Starting phenix.real_space_refine on Fri Aug 22 12:38:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sl0_40570/08_2025/8sl0_40570.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sl0_40570/08_2025/8sl0_40570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sl0_40570/08_2025/8sl0_40570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sl0_40570/08_2025/8sl0_40570.map" model { file = "/net/cci-nas-00/data/ceres_data/8sl0_40570/08_2025/8sl0_40570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sl0_40570/08_2025/8sl0_40570.cif" } resolution = 3.3 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= 0.034 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 2 5.16 5 C 1107 2.51 5 N 297 2.21 5 O 331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 1737 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 10, 'TRANS': 217} Time building chain proxies: 0.78, per 1000 atoms: 0.45 Number of scatterers: 1737 At special positions: 0 Unit cell: (90.153, 64.395, 70.119, 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 2 16.00 O 331 8.00 N 297 7.00 C 1107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.15 Conformation dependent library (CDL) restraints added in 76.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 410 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 13.2% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'A' and resid 139 through 147 removed outlier: 3.593A pdb=" N GLN A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 24 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 18 through 24 current: chain 'A' and resid 39 through 42 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 39 through 42 current: chain 'A' and resid 97 through 120 removed outlier: 7.586A pdb=" N ALA A 97 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 180 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 99 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU A 178 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA A 101 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE A 176 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR A 103 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY A 174 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 105 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY A 172 " --> pdb=" O GLN A 105 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG A 107 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS A 170 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 109 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA A 168 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE A 111 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 166 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE A 113 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE A 164 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ASN A 115 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN A 162 " --> pdb=" O ASN A 115 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 189 through 205 current: chain 'A' and resid 228 through 231 35 hydrogen bonds defined for protein. 96 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: 0.20 Time building geometry restraints manager: 0.21 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: 579 1.34 - 1.46: 309 1.46 - 1.57: 873 1.57 - 1.69: 0 1.69 - 1.81: 3 Bond restraints: 1764 Sorted by residual: bond pdb=" C GLU A 219 " pdb=" N ILE A 220 " ideal model delta sigma weight residual 1.330 1.305 0.025 1.97e-02 2.58e+03 1.63e+00 bond pdb=" N SER A 55 " pdb=" CA SER A 55 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.29e-02 6.01e+03 4.82e-01 bond pdb=" N GLU A 182 " pdb=" CA GLU A 182 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.29e-02 6.01e+03 4.80e-01 bond pdb=" CA VAL A 89 " pdb=" CB VAL A 89 " ideal model delta sigma weight residual 1.540 1.550 -0.009 1.36e-02 5.41e+03 4.79e-01 bond pdb=" CA ASP A 6 " pdb=" C ASP A 6 " ideal model delta sigma weight residual 1.525 1.538 -0.013 2.10e-02 2.27e+03 4.09e-01 ... (remaining 1759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 2342 1.80 - 3.61: 35 3.61 - 5.41: 2 5.41 - 7.21: 3 7.21 - 9.01: 2 Bond angle restraints: 2384 Sorted by residual: angle pdb=" C GLU A 182 " pdb=" CA GLU A 182 " pdb=" CB GLU A 182 " ideal model delta sigma weight residual 110.42 115.84 -5.42 1.99e+00 2.53e-01 7.41e+00 angle pdb=" C SER A 55 " pdb=" CA SER A 55 " pdb=" CB SER A 55 " ideal model delta sigma weight residual 110.42 115.74 -5.32 1.99e+00 2.53e-01 7.13e+00 angle pdb=" CA LEU A 30 " pdb=" CB LEU A 30 " pdb=" CG LEU A 30 " ideal model delta sigma weight residual 116.30 125.31 -9.01 3.50e+00 8.16e-02 6.63e+00 angle pdb=" CA LEU A 90 " pdb=" CB LEU A 90 " pdb=" CG LEU A 90 " ideal model delta sigma weight residual 116.30 124.68 -8.38 3.50e+00 8.16e-02 5.74e+00 angle pdb=" C SER A 88 " pdb=" N VAL A 89 " pdb=" CA VAL A 89 " ideal model delta sigma weight residual 121.97 126.07 -4.10 1.80e+00 3.09e-01 5.18e+00 ... (remaining 2379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 943 17.60 - 35.20: 94 35.20 - 52.80: 23 52.80 - 70.40: 6 70.40 - 88.00: 4 Dihedral angle restraints: 1070 sinusoidal: 426 harmonic: 644 Sorted by residual: dihedral pdb=" CA ASN A 115 " pdb=" CB ASN A 115 " pdb=" CG ASN A 115 " pdb=" OD1 ASN A 115 " ideal model delta sinusoidal sigma weight residual 120.00 -168.87 -71.13 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ARG A 14 " pdb=" C ARG A 14 " pdb=" N LEU A 15 " pdb=" CA LEU A 15 " ideal model delta harmonic sigma weight residual 180.00 163.99 16.01 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA GLN A 28 " pdb=" CB GLN A 28 " pdb=" CG GLN A 28 " pdb=" CD GLN A 28 " ideal model delta sinusoidal sigma weight residual 180.00 120.32 59.68 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 158 0.028 - 0.056: 61 0.056 - 0.083: 26 0.083 - 0.111: 22 0.111 - 0.139: 7 Chirality restraints: 274 Sorted by residual: chirality pdb=" CB VAL A 89 " pdb=" CA VAL A 89 " pdb=" CG1 VAL A 89 " pdb=" CG2 VAL A 89 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE A 99 " pdb=" N ILE A 99 " pdb=" C ILE A 99 " pdb=" CB ILE A 99 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE A 27 " pdb=" N ILE A 27 " pdb=" C ILE A 27 " pdb=" CB ILE A 27 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 271 not shown) Planarity restraints: 312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 180 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.26e+00 pdb=" N PRO A 181 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 28 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A 29 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 187 " -0.004 2.00e-02 2.50e+03 7.79e-03 6.07e-01 pdb=" C VAL A 187 " 0.013 2.00e-02 2.50e+03 pdb=" O VAL A 187 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY A 188 " -0.005 2.00e-02 2.50e+03 ... (remaining 309 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 140 2.74 - 3.28: 1782 3.28 - 3.82: 2699 3.82 - 4.36: 3065 4.36 - 4.90: 5315 Nonbonded interactions: 13001 Sorted by model distance: nonbonded pdb=" O CYS A 217 " pdb=" OG SER A 232 " model vdw 2.201 3.040 nonbonded pdb=" NH2 ARG A 151 " pdb=" OE1 GLU A 219 " model vdw 2.344 3.120 nonbonded pdb=" ND1 HIS A 31 " pdb=" OH TYR A 42 " model vdw 2.391 3.120 nonbonded pdb=" OH TYR A 103 " pdb=" OE1 GLN A 105 " model vdw 2.418 3.040 nonbonded pdb=" O SER A 201 " pdb=" OG SER A 201 " model vdw 2.477 3.040 ... (remaining 12996 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: 17.990 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.280 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 0.025 1764 Z= 0.152 Angle : 0.622 9.015 2384 Z= 0.316 Chirality : 0.046 0.139 274 Planarity : 0.004 0.038 312 Dihedral : 15.999 87.997 660 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.41 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 29.95 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.56), residues: 226 helix: -0.33 (1.25), residues: 22 sheet: -0.31 (0.52), residues: 110 loop : -2.27 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 110 TYR 0.007 0.001 TYR A 42 PHE 0.003 0.001 PHE A 164 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 1764) covalent geometry : angle 0.62249 ( 2384) hydrogen bonds : bond 0.17267 ( 35) hydrogen bonds : angle 5.21109 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.077 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.2074 time to fit residues: 1.6520 Evaluate side-chains 5 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.0370 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.057096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.048175 restraints weight = 8441.537| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 4.04 r_work: 0.3111 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1764 Z= 0.112 Angle : 0.586 8.579 2384 Z= 0.282 Chirality : 0.046 0.140 274 Planarity : 0.004 0.037 312 Dihedral : 4.057 15.425 242 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.96 % Favored : 91.59 % Rotamer: Outliers : 1.60 % Allowed : 29.95 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.56), residues: 226 helix: -0.54 (1.08), residues: 26 sheet: -0.24 (0.52), residues: 110 loop : -2.34 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 110 TYR 0.008 0.001 TYR A 11 PHE 0.004 0.001 PHE A 129 HIS 0.001 0.000 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 1764) covalent geometry : angle 0.58558 ( 2384) hydrogen bonds : bond 0.02981 ( 35) hydrogen bonds : angle 4.88126 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.080 Fit side-chains REVERT: A 145 TYR cc_start: 0.9282 (m-80) cc_final: 0.9059 (m-80) outliers start: 3 outliers final: 3 residues processed: 9 average time/residue: 0.1686 time to fit residues: 1.7020 Evaluate side-chains 9 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.055296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.046524 restraints weight = 8485.026| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.93 r_work: 0.3077 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1764 Z= 0.178 Angle : 0.595 7.734 2384 Z= 0.292 Chirality : 0.046 0.140 274 Planarity : 0.004 0.034 312 Dihedral : 4.161 16.855 242 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.73 % Favored : 89.82 % Rotamer: Outliers : 6.42 % Allowed : 26.20 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.56), residues: 226 helix: -0.66 (1.02), residues: 26 sheet: -0.25 (0.52), residues: 110 loop : -2.36 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 14 TYR 0.008 0.001 TYR A 11 PHE 0.004 0.001 PHE A 129 HIS 0.001 0.000 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 1764) covalent geometry : angle 0.59543 ( 2384) hydrogen bonds : bond 0.02891 ( 35) hydrogen bonds : angle 4.80836 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 5 time to evaluate : 0.082 Fit side-chains REVERT: A 76 ASN cc_start: 0.9296 (OUTLIER) cc_final: 0.8852 (p0) outliers start: 12 outliers final: 9 residues processed: 16 average time/residue: 0.1054 time to fit residues: 1.9793 Evaluate side-chains 15 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 5 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.055696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.046951 restraints weight = 8464.525| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.92 r_work: 0.3076 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1764 Z= 0.151 Angle : 0.605 12.985 2384 Z= 0.287 Chirality : 0.046 0.146 274 Planarity : 0.004 0.035 312 Dihedral : 4.119 16.308 242 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.18 % Favored : 89.38 % Rotamer: Outliers : 7.49 % Allowed : 25.67 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.56), residues: 226 helix: -0.54 (1.01), residues: 26 sheet: -0.19 (0.51), residues: 110 loop : -2.36 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 14 TYR 0.009 0.001 TYR A 11 PHE 0.004 0.001 PHE A 129 HIS 0.000 0.000 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 1764) covalent geometry : angle 0.60509 ( 2384) hydrogen bonds : bond 0.02600 ( 35) hydrogen bonds : angle 4.77304 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 5 time to evaluate : 0.074 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 18 average time/residue: 0.0928 time to fit residues: 1.9159 Evaluate side-chains 17 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 5 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 0.0070 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.9200 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.055294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.046717 restraints weight = 8429.591| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.90 r_work: 0.3068 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1764 Z= 0.171 Angle : 0.634 10.961 2384 Z= 0.297 Chirality : 0.047 0.138 274 Planarity : 0.004 0.034 312 Dihedral : 4.132 16.396 242 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.18 % Favored : 89.38 % Rotamer: Outliers : 7.49 % Allowed : 26.20 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.55), residues: 226 helix: -0.37 (1.02), residues: 26 sheet: -0.18 (0.51), residues: 110 loop : -2.37 (0.59), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 14 TYR 0.008 0.001 TYR A 11 PHE 0.004 0.001 PHE A 129 HIS 0.001 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 1764) covalent geometry : angle 0.63413 ( 2384) hydrogen bonds : bond 0.02623 ( 35) hydrogen bonds : angle 4.72817 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 5 time to evaluate : 0.073 Fit side-chains outliers start: 14 outliers final: 14 residues processed: 18 average time/residue: 0.0959 time to fit residues: 1.9698 Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 5 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.055368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.046714 restraints weight = 8618.109| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.95 r_work: 0.3069 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1764 Z= 0.154 Angle : 0.599 10.434 2384 Z= 0.285 Chirality : 0.046 0.143 274 Planarity : 0.004 0.038 312 Dihedral : 4.096 16.146 242 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.06 % Favored : 88.50 % Rotamer: Outliers : 6.95 % Allowed : 26.20 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.56), residues: 226 helix: -0.19 (1.05), residues: 26 sheet: -0.19 (0.51), residues: 110 loop : -2.34 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 14 TYR 0.008 0.001 TYR A 11 PHE 0.005 0.001 PHE A 129 HIS 0.000 0.000 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 1764) covalent geometry : angle 0.59932 ( 2384) hydrogen bonds : bond 0.02532 ( 35) hydrogen bonds : angle 4.70252 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 6 time to evaluate : 0.076 Fit side-chains REVERT: A 145 TYR cc_start: 0.9312 (m-80) cc_final: 0.9010 (m-80) outliers start: 13 outliers final: 11 residues processed: 18 average time/residue: 0.1170 time to fit residues: 2.3534 Evaluate side-chains 17 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 6 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 3 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.055069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.046594 restraints weight = 8481.156| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.88 r_work: 0.3062 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1764 Z= 0.159 Angle : 0.611 10.090 2384 Z= 0.292 Chirality : 0.046 0.141 274 Planarity : 0.004 0.037 312 Dihedral : 4.111 15.981 242 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.62 % Favored : 88.94 % Rotamer: Outliers : 6.95 % Allowed : 25.67 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.56), residues: 226 helix: -0.14 (1.04), residues: 26 sheet: -0.20 (0.51), residues: 110 loop : -2.13 (0.62), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 14 TYR 0.008 0.001 TYR A 11 PHE 0.005 0.001 PHE A 129 HIS 0.000 0.000 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 1764) covalent geometry : angle 0.61074 ( 2384) hydrogen bonds : bond 0.02498 ( 35) hydrogen bonds : angle 4.67845 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 6 time to evaluate : 0.074 Fit side-chains REVERT: A 145 TYR cc_start: 0.9305 (m-80) cc_final: 0.9000 (m-80) outliers start: 13 outliers final: 13 residues processed: 18 average time/residue: 0.0896 time to fit residues: 1.8474 Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 6 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.055511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.047019 restraints weight = 8406.387| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.88 r_work: 0.3080 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1764 Z= 0.137 Angle : 0.594 9.916 2384 Z= 0.283 Chirality : 0.046 0.144 274 Planarity : 0.004 0.039 312 Dihedral : 4.013 15.502 242 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.62 % Favored : 88.94 % Rotamer: Outliers : 6.95 % Allowed : 25.67 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.57), residues: 226 helix: -0.01 (1.06), residues: 26 sheet: -0.18 (0.52), residues: 110 loop : -1.99 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 14 TYR 0.008 0.001 TYR A 11 PHE 0.005 0.001 PHE A 129 HIS 0.000 0.000 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 1764) covalent geometry : angle 0.59381 ( 2384) hydrogen bonds : bond 0.02394 ( 35) hydrogen bonds : angle 4.65459 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 6 time to evaluate : 0.070 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 18 average time/residue: 0.0859 time to fit residues: 1.7821 Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 6 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.055086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.046609 restraints weight = 8588.052| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.89 r_work: 0.3072 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1764 Z= 0.159 Angle : 0.596 9.819 2384 Z= 0.287 Chirality : 0.046 0.143 274 Planarity : 0.004 0.038 312 Dihedral : 4.050 15.490 242 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.06 % Favored : 88.50 % Rotamer: Outliers : 7.49 % Allowed : 25.67 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.58), residues: 226 helix: -0.11 (1.04), residues: 26 sheet: -0.14 (0.52), residues: 110 loop : -1.92 (0.65), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 151 TYR 0.008 0.001 TYR A 11 PHE 0.005 0.001 PHE A 129 HIS 0.000 0.000 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 1764) covalent geometry : angle 0.59603 ( 2384) hydrogen bonds : bond 0.02523 ( 35) hydrogen bonds : angle 4.65072 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 6 time to evaluate : 0.074 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 19 average time/residue: 0.1007 time to fit residues: 2.1514 Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 6 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 13 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 20 optimal weight: 0.0070 chunk 0 optimal weight: 1.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.056366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.048033 restraints weight = 8273.638| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.85 r_work: 0.3116 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1764 Z= 0.097 Angle : 0.584 10.109 2384 Z= 0.274 Chirality : 0.046 0.142 274 Planarity : 0.004 0.040 312 Dihedral : 3.826 14.882 242 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.18 % Favored : 89.38 % Rotamer: Outliers : 5.88 % Allowed : 27.27 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.59), residues: 226 helix: 0.06 (1.08), residues: 26 sheet: -0.04 (0.53), residues: 110 loop : -1.77 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 151 TYR 0.009 0.001 TYR A 11 PHE 0.005 0.001 PHE A 129 HIS 0.001 0.000 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 1764) covalent geometry : angle 0.58393 ( 2384) hydrogen bonds : bond 0.02097 ( 35) hydrogen bonds : angle 4.53053 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 6 time to evaluate : 0.101 Fit side-chains REVERT: A 104 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8011 (p0) REVERT: A 145 TYR cc_start: 0.9022 (m-80) cc_final: 0.8654 (m-80) outliers start: 11 outliers final: 9 residues processed: 16 average time/residue: 0.1190 time to fit residues: 2.1877 Evaluate side-chains 16 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 6 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.055582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.047089 restraints weight = 8571.158| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.95 r_work: 0.3080 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1764 Z= 0.148 Angle : 0.592 9.804 2384 Z= 0.284 Chirality : 0.046 0.143 274 Planarity : 0.004 0.037 312 Dihedral : 3.914 15.013 242 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.62 % Favored : 88.94 % Rotamer: Outliers : 5.35 % Allowed : 27.27 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.59), residues: 226 helix: 0.14 (1.08), residues: 26 sheet: -0.06 (0.53), residues: 110 loop : -1.74 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 14 TYR 0.008 0.001 TYR A 11 PHE 0.005 0.001 PHE A 129 HIS 0.000 0.000 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 1764) covalent geometry : angle 0.59209 ( 2384) hydrogen bonds : bond 0.02444 ( 35) hydrogen bonds : angle 4.57544 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1120.57 seconds wall clock time: 20 minutes 23.63 seconds (1223.63 seconds total)