Starting phenix.real_space_refine on Fri Aug 22 12:37:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vhv_43242/08_2025/8vhv_43242.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vhv_43242/08_2025/8vhv_43242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vhv_43242/08_2025/8vhv_43242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vhv_43242/08_2025/8vhv_43242.map" model { file = "/net/cci-nas-00/data/ceres_data/8vhv_43242/08_2025/8vhv_43242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vhv_43242/08_2025/8vhv_43242.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 11 5.16 5 C 878 2.51 5 N 219 2.21 5 O 227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1335 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Time building chain proxies: 0.54, per 1000 atoms: 0.40 Number of scatterers: 1335 At special positions: 0 Unit cell: (41.85, 51.15, 82.77, 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 11 16.00 O 227 8.00 N 219 7.00 C 878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 39 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 76 " distance=2.02 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: 0.07 Conformation dependent library (CDL) restraints added in 38.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 310 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 1 sheets defined 67.4% alpha, 8.7% 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 6 through 28 Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 104 through 122 Processing helix chain 'A' and resid 131 through 159 removed outlier: 3.720A pdb=" N LEU A 135 " --> pdb=" O HIS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 206 removed outlier: 3.821A pdb=" N GLN A 206 " --> pdb=" O ASP A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 78 removed outlier: 4.082A pdb=" N LEU A 75 " --> pdb=" O CYS A 67 " (cutoff:3.500A) 104 hydrogen bonds defined for protein. 303 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: 0.12 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: 1.23 - 1.34: 403 1.34 - 1.46: 301 1.46 - 1.58: 644 1.58 - 1.69: 0 1.69 - 1.81: 17 Bond restraints: 1365 Sorted by residual: bond pdb=" N ARG A 5 " pdb=" CA ARG A 5 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 bond pdb=" C VAL A 142 " pdb=" O VAL A 142 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.12e-02 7.97e+03 4.27e-01 bond pdb=" CA CYS A 66 " pdb=" CB CYS A 66 " ideal model delta sigma weight residual 1.534 1.519 0.016 2.47e-02 1.64e+03 4.00e-01 bond pdb=" C GLU A 69 " pdb=" O GLU A 69 " ideal model delta sigma weight residual 1.232 1.226 0.006 1.01e-02 9.80e+03 3.58e-01 bond pdb=" CA GLU A 190 " pdb=" C GLU A 190 " ideal model delta sigma weight residual 1.523 1.531 -0.007 1.30e-02 5.92e+03 3.32e-01 ... (remaining 1360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 1733 1.14 - 2.29: 89 2.29 - 3.43: 11 3.43 - 4.57: 4 4.57 - 5.71: 3 Bond angle restraints: 1840 Sorted by residual: angle pdb=" N PHE A 106 " pdb=" CA PHE A 106 " pdb=" C PHE A 106 " ideal model delta sigma weight residual 109.81 115.52 -5.71 2.21e+00 2.05e-01 6.68e+00 angle pdb=" C ARG A 130 " pdb=" N HIS A 131 " pdb=" CA HIS A 131 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.99e+00 angle pdb=" N HIS A 131 " pdb=" CA HIS A 131 " pdb=" C HIS A 131 " ideal model delta sigma weight residual 110.80 115.40 -4.60 2.13e+00 2.20e-01 4.67e+00 angle pdb=" N GLY A 70 " pdb=" CA GLY A 70 " pdb=" C GLY A 70 " ideal model delta sigma weight residual 111.19 114.21 -3.02 1.45e+00 4.76e-01 4.32e+00 angle pdb=" N GLU A 69 " pdb=" CA GLU A 69 " pdb=" C GLU A 69 " ideal model delta sigma weight residual 110.06 112.93 -2.87 1.43e+00 4.89e-01 4.02e+00 ... (remaining 1835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.64: 582 8.64 - 17.28: 123 17.28 - 25.92: 42 25.92 - 34.55: 19 34.55 - 43.19: 10 Dihedral angle restraints: 776 sinusoidal: 290 harmonic: 486 Sorted by residual: dihedral pdb=" CA THR A 129 " pdb=" C THR A 129 " pdb=" N ARG A 130 " pdb=" CA ARG A 130 " ideal model delta harmonic sigma weight residual 180.00 157.85 22.15 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LEU A 119 " pdb=" C LEU A 119 " pdb=" N CYS A 120 " pdb=" CA CYS A 120 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PHE A 106 " pdb=" C PHE A 106 " pdb=" N PRO A 107 " pdb=" CA PRO A 107 " ideal model delta harmonic sigma weight residual 180.00 162.61 17.39 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 773 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.027: 103 0.027 - 0.054: 76 0.054 - 0.080: 22 0.080 - 0.106: 4 0.106 - 0.133: 4 Chirality restraints: 209 Sorted by residual: chirality pdb=" CA PRO A 107 " pdb=" N PRO A 107 " pdb=" C PRO A 107 " pdb=" CB PRO A 107 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA LEU A 68 " pdb=" N LEU A 68 " pdb=" C LEU A 68 " pdb=" CB LEU A 68 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA VAL A 56 " pdb=" N VAL A 56 " pdb=" C VAL A 56 " pdb=" CB VAL A 56 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 206 not shown) Planarity restraints: 222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 110 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C SER A 110 " -0.041 2.00e-02 2.50e+03 pdb=" O SER A 110 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A 111 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 64 " -0.147 9.50e-02 1.11e+02 6.64e-02 3.14e+00 pdb=" NE ARG A 64 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 64 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 64 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 64 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 200 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C PHE A 200 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE A 200 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 201 " -0.010 2.00e-02 2.50e+03 ... (remaining 219 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 437 2.84 - 3.35: 1365 3.35 - 3.87: 2184 3.87 - 4.38: 2338 4.38 - 4.90: 4104 Nonbonded interactions: 10428 Sorted by model distance: nonbonded pdb=" O LYS A 128 " pdb=" OG1 THR A 129 " model vdw 2.325 3.040 nonbonded pdb=" O SER A 35 " pdb=" O THR A 58 " model vdw 2.496 3.040 nonbonded pdb=" O SER A 103 " pdb=" OG SER A 104 " model vdw 2.511 3.040 nonbonded pdb=" OG SER A 60 " pdb=" OG1 THR A 65 " model vdw 2.519 3.040 nonbonded pdb=" OD2 ASP A 30 " pdb=" NH1 ARG A 64 " model vdw 2.539 3.120 ... (remaining 10423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 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: 0.000 Process input model: 2.790 Find NCS groups from input model: 0.000 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:5.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5423 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 : 0.003 0.031 1367 Z= 0.164 Angle : 0.642 5.714 1844 Z= 0.390 Chirality : 0.038 0.133 209 Planarity : 0.009 0.066 222 Dihedral : 12.389 43.192 460 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % 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: 0.22 (0.60), residues: 164 helix: 0.86 (0.44), residues: 109 sheet: -0.20 (1.97), residues: 10 loop : -1.40 (0.84), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.003 ARG A 64 TYR 0.016 0.004 TYR A 180 PHE 0.016 0.002 PHE A 96 TRP 0.014 0.003 TRP A 177 HIS 0.004 0.002 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 1365) covalent geometry : angle 0.64159 ( 1840) SS BOND : bond 0.00543 ( 2) SS BOND : angle 0.72632 ( 4) hydrogen bonds : bond 0.14511 ( 104) hydrogen bonds : angle 5.57714 ( 303) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.028 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2266 time to fit residues: 7.7337 Evaluate side-chains 27 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 12 optimal weight: 0.1980 chunk 13 optimal weight: 0.0970 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.0870 chunk 16 optimal weight: 0.0870 chunk 15 optimal weight: 0.0970 chunk 9 optimal weight: 0.2980 chunk 11 optimal weight: 0.0980 chunk 6 optimal weight: 0.0570 chunk 4 optimal weight: 0.3980 chunk 3 optimal weight: 0.0970 overall best weight: 0.0850 ------------------------------------------------------------------------------- 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 = 0.4755 r_free = 0.4755 target = 0.277892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.274624 restraints weight = 1218.753| |-----------------------------------------------------------------------------| r_work (start): 0.4729 rms_B_bonded: 0.26 r_work: 0.4701 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.4656 rms_B_bonded: 1.50 restraints_weight: 0.2500 r_work (final): 0.4656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5367 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1367 Z= 0.126 Angle : 0.541 7.401 1844 Z= 0.291 Chirality : 0.041 0.119 209 Planarity : 0.003 0.032 222 Dihedral : 4.692 16.089 183 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 6.47 % Allowed : 9.35 % Favored : 84.17 % 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: 2.66 (0.70), residues: 164 helix: 2.85 (0.50), residues: 111 sheet: -0.24 (1.96), residues: 10 loop : -0.78 (1.03), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 36 TYR 0.011 0.002 TYR A 175 PHE 0.008 0.001 PHE A 179 TRP 0.019 0.002 TRP A 177 HIS 0.002 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 1365) covalent geometry : angle 0.54138 ( 1840) SS BOND : bond 0.00133 ( 2) SS BOND : angle 0.35851 ( 4) hydrogen bonds : bond 0.04503 ( 104) hydrogen bonds : angle 3.82461 ( 303) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.027 Fit side-chains REVERT: A 94 GLU cc_start: 0.5096 (OUTLIER) cc_final: 0.4806 (mp0) outliers start: 9 outliers final: 2 residues processed: 33 average time/residue: 0.1624 time to fit residues: 5.5208 Evaluate side-chains 26 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 0 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 14 optimal weight: 0.2980 chunk 1 optimal weight: 0.2980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.271400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.268307 restraints weight = 1172.356| |-----------------------------------------------------------------------------| r_work (start): 0.4676 rms_B_bonded: 0.25 r_work: 0.4647 rms_B_bonded: 0.60 restraints_weight: 0.5000 r_work: 0.4603 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work (final): 0.4603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5575 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 1367 Z= 0.240 Angle : 0.723 8.578 1844 Z= 0.372 Chirality : 0.047 0.170 209 Planarity : 0.004 0.033 222 Dihedral : 5.132 18.197 183 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 9.35 % Allowed : 10.07 % Favored : 80.58 % 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: 2.39 (0.72), residues: 164 helix: 2.56 (0.50), residues: 112 sheet: -0.58 (1.77), residues: 10 loop : -0.62 (1.19), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 36 TYR 0.017 0.003 TYR A 34 PHE 0.008 0.002 PHE A 140 TRP 0.020 0.003 TRP A 177 HIS 0.004 0.002 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 1365) covalent geometry : angle 0.72358 ( 1840) SS BOND : bond 0.00372 ( 2) SS BOND : angle 0.43502 ( 4) hydrogen bonds : bond 0.05805 ( 104) hydrogen bonds : angle 4.08502 ( 303) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.030 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 30 average time/residue: 0.1720 time to fit residues: 5.3133 Evaluate side-chains 25 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 0.0980 chunk 2 optimal weight: 0.4980 chunk 13 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 0.0670 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 1 optimal weight: 0.2980 chunk 0 optimal weight: 0.3980 overall best weight: 0.1916 ------------------------------------------------------------------------------- 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 = 0.4718 r_free = 0.4718 target = 0.274077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.270946 restraints weight = 1177.884| |-----------------------------------------------------------------------------| r_work (start): 0.4692 rms_B_bonded: 0.25 r_work: 0.4662 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.4616 rms_B_bonded: 1.56 restraints_weight: 0.2500 r_work (final): 0.4616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5521 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1367 Z= 0.168 Angle : 0.596 6.331 1844 Z= 0.314 Chirality : 0.043 0.145 209 Planarity : 0.003 0.035 222 Dihedral : 4.761 15.670 183 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 9.35 % Allowed : 11.51 % Favored : 79.14 % 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: 2.14 (0.69), residues: 164 helix: 2.61 (0.49), residues: 114 sheet: -0.53 (1.76), residues: 10 loop : -1.76 (0.97), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 36 TYR 0.013 0.002 TYR A 175 PHE 0.007 0.001 PHE A 179 TRP 0.018 0.002 TRP A 177 HIS 0.002 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 1365) covalent geometry : angle 0.59610 ( 1840) SS BOND : bond 0.00276 ( 2) SS BOND : angle 0.41765 ( 4) hydrogen bonds : bond 0.05106 ( 104) hydrogen bonds : angle 3.86566 ( 303) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.048 Fit side-chains REVERT: A 94 GLU cc_start: 0.5240 (OUTLIER) cc_final: 0.5031 (mp0) outliers start: 13 outliers final: 5 residues processed: 31 average time/residue: 0.2730 time to fit residues: 8.7217 Evaluate side-chains 27 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 195 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 0.0020 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.0980 chunk 16 optimal weight: 0.0980 chunk 2 optimal weight: 0.1980 chunk 1 optimal weight: 0.0980 chunk 11 optimal weight: 0.0870 chunk 12 optimal weight: 0.0980 chunk 7 optimal weight: 0.0870 chunk 15 optimal weight: 0.2980 chunk 0 optimal weight: 0.4980 overall best weight: 0.0744 ------------------------------------------------------------------------------- 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 = 0.4756 r_free = 0.4756 target = 0.278861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.275584 restraints weight = 1193.359| |-----------------------------------------------------------------------------| r_work (start): 0.4732 rms_B_bonded: 0.28 r_work: 0.4701 rms_B_bonded: 0.70 restraints_weight: 0.5000 r_work: 0.4657 rms_B_bonded: 1.57 restraints_weight: 0.2500 r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5392 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1367 Z= 0.120 Angle : 0.504 5.984 1844 Z= 0.270 Chirality : 0.040 0.119 209 Planarity : 0.003 0.031 222 Dihedral : 4.311 16.532 183 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 7.19 % Allowed : 13.67 % Favored : 79.14 % 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: 2.56 (0.69), residues: 164 helix: 2.94 (0.48), residues: 114 sheet: -0.67 (1.67), residues: 10 loop : -1.58 (1.02), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 101 TYR 0.009 0.001 TYR A 175 PHE 0.008 0.001 PHE A 106 TRP 0.015 0.001 TRP A 177 HIS 0.002 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 1365) covalent geometry : angle 0.50380 ( 1840) SS BOND : bond 0.00125 ( 2) SS BOND : angle 0.48036 ( 4) hydrogen bonds : bond 0.04460 ( 104) hydrogen bonds : angle 3.63313 ( 303) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.051 Fit side-chains REVERT: A 94 GLU cc_start: 0.5077 (OUTLIER) cc_final: 0.4839 (mp0) outliers start: 10 outliers final: 3 residues processed: 31 average time/residue: 0.3448 time to fit residues: 10.9470 Evaluate side-chains 28 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 0.3980 chunk 5 optimal weight: 0.0970 chunk 10 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 16 optimal weight: 0.0870 chunk 7 optimal weight: 0.0570 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 overall best weight: 0.1072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.277830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.274500 restraints weight = 1200.191| |-----------------------------------------------------------------------------| r_work (start): 0.4723 rms_B_bonded: 0.29 r_work: 0.4694 rms_B_bonded: 0.68 restraints_weight: 0.5000 r_work: 0.4648 rms_B_bonded: 1.59 restraints_weight: 0.2500 r_work (final): 0.4648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5418 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1367 Z= 0.131 Angle : 0.536 7.551 1844 Z= 0.282 Chirality : 0.040 0.114 209 Planarity : 0.003 0.031 222 Dihedral : 4.383 16.063 183 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 6.47 % Allowed : 17.27 % Favored : 76.26 % 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: 2.48 (0.69), residues: 164 helix: 2.93 (0.48), residues: 114 sheet: -0.73 (1.62), residues: 10 loop : -1.75 (0.99), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 203 TYR 0.010 0.002 TYR A 175 PHE 0.008 0.001 PHE A 106 TRP 0.014 0.001 TRP A 177 HIS 0.002 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 1365) covalent geometry : angle 0.53589 ( 1840) SS BOND : bond 0.00187 ( 2) SS BOND : angle 0.56330 ( 4) hydrogen bonds : bond 0.04603 ( 104) hydrogen bonds : angle 3.69544 ( 303) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.048 Fit side-chains REVERT: A 94 GLU cc_start: 0.5202 (OUTLIER) cc_final: 0.4973 (mp0) outliers start: 9 outliers final: 1 residues processed: 32 average time/residue: 0.2781 time to fit residues: 9.1736 Evaluate side-chains 27 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 2 optimal weight: 0.4980 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 0.0770 chunk 6 optimal weight: 0.4980 chunk 15 optimal weight: 0.1980 chunk 13 optimal weight: 0.0980 chunk 1 optimal weight: 0.0980 chunk 5 optimal weight: 0.0770 chunk 8 optimal weight: 0.0870 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 0.8980 overall best weight: 0.0874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.278600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.275389 restraints weight = 1178.802| |-----------------------------------------------------------------------------| r_work (start): 0.4733 rms_B_bonded: 0.27 r_work: 0.4707 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.4665 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work (final): 0.4665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5372 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 1367 Z= 0.126 Angle : 0.519 7.607 1844 Z= 0.274 Chirality : 0.039 0.115 209 Planarity : 0.003 0.030 222 Dihedral : 4.258 15.601 183 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.88 % Allowed : 21.58 % Favored : 75.54 % 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: 2.58 (0.69), residues: 164 helix: 3.03 (0.48), residues: 114 sheet: -0.89 (1.56), residues: 10 loop : -1.75 (1.01), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 203 TYR 0.009 0.001 TYR A 175 PHE 0.009 0.001 PHE A 106 TRP 0.013 0.002 TRP A 177 HIS 0.002 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 1365) covalent geometry : angle 0.51905 ( 1840) SS BOND : bond 0.00179 ( 2) SS BOND : angle 0.56261 ( 4) hydrogen bonds : bond 0.04535 ( 104) hydrogen bonds : angle 3.67931 ( 303) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.051 Fit side-chains REVERT: A 94 GLU cc_start: 0.5096 (OUTLIER) cc_final: 0.4891 (mp0) outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.3472 time to fit residues: 9.6129 Evaluate side-chains 29 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 3 optimal weight: 0.3980 chunk 10 optimal weight: 0.3980 chunk 8 optimal weight: 0.0970 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 6 optimal weight: 0.0670 chunk 16 optimal weight: 0.0770 chunk 7 optimal weight: 0.3980 chunk 2 optimal weight: 0.0870 chunk 14 optimal weight: 0.1980 overall best weight: 0.1052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.278583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.275242 restraints weight = 1182.386| |-----------------------------------------------------------------------------| r_work (start): 0.4732 rms_B_bonded: 0.27 r_work: 0.4705 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.4662 rms_B_bonded: 1.43 restraints_weight: 0.2500 r_work (final): 0.4662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5390 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 1367 Z= 0.139 Angle : 0.580 9.471 1844 Z= 0.298 Chirality : 0.040 0.114 209 Planarity : 0.003 0.030 222 Dihedral : 4.328 15.553 183 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 7.19 % Allowed : 17.99 % Favored : 74.82 % 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: 2.40 (0.67), residues: 164 helix: 2.90 (0.47), residues: 114 sheet: -0.89 (1.55), residues: 10 loop : -1.86 (0.98), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 36 TYR 0.010 0.002 TYR A 34 PHE 0.008 0.001 PHE A 106 TRP 0.012 0.002 TRP A 177 HIS 0.002 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 1365) covalent geometry : angle 0.58050 ( 1840) SS BOND : bond 0.00177 ( 2) SS BOND : angle 0.55551 ( 4) hydrogen bonds : bond 0.04595 ( 104) hydrogen bonds : angle 3.85365 ( 303) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.055 Fit side-chains REVERT: A 40 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.5789 (tmtt) REVERT: A 94 GLU cc_start: 0.5155 (OUTLIER) cc_final: 0.4948 (mp0) outliers start: 10 outliers final: 5 residues processed: 32 average time/residue: 0.2620 time to fit residues: 8.6345 Evaluate side-chains 31 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 15 optimal weight: 0.0980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 chunk 3 optimal weight: 0.3980 chunk 8 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 12 optimal weight: 0.0970 chunk 11 optimal weight: 0.1980 chunk 5 optimal weight: 0.0980 chunk 7 optimal weight: 0.0980 overall best weight: 0.0956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.278899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.275524 restraints weight = 1174.829| |-----------------------------------------------------------------------------| r_work (start): 0.4734 rms_B_bonded: 0.27 r_work: 0.4706 rms_B_bonded: 0.63 restraints_weight: 0.5000 r_work: 0.4666 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work (final): 0.4666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5371 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 1367 Z= 0.137 Angle : 0.576 9.032 1844 Z= 0.297 Chirality : 0.039 0.114 209 Planarity : 0.003 0.029 222 Dihedral : 4.277 15.424 183 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 5.76 % Allowed : 18.71 % Favored : 75.54 % 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: 2.42 (0.67), residues: 164 helix: 2.93 (0.46), residues: 114 sheet: -0.90 (1.52), residues: 10 loop : -1.91 (0.97), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 203 TYR 0.009 0.001 TYR A 175 PHE 0.007 0.001 PHE A 106 TRP 0.012 0.001 TRP A 177 HIS 0.002 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 1365) covalent geometry : angle 0.57579 ( 1840) SS BOND : bond 0.00171 ( 2) SS BOND : angle 0.57747 ( 4) hydrogen bonds : bond 0.04542 ( 104) hydrogen bonds : angle 3.85984 ( 303) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.047 Fit side-chains REVERT: A 40 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.5795 (tmtt) outliers start: 8 outliers final: 4 residues processed: 30 average time/residue: 0.2736 time to fit residues: 8.4545 Evaluate side-chains 30 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 3 optimal weight: 0.0970 chunk 4 optimal weight: 0.0570 chunk 16 optimal weight: 0.0870 chunk 0 optimal weight: 1.0980 chunk 10 optimal weight: 0.0770 chunk 5 optimal weight: 0.0980 chunk 12 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 overall best weight: 0.0832 ------------------------------------------------------------------------------- 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 = 0.4757 r_free = 0.4757 target = 0.278748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.275663 restraints weight = 1166.390| |-----------------------------------------------------------------------------| r_work (start): 0.4739 rms_B_bonded: 0.25 r_work: 0.4713 rms_B_bonded: 0.59 restraints_weight: 0.5000 r_work: 0.4673 rms_B_bonded: 1.33 restraints_weight: 0.2500 r_work (final): 0.4673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5344 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 1367 Z= 0.132 Angle : 0.577 9.017 1844 Z= 0.297 Chirality : 0.039 0.120 209 Planarity : 0.003 0.029 222 Dihedral : 4.219 15.240 183 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.60 % Allowed : 21.58 % Favored : 74.82 % 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: 2.53 (0.67), residues: 164 helix: 3.02 (0.46), residues: 114 sheet: -0.93 (1.51), residues: 10 loop : -1.87 (0.97), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 203 TYR 0.008 0.001 TYR A 175 PHE 0.007 0.001 PHE A 106 TRP 0.011 0.001 TRP A 177 HIS 0.002 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 1365) covalent geometry : angle 0.57673 ( 1840) SS BOND : bond 0.00149 ( 2) SS BOND : angle 0.58793 ( 4) hydrogen bonds : bond 0.04446 ( 104) hydrogen bonds : angle 3.86827 ( 303) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 328 Ramachandran restraints generated. 164 Oldfield, 0 Emsley, 164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.029 Fit side-chains REVERT: A 40 LYS cc_start: 0.6657 (OUTLIER) cc_final: 0.5770 (tmtt) outliers start: 5 outliers final: 4 residues processed: 27 average time/residue: 0.2418 time to fit residues: 6.7443 Evaluate side-chains 33 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 188 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 0.0970 chunk 5 optimal weight: 0.0980 chunk 1 optimal weight: 0.2980 chunk 3 optimal weight: 0.1980 chunk 13 optimal weight: 0.0870 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.0970 chunk 15 optimal weight: 0.0980 chunk 6 optimal weight: 0.4980 chunk 0 optimal weight: 0.0970 chunk 4 optimal weight: 0.3980 overall best weight: 0.0952 ------------------------------------------------------------------------------- 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 = 0.4750 r_free = 0.4750 target = 0.277922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.274641 restraints weight = 1184.656| |-----------------------------------------------------------------------------| r_work (start): 0.4732 rms_B_bonded: 0.27 r_work: 0.4703 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.4660 rms_B_bonded: 1.49 restraints_weight: 0.2500 r_work (final): 0.4660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5374 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1367 Z= 0.122 Angle : 0.538 8.796 1844 Z= 0.275 Chirality : 0.039 0.113 209 Planarity : 0.003 0.030 222 Dihedral : 4.204 15.078 183 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.32 % Allowed : 20.86 % Favored : 74.82 % 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: 2.74 (0.67), residues: 164 helix: 3.20 (0.46), residues: 114 sheet: -0.90 (1.52), residues: 10 loop : -1.87 (0.96), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 36 TYR 0.008 0.001 TYR A 175 PHE 0.006 0.001 PHE A 179 TRP 0.011 0.001 TRP A 177 HIS 0.002 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 1365) covalent geometry : angle 0.53777 ( 1840) SS BOND : bond 0.00174 ( 2) SS BOND : angle 0.56849 ( 4) hydrogen bonds : bond 0.04413 ( 104) hydrogen bonds : angle 3.63150 ( 303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 861.56 seconds wall clock time: 15 minutes 54.13 seconds (954.13 seconds total)