigma weight residual 180.00 151.14 28.86 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASN A 55 " pdb=" C ASN A 55 " pdb=" N ARG A 56 " pdb=" CA ARG A 56 " ideal model delta harmonic sigma weight residual 180.00 151.16 28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA LYS B 113 " pdb=" C LYS B 113 " pdb=" N ASP B 114 " pdb=" CA ASP B 114 " ideal model delta harmonic sigma weight residual -180.00 -156.91 -23.09 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 1091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 162 0.034 - 0.069: 82 0.069 - 0.103: 30 0.103 - 0.137: 10 0.137 - 0.171: 6 Chirality restraints: 290 Sorted by residual: chirality pdb=" CA ILE A 128 " pdb=" N ILE A 128 " pdb=" C ILE A 128 " pdb=" CB ILE A 128 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" CA ILE B 128 " pdb=" N ILE B 128 " pdb=" C ILE B 128 " pdb=" CB ILE B 128 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CB THR A 45 " pdb=" CA THR A 45 " pdb=" OG1 THR A 45 " pdb=" CG2 THR A 45 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 287 not shown) Planarity restraints: 320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 4 " -0.014 2.00e-02 2.50e+03 1.14e-02 2.27e+00 pdb=" CG PHE B 4 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE B 4 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 4 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 4 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 4 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 4 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 4 " -0.014 2.00e-02 2.50e+03 1.14e-02 2.26e+00 pdb=" CG PHE A 4 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 4 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 4 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 4 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 4 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 4 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 116 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A 117 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.020 5.00e-02 4.00e+02 ... (remaining 317 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 280 2.76 - 3.30: 1705 3.30 - 3.83: 3045 3.83 - 4.37: 3731 4.37 - 4.90: 6444 Nonbonded interactions: 15205 Sorted by model distance: nonbonded pdb=" O GLY A 110 " pdb=" ND2 ASN A 116 " model vdw 2.231 3.120 nonbonded pdb=" O GLY B 110 " pdb=" ND2 ASN B 116 " model vdw 2.231 3.120 nonbonded pdb=" NH2 ARG A 56 " pdb=" OD1 ASN B 125 " model vdw 2.328 3.120 nonbonded pdb=" OD1 ASN A 125 " pdb=" NH2 ARG B 56 " model vdw 2.380 3.120 nonbonded pdb=" O ALA B 41 " pdb=" NH2 ARG B 83 " model vdw 2.407 3.120 ... (remaining 15200 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' } 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: 0.810 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 2.460 Find NCS groups from input model: 0.010 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:4.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.008 0.053 1820 Z= 0.353 Angle : 0.716 5.839 2476 Z= 0.397 Chirality : 0.051 0.171 290 Planarity : 0.004 0.036 320 Dihedral : 12.615 84.198 646 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 0.24 (0.54), residues: 230 helix: 0.37 (0.67), residues: 52 sheet: 0.45 (0.58), residues: 78 loop : -0.03 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 38 TYR 0.008 0.002 TYR A 129 PHE 0.025 0.003 PHE A 4 TRP 0.015 0.004 TRP A 32 Details of bonding type rmsd covalent geometry : bond 0.00839 ( 1820) covalent geometry : angle 0.71565 ( 2476) hydrogen bonds : bond 0.14543 ( 94) hydrogen bonds : angle 6.53616 ( 270) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.071 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.8148 time to fit residues: 40.4560 Evaluate side-chains 43 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.146929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126233 restraints weight = 1903.332| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.81 r_work: 0.3369 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 1820 Z= 0.224 Angle : 0.585 5.697 2476 Z= 0.317 Chirality : 0.047 0.150 290 Planarity : 0.005 0.035 320 Dihedral : 5.635 27.855 252 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.61 % Allowed : 9.79 % Favored : 86.60 % 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 aren not related in a simple way. whole: 0.50 (0.54), residues: 230 helix: 1.09 (0.67), residues: 52 sheet: 0.17 (0.56), residues: 78 loop : 0.23 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 49 TYR 0.009 0.002 TYR A 42 PHE 0.016 0.002 PHE B 4 TRP 0.014 0.003 TRP B 32 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 1820) covalent geometry : angle 0.58479 ( 2476) hydrogen bonds : bond 0.04463 ( 94) hydrogen bonds : angle 5.50837 ( 270) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.077 Fit side-chains REVERT: B 103 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8426 (tm) outliers start: 7 outliers final: 2 residues processed: 50 average time/residue: 0.8039 time to fit residues: 40.6898 Evaluate side-chains 50 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.151472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130936 restraints weight = 1921.986| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.83 r_work: 0.3468 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1820 Z= 0.129 Angle : 0.499 5.395 2476 Z= 0.269 Chirality : 0.045 0.146 290 Planarity : 0.004 0.036 320 Dihedral : 4.903 24.545 252 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.12 % Allowed : 12.89 % Favored : 82.99 % 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 aren not related in a simple way. whole: 0.88 (0.56), residues: 230 helix: 1.76 (0.71), residues: 52 sheet: 0.32 (0.54), residues: 88 loop : 0.34 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.007 0.001 TYR B 42 PHE 0.011 0.002 PHE B 4 TRP 0.012 0.002 TRP B 32 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 1820) covalent geometry : angle 0.49935 ( 2476) hydrogen bonds : bond 0.03524 ( 94) hydrogen bonds : angle 5.25870 ( 270) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.069 Fit side-chains REVERT: A 25 PHE cc_start: 0.8466 (t80) cc_final: 0.8125 (t80) outliers start: 8 outliers final: 1 residues processed: 55 average time/residue: 0.7449 time to fit residues: 41.4916 Evaluate side-chains 52 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.149977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129175 restraints weight = 1856.624| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.80 r_work: 0.3449 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 1820 Z= 0.159 Angle : 0.521 5.481 2476 Z= 0.278 Chirality : 0.045 0.145 290 Planarity : 0.005 0.036 320 Dihedral : 5.024 25.008 252 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.09 % Allowed : 14.43 % Favored : 82.47 % 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 aren not related in a simple way. whole: 0.90 (0.56), residues: 230 helix: 1.72 (0.72), residues: 52 sheet: 0.30 (0.54), residues: 88 loop : 0.43 (0.69), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.008 0.001 TYR B 58 PHE 0.010 0.002 PHE B 4 TRP 0.012 0.002 TRP B 32 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 1820) covalent geometry : angle 0.52111 ( 2476) hydrogen bonds : bond 0.03754 ( 94) hydrogen bonds : angle 5.28021 ( 270) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.083 Fit side-chains REVERT: B 89 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7790 (mm-30) outliers start: 6 outliers final: 2 residues processed: 54 average time/residue: 0.7696 time to fit residues: 42.0839 Evaluate side-chains 54 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.151434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.130592 restraints weight = 1905.804| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.83 r_work: 0.3405 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1820 Z= 0.145 Angle : 0.510 5.446 2476 Z= 0.272 Chirality : 0.045 0.144 290 Planarity : 0.004 0.036 320 Dihedral : 4.918 24.628 252 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.09 % Allowed : 17.01 % Favored : 79.90 % 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 aren not related in a simple way. whole: 0.97 (0.56), residues: 230 helix: 1.80 (0.73), residues: 52 sheet: 0.30 (0.54), residues: 88 loop : 0.50 (0.69), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.009 0.001 TYR B 42 PHE 0.009 0.002 PHE A 4 TRP 0.012 0.002 TRP B 32 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 1820) covalent geometry : angle 0.50951 ( 2476) hydrogen bonds : bond 0.03550 ( 94) hydrogen bonds : angle 5.26138 ( 270) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.072 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.7894 time to fit residues: 43.1459 Evaluate side-chains 55 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 45 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.151229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.130475 restraints weight = 1884.290| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.81 r_work: 0.3400 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1820 Z= 0.150 Angle : 0.509 5.456 2476 Z= 0.271 Chirality : 0.045 0.144 290 Planarity : 0.004 0.035 320 Dihedral : 4.936 24.713 252 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.09 % Allowed : 18.04 % Favored : 78.87 % 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 aren not related in a simple way. whole: 1.01 (0.57), residues: 230 helix: 1.82 (0.73), residues: 52 sheet: 0.31 (0.54), residues: 88 loop : 0.56 (0.70), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.008 0.001 TYR B 58 PHE 0.008 0.001 PHE A 4 TRP 0.012 0.002 TRP B 32 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 1820) covalent geometry : angle 0.50929 ( 2476) hydrogen bonds : bond 0.03553 ( 94) hydrogen bonds : angle 5.24798 ( 270) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.072 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 0.7476 time to fit residues: 40.1024 Evaluate side-chains 54 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 45 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.152287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131568 restraints weight = 1855.712| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.80 r_work: 0.3460 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1820 Z= 0.139 Angle : 0.507 5.429 2476 Z= 0.270 Chirality : 0.045 0.144 290 Planarity : 0.004 0.036 320 Dihedral : 4.871 24.709 252 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.06 % Allowed : 19.07 % Favored : 78.87 % 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 aren not related in a simple way. whole: 1.03 (0.57), residues: 230 helix: 1.85 (0.73), residues: 52 sheet: 0.31 (0.54), residues: 88 loop : 0.57 (0.69), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 49 TYR 0.009 0.001 TYR B 42 PHE 0.007 0.001 PHE A 4 TRP 0.012 0.002 TRP B 32 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 1820) covalent geometry : angle 0.50743 ( 2476) hydrogen bonds : bond 0.03473 ( 94) hydrogen bonds : angle 5.21135 ( 270) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.068 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 0.7298 time to fit residues: 39.1621 Evaluate side-chains 54 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 45 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.128869 restraints weight = 1870.055| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.83 r_work: 0.3385 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 1820 Z= 0.167 Angle : 0.525 5.496 2476 Z= 0.279 Chirality : 0.045 0.144 290 Planarity : 0.005 0.037 320 Dihedral : 5.042 25.338 252 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.06 % Allowed : 19.07 % Favored : 78.87 % 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 aren not related in a simple way. whole: 0.94 (0.56), residues: 230 helix: 1.75 (0.72), residues: 52 sheet: 0.28 (0.54), residues: 88 loop : 0.51 (0.69), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 49 TYR 0.012 0.002 TYR B 42 PHE 0.008 0.001 PHE A 4 TRP 0.012 0.002 TRP B 32 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 1820) covalent geometry : angle 0.52515 ( 2476) hydrogen bonds : bond 0.03690 ( 94) hydrogen bonds : angle 5.26828 ( 270) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.061 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 0.6840 time to fit residues: 36.7106 Evaluate side-chains 54 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 45 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.130748 restraints weight = 1857.121| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.79 r_work: 0.3452 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1820 Z= 0.153 Angle : 0.516 5.464 2476 Z= 0.274 Chirality : 0.045 0.143 290 Planarity : 0.004 0.037 320 Dihedral : 4.976 25.007 252 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.58 % Allowed : 18.56 % Favored : 78.87 % 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 aren not related in a simple way. whole: 1.03 (0.55), residues: 230 helix: 1.78 (0.73), residues: 52 sheet: 0.10 (0.55), residues: 78 loop : 0.79 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 49 TYR 0.012 0.002 TYR B 42 PHE 0.007 0.001 PHE A 4 TRP 0.012 0.002 TRP B 32 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 1820) covalent geometry : angle 0.51595 ( 2476) hydrogen bonds : bond 0.03592 ( 94) hydrogen bonds : angle 5.23680 ( 270) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.083 Fit side-chains REVERT: B 89 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7750 (mm-30) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.7717 time to fit residues: 41.3911 Evaluate side-chains 55 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131476 restraints weight = 1847.031| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.78 r_work: 0.3461 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1820 Z= 0.142 Angle : 0.510 5.433 2476 Z= 0.271 Chirality : 0.045 0.142 290 Planarity : 0.005 0.037 320 Dihedral : 4.910 25.004 252 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.06 % Allowed : 19.07 % Favored : 78.87 % 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 aren not related in a simple way. whole: 1.01 (0.56), residues: 230 helix: 1.83 (0.73), residues: 52 sheet: 0.35 (0.54), residues: 88 loop : 0.50 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 49 TYR 0.012 0.002 TYR B 42 PHE 0.007 0.001 PHE A 4 TRP 0.013 0.002 TRP B 32 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 1820) covalent geometry : angle 0.50994 ( 2476) hydrogen bonds : bond 0.03500 ( 94) hydrogen bonds : angle 5.22537 ( 270) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.065 Fit side-chains REVERT: B 89 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7740 (mm-30) outliers start: 4 outliers final: 3 residues processed: 52 average time/residue: 0.6180 time to fit residues: 32.5426 Evaluate side-chains 55 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131149 restraints weight = 1875.286| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.81 r_work: 0.3470 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1820 Z= 0.130 Angle : 0.502 5.401 2476 Z= 0.266 Chirality : 0.045 0.141 290 Planarity : 0.005 0.038 320 Dihedral : 4.798 24.447 252 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.06 % Allowed : 19.59 % Favored : 78.35 % 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 aren not related in a simple way. whole: 1.10 (0.56), residues: 230 helix: 1.90 (0.73), residues: 52 sheet: 0.41 (0.54), residues: 88 loop : 0.56 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.011 0.001 TYR B 42 PHE 0.007 0.001 PHE A 4 TRP 0.013 0.002 TRP B 32 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 1820) covalent geometry : angle 0.50216 ( 2476) hydrogen bonds : bond 0.03386 ( 94) hydrogen bonds : angle 5.17341 ( 270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1147.63 seconds wall clock time: 20 minutes 58.81 seconds (1258.81 seconds total)