Starting phenix.real_space_refine on Fri May 9 12:42:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vhv_43242/05_2025/8vhv_43242.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vhv_43242/05_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_43242/05_2025/8vhv_43242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vhv_43242/05_2025/8vhv_43242.map" model { file = "/net/cci-nas-00/data/ceres_data/8vhv_43242/05_2025/8vhv_43242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vhv_43242/05_2025/8vhv_43242.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.16, per 1000 atoms: 2.37 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: 0.34 Conformation dependent library (CDL) restraints added in 181.0 milliseconds 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: 0.15 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: 0.35 Time building geometry restraints manager: 0.42 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.250 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.060 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.003 TRP A 177 HIS 0.004 0.002 HIS A 59 PHE 0.016 0.002 PHE A 96 TYR 0.016 0.004 TYR A 180 ARG 0.012 0.003 ARG A 64 Details of bonding type rmsd hydrogen bonds : bond 0.14511 ( 104) hydrogen bonds : angle 5.57714 ( 303) SS BOND : bond 0.00543 ( 2) SS BOND : angle 0.72632 ( 4) covalent geometry : bond 0.00305 ( 1365) covalent geometry : angle 0.64159 ( 1840) *********************** 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 : 0.146 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.5678 time to fit residues: 19.3649 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 : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 0.0980 chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 0.2980 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 0.3980 chunk 6 optimal weight: 0.3980 chunk 13 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 15 optimal weight: 0.2980 chunk 10 optimal weight: 0.1980 overall best weight: 0.1780 ------------------------------------------------------------------------------- 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 = 0.4727 r_free = 0.4727 target = 0.274512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.271260 restraints weight = 1235.850| |-----------------------------------------------------------------------------| r_work (start): 0.4699 rms_B_bonded: 0.26 r_work: 0.4667 rms_B_bonded: 0.70 restraints_weight: 0.5000 r_work: 0.4617 rms_B_bonded: 1.61 restraints_weight: 0.2500 r_work (final): 0.4617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5487 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1367 Z= 0.161 Angle : 0.619 7.744 1844 Z= 0.328 Chirality : 0.044 0.147 209 Planarity : 0.004 0.034 222 Dihedral : 4.970 15.374 183 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 7.91 % Allowed : 8.63 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.71), residues: 164 helix: 2.54 (0.49), residues: 112 sheet: -0.34 (1.97), residues: 10 loop : -0.56 (1.15), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 177 HIS 0.003 0.001 HIS A 59 PHE 0.007 0.001 PHE A 115 TYR 0.013 0.002 TYR A 175 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.05118 ( 104) hydrogen bonds : angle 4.00696 ( 303) SS BOND : bond 0.00239 ( 2) SS BOND : angle 0.29095 ( 4) covalent geometry : bond 0.00338 ( 1365) covalent geometry : angle 0.61998 ( 1840) *********************** 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 40 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.144 Fit side-chains REVERT: A 40 LYS cc_start: 0.6787 (OUTLIER) cc_final: 0.6488 (tmtt) outliers start: 11 outliers final: 4 residues processed: 35 average time/residue: 0.5157 time to fit residues: 18.6806 Evaluate side-chains 31 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 195 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 0.0870 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 0.0870 chunk 2 optimal weight: 0.0870 chunk 16 optimal weight: 0.2980 chunk 6 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 11 optimal weight: 0.0870 chunk 13 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 overall best weight: 0.0892 ------------------------------------------------------------------------------- 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 = 0.4754 r_free = 0.4754 target = 0.278359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.275226 restraints weight = 1205.820| |-----------------------------------------------------------------------------| r_work (start): 0.4724 rms_B_bonded: 0.25 r_work: 0.4701 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.4660 rms_B_bonded: 1.34 restraints_weight: 0.2500 r_work (final): 0.4660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5375 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1367 Z= 0.124 Angle : 0.539 7.192 1844 Z= 0.282 Chirality : 0.041 0.138 209 Planarity : 0.003 0.035 222 Dihedral : 4.469 15.763 183 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 7.91 % Allowed : 9.35 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.70), residues: 164 helix: 2.83 (0.50), residues: 114 sheet: -0.50 (1.80), residues: 10 loop : -1.48 (1.02), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 177 HIS 0.002 0.001 HIS A 59 PHE 0.007 0.001 PHE A 179 TYR 0.009 0.002 TYR A 173 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 104) hydrogen bonds : angle 3.72741 ( 303) SS BOND : bond 0.00194 ( 2) SS BOND : angle 0.47337 ( 4) covalent geometry : bond 0.00258 ( 1365) covalent geometry : angle 0.53942 ( 1840) *********************** 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 43 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.145 Fit side-chains REVERT: A 23 MET cc_start: 0.7031 (tpt) cc_final: 0.6598 (tpt) REVERT: A 40 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.6181 (tmtt) outliers start: 11 outliers final: 3 residues processed: 39 average time/residue: 0.5728 time to fit residues: 23.0034 Evaluate side-chains 33 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 153 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 10 optimal weight: 0.2980 chunk 6 optimal weight: 0.3980 chunk 12 optimal weight: 0.1980 chunk 13 optimal weight: 0.0870 chunk 4 optimal weight: 0.4980 chunk 16 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 0.0970 chunk 14 optimal weight: 0.0980 overall best weight: 0.1154 ------------------------------------------------------------------------------- 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 = 0.4739 r_free = 0.4739 target = 0.276787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.273733 restraints weight = 1194.079| |-----------------------------------------------------------------------------| r_work (start): 0.4715 rms_B_bonded: 0.27 r_work: 0.4672 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.4617 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.4617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5459 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1367 Z= 0.129 Angle : 0.519 4.705 1844 Z= 0.279 Chirality : 0.040 0.116 209 Planarity : 0.003 0.034 222 Dihedral : 4.445 15.640 183 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 7.91 % Allowed : 14.39 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.70), residues: 164 helix: 2.93 (0.49), residues: 113 sheet: -0.63 (1.72), residues: 10 loop : -1.24 (1.07), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 177 HIS 0.002 0.001 HIS A 59 PHE 0.006 0.001 PHE A 179 TYR 0.011 0.002 TYR A 175 ARG 0.001 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 104) hydrogen bonds : angle 3.70042 ( 303) SS BOND : bond 0.00201 ( 2) SS BOND : angle 0.49290 ( 4) covalent geometry : bond 0.00267 ( 1365) covalent geometry : angle 0.51940 ( 1840) *********************** 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 39 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.125 Fit side-chains REVERT: A 23 MET cc_start: 0.7146 (tpt) cc_final: 0.6890 (tpt) REVERT: A 40 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6170 (tmtt) outliers start: 11 outliers final: 6 residues processed: 34 average time/residue: 0.4777 time to fit residues: 16.8071 Evaluate side-chains 33 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 105 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 0.0970 chunk 16 optimal weight: 0.0770 chunk 6 optimal weight: 0.2980 chunk 7 optimal weight: 0.0670 chunk 5 optimal weight: 0.3980 chunk 10 optimal weight: 0.0870 chunk 8 optimal weight: 0.0980 chunk 1 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 overall best weight: 0.0830 ------------------------------------------------------------------------------- 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 = 0.4753 r_free = 0.4753 target = 0.278466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.275361 restraints weight = 1198.715| |-----------------------------------------------------------------------------| r_work (start): 0.4730 rms_B_bonded: 0.27 r_work: 0.4703 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.4658 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work (final): 0.4658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5374 moved from start: 0.2751 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= 0.119 Angle : 0.537 8.348 1844 Z= 0.273 Chirality : 0.039 0.116 209 Planarity : 0.003 0.033 222 Dihedral : 4.274 15.954 183 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 7.19 % Allowed : 14.39 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.70), residues: 164 helix: 2.98 (0.49), residues: 114 sheet: -0.65 (1.71), residues: 10 loop : -1.55 (1.02), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 177 HIS 0.002 0.001 HIS A 59 PHE 0.006 0.001 PHE A 179 TYR 0.010 0.001 TYR A 34 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 104) hydrogen bonds : angle 3.60453 ( 303) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.55371 ( 4) covalent geometry : bond 0.00245 ( 1365) covalent geometry : angle 0.53704 ( 1840) *********************** 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 37 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.144 Fit side-chains REVERT: A 40 LYS cc_start: 0.6560 (OUTLIER) cc_final: 0.6104 (tmtt) outliers start: 10 outliers final: 6 residues processed: 34 average time/residue: 0.4996 time to fit residues: 17.6245 Evaluate side-chains 32 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 105 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 7 optimal weight: 0.0870 chunk 15 optimal weight: 0.1980 chunk 8 optimal weight: 0.0970 chunk 1 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.0870 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.0770 chunk 11 optimal weight: 0.2980 chunk 3 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 overall best weight: 0.0870 ------------------------------------------------------------------------------- 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 = 0.4753 r_free = 0.4753 target = 0.278606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.275325 restraints weight = 1185.290| |-----------------------------------------------------------------------------| r_work (start): 0.4729 rms_B_bonded: 0.28 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: 0.5374 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1367 Z= 0.116 Angle : 0.511 7.161 1844 Z= 0.267 Chirality : 0.038 0.114 209 Planarity : 0.003 0.032 222 Dihedral : 4.204 15.125 183 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.70), residues: 164 helix: 3.10 (0.49), residues: 114 sheet: -0.68 (1.64), residues: 10 loop : -1.77 (1.03), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 177 HIS 0.002 0.001 HIS A 59 PHE 0.006 0.001 PHE A 179 TYR 0.008 0.001 TYR A 175 ARG 0.001 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 104) hydrogen bonds : angle 3.55846 ( 303) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.54804 ( 4) covalent geometry : bond 0.00240 ( 1365) covalent geometry : angle 0.51128 ( 1840) *********************** 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 36 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.146 Fit side-chains REVERT: A 40 LYS cc_start: 0.6491 (OUTLIER) cc_final: 0.6031 (tmtt) outliers start: 9 outliers final: 4 residues processed: 33 average time/residue: 0.5312 time to fit residues: 18.1409 Evaluate side-chains 31 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.130 ------------------------------------------------------------------------------- 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 153 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.0970 chunk 16 optimal weight: 0.2980 chunk 8 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.0870 chunk 3 optimal weight: 0.1980 chunk 6 optimal weight: 0.0770 chunk 10 optimal weight: 0.0980 chunk 14 optimal weight: 0.0870 overall best weight: 0.0892 ------------------------------------------------------------------------------- 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 = 0.4756 r_free = 0.4756 target = 0.278628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.275293 restraints weight = 1249.377| |-----------------------------------------------------------------------------| r_work (start): 0.4731 rms_B_bonded: 0.29 r_work: 0.4705 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.4657 rms_B_bonded: 1.59 restraints_weight: 0.2500 r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5372 moved from start: 0.2943 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= 0.121 Angle : 0.553 8.563 1844 Z= 0.279 Chirality : 0.039 0.114 209 Planarity : 0.003 0.032 222 Dihedral : 4.204 15.000 183 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 5.04 % Allowed : 19.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.69), residues: 164 helix: 3.08 (0.48), residues: 114 sheet: -0.67 (1.64), residues: 10 loop : -1.79 (1.01), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 177 HIS 0.002 0.001 HIS A 59 PHE 0.006 0.001 PHE A 106 TYR 0.010 0.001 TYR A 34 ARG 0.001 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 104) hydrogen bonds : angle 3.61154 ( 303) SS BOND : bond 0.00167 ( 2) SS BOND : angle 0.54415 ( 4) covalent geometry : bond 0.00255 ( 1365) covalent geometry : angle 0.55338 ( 1840) *********************** 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 36 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.143 Fit side-chains REVERT: A 40 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.5991 (tmtt) outliers start: 7 outliers final: 5 residues processed: 34 average time/residue: 0.5100 time to fit residues: 17.9669 Evaluate side-chains 35 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 153 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 0.0770 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 12 optimal weight: 0.0970 chunk 2 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 15 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 overall best weight: 0.1734 ------------------------------------------------------------------------------- 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 = 0.4732 r_free = 0.4732 target = 0.275690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.272369 restraints weight = 1186.776| |-----------------------------------------------------------------------------| r_work (start): 0.4703 rms_B_bonded: 0.27 r_work: 0.4674 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.4630 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work (final): 0.4630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5453 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 1367 Z= 0.160 Angle : 0.584 7.970 1844 Z= 0.304 Chirality : 0.040 0.130 209 Planarity : 0.003 0.032 222 Dihedral : 4.479 14.584 183 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.04 % Allowed : 19.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.68), residues: 164 helix: 2.90 (0.48), residues: 114 sheet: -0.62 (1.65), residues: 10 loop : -2.13 (0.92), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 177 HIS 0.002 0.001 HIS A 204 PHE 0.007 0.001 PHE A 186 TYR 0.011 0.002 TYR A 34 ARG 0.001 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 104) hydrogen bonds : angle 3.81860 ( 303) SS BOND : bond 0.00250 ( 2) SS BOND : angle 0.49740 ( 4) covalent geometry : bond 0.00365 ( 1365) covalent geometry : angle 0.58439 ( 1840) *********************** 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 36 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.139 Fit side-chains REVERT: A 40 LYS cc_start: 0.6733 (OUTLIER) cc_final: 0.6391 (tmtt) outliers start: 7 outliers final: 4 residues processed: 34 average time/residue: 0.5992 time to fit residues: 21.0601 Evaluate side-chains 34 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 188 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.0870 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 0.0670 chunk 8 optimal weight: 0.2980 chunk 15 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 6 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 overall best weight: 0.1696 ------------------------------------------------------------------------------- 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 = 0.4729 r_free = 0.4729 target = 0.275219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.272126 restraints weight = 1169.812| |-----------------------------------------------------------------------------| r_work (start): 0.4706 rms_B_bonded: 0.25 r_work: 0.4676 rms_B_bonded: 0.64 restraints_weight: 0.5000 r_work: 0.4633 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work (final): 0.4633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5460 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 1367 Z= 0.166 Angle : 0.612 7.830 1844 Z= 0.324 Chirality : 0.041 0.128 209 Planarity : 0.003 0.032 222 Dihedral : 4.513 14.434 183 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.04 % Allowed : 20.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.66), residues: 164 helix: 2.74 (0.46), residues: 114 sheet: -0.60 (1.65), residues: 10 loop : -2.34 (0.89), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 177 HIS 0.002 0.001 HIS A 59 PHE 0.006 0.001 PHE A 115 TYR 0.011 0.002 TYR A 34 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04788 ( 104) hydrogen bonds : angle 4.02276 ( 303) SS BOND : bond 0.00241 ( 2) SS BOND : angle 0.46096 ( 4) covalent geometry : bond 0.00393 ( 1365) covalent geometry : angle 0.61214 ( 1840) *********************** 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 37 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.140 Fit side-chains REVERT: A 40 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6465 (tmtt) outliers start: 7 outliers final: 4 residues processed: 35 average time/residue: 0.5179 time to fit residues: 18.7363 Evaluate side-chains 35 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 188 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 11 optimal weight: 0.0770 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 15 optimal weight: 0.2980 chunk 2 optimal weight: 0.2980 chunk 4 optimal weight: 0.0470 chunk 8 optimal weight: 0.0980 overall best weight: 0.1236 ------------------------------------------------------------------------------- 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 = 0.4738 r_free = 0.4738 target = 0.276069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.273009 restraints weight = 1207.147| |-----------------------------------------------------------------------------| r_work (start): 0.4716 rms_B_bonded: 0.26 r_work: 0.4688 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.4646 rms_B_bonded: 1.38 restraints_weight: 0.2500 r_work (final): 0.4646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5415 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 1367 Z= 0.148 Angle : 0.598 8.257 1844 Z= 0.314 Chirality : 0.040 0.119 209 Planarity : 0.003 0.032 222 Dihedral : 4.379 14.321 183 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.04 % Allowed : 19.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.67), residues: 164 helix: 2.79 (0.46), residues: 114 sheet: -0.66 (1.61), residues: 10 loop : -2.30 (0.90), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 177 HIS 0.002 0.001 HIS A 59 PHE 0.007 0.001 PHE A 106 TYR 0.009 0.002 TYR A 175 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04581 ( 104) hydrogen bonds : angle 3.98328 ( 303) SS BOND : bond 0.00203 ( 2) SS BOND : angle 0.47292 ( 4) covalent geometry : bond 0.00354 ( 1365) covalent geometry : angle 0.59820 ( 1840) ********************** 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 38 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.154 Fit side-chains REVERT: A 40 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6243 (tmtt) outliers start: 7 outliers final: 5 residues processed: 36 average time/residue: 0.4252 time to fit residues: 15.9538 Evaluate side-chains 36 residues out of total 139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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 188 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 16 optimal weight: 0.1980 chunk 11 optimal weight: 0.0980 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 0.0670 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 7 optimal weight: 0.3980 chunk 10 optimal weight: 0.0670 chunk 14 optimal weight: 0.0980 chunk 1 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 overall best weight: 0.1056 ------------------------------------------------------------------------------- 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 = 0.4744 r_free = 0.4744 target = 0.276882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.273824 restraints weight = 1226.140| |-----------------------------------------------------------------------------| r_work (start): 0.4720 rms_B_bonded: 0.26 r_work: 0.4693 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.4649 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work (final): 0.4649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5394 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 1367 Z= 0.144 Angle : 0.633 9.704 1844 Z= 0.318 Chirality : 0.040 0.120 209 Planarity : 0.003 0.032 222 Dihedral : 4.327 14.314 183 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 5.76 % Allowed : 19.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.67), residues: 164 helix: 2.83 (0.46), residues: 114 sheet: -0.71 (1.61), residues: 10 loop : -2.15 (0.94), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 177 HIS 0.002 0.001 HIS A 59 PHE 0.007 0.001 PHE A 106 TYR 0.010 0.002 TYR A 34 ARG 0.001 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 104) hydrogen bonds : angle 3.94358 ( 303) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.50966 ( 4) covalent geometry : bond 0.00345 ( 1365) covalent geometry : angle 0.63348 ( 1840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1753.04 seconds wall clock time: 31 minutes 6.52 seconds (1866.52 seconds total)