Starting phenix.real_space_refine on Sat May 2 05:43:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x3y_66514/05_2026/9x3y_66514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x3y_66514/05_2026/9x3y_66514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x3y_66514/05_2026/9x3y_66514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x3y_66514/05_2026/9x3y_66514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x3y_66514/05_2026/9x3y_66514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x3y_66514/05_2026/9x3y_66514.map" } resolution = 2.77 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= 0.002 sd= 0.144 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 16 5.16 5 C 1366 2.51 5 N 302 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 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2015 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1960 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 55 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Time building chain proxies: 0.89, per 1000 atoms: 0.44 Number of scatterers: 2015 At special positions: 0 Unit cell: (58.93, 63.08, 63.91, 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 16 16.00 O 331 8.00 N 302 7.00 C 1366 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.12 Conformation dependent library (CDL) restraints added in 57.1 milliseconds 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 480 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 87.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'R' and resid 33 through 60 removed outlier: 3.531A pdb=" N TRP R 37 " --> pdb=" O PRO R 33 " (cutoff:3.500A) Proline residue: R 44 - end of helix Processing helix chain 'R' and resid 64 through 93 removed outlier: 3.562A pdb=" N VAL R 68 " --> pdb=" O ASN R 64 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR R 69 " --> pdb=" O PRO R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 136 removed outlier: 3.679A pdb=" N VAL R 134 " --> pdb=" O ARG R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 143 Processing helix chain 'R' and resid 147 through 171 Processing helix chain 'R' and resid 182 through 197 Processing helix chain 'R' and resid 198 through 216 Processing helix chain 'R' and resid 226 through 241 Processing helix chain 'R' and resid 241 through 255 removed outlier: 4.638A pdb=" N ARG R 245 " --> pdb=" O ALA R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 281 Proline residue: R 277 - end of helix 164 hydrogen bonds defined for protein. 492 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: 0.26 Time building geometry restraints manager: 0.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 280 1.31 - 1.43: 613 1.43 - 1.56: 1156 1.56 - 1.68: 0 1.68 - 1.81: 24 Bond restraints: 2073 Sorted by residual: bond pdb=" CA GLN L 16 " pdb=" C GLN L 16 " ideal model delta sigma weight residual 1.525 1.433 0.092 2.10e-02 2.27e+03 1.90e+01 bond pdb=" C GLN L 16 " pdb=" O GLN L 16 " ideal model delta sigma weight residual 1.231 1.181 0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" CA GLN L 16 " pdb=" CB GLN L 16 " ideal model delta sigma weight residual 1.530 1.488 0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" CD GLN L 16 " pdb=" NE2 GLN L 16 " ideal model delta sigma weight residual 1.328 1.288 0.040 2.10e-02 2.27e+03 3.68e+00 bond pdb=" N PHE L 11 " pdb=" CA PHE L 11 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 ... (remaining 2068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.83: 2826 6.83 - 13.66: 0 13.66 - 20.49: 0 20.49 - 27.32: 0 27.32 - 34.15: 1 Bond angle restraints: 2827 Sorted by residual: angle pdb=" N GLN L 16 " pdb=" CA GLN L 16 " pdb=" C GLN L 16 " ideal model delta sigma weight residual 111.00 76.85 34.15 2.80e+00 1.28e-01 1.49e+02 angle pdb=" N GLN L 16 " pdb=" CA GLN L 16 " pdb=" CB GLN L 16 " ideal model delta sigma weight residual 110.50 117.27 -6.77 1.70e+00 3.46e-01 1.58e+01 angle pdb=" N VAL R 134 " pdb=" CA VAL R 134 " pdb=" C VAL R 134 " ideal model delta sigma weight residual 112.96 109.40 3.56 1.00e+00 1.00e+00 1.27e+01 angle pdb=" O PRO L 15 " pdb=" C PRO L 15 " pdb=" N GLN L 16 " ideal model delta sigma weight residual 122.64 118.68 3.96 1.35e+00 5.49e-01 8.59e+00 angle pdb=" C PRO L 15 " pdb=" N GLN L 16 " pdb=" CA GLN L 16 " ideal model delta sigma weight residual 121.70 126.39 -4.69 1.80e+00 3.09e-01 6.80e+00 ... (remaining 2822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.84: 1002 11.84 - 23.67: 122 23.67 - 35.51: 47 35.51 - 47.35: 15 47.35 - 59.18: 3 Dihedral angle restraints: 1189 sinusoidal: 449 harmonic: 740 Sorted by residual: dihedral pdb=" C GLN L 16 " pdb=" N GLN L 16 " pdb=" CA GLN L 16 " pdb=" CB GLN L 16 " ideal model delta harmonic sigma weight residual -122.60 -107.17 -15.43 0 2.50e+00 1.60e-01 3.81e+01 dihedral pdb=" CA PHE L 13 " pdb=" C PHE L 13 " pdb=" N GLN L 14 " pdb=" CA GLN L 14 " ideal model delta harmonic sigma weight residual -180.00 -161.70 -18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" N GLN L 16 " pdb=" C GLN L 16 " pdb=" CA GLN L 16 " pdb=" CB GLN L 16 " ideal model delta harmonic sigma weight residual 122.80 114.47 8.33 0 2.50e+00 1.60e-01 1.11e+01 ... (remaining 1186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 228 0.031 - 0.062: 70 0.062 - 0.093: 36 0.093 - 0.125: 5 0.125 - 0.156: 1 Chirality restraints: 340 Sorted by residual: chirality pdb=" CA ILE R 32 " pdb=" N ILE R 32 " pdb=" C ILE R 32 " pdb=" CB ILE R 32 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CA PRO R 65 " pdb=" N PRO R 65 " pdb=" C PRO R 65 " pdb=" CB PRO R 65 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.25e-01 chirality pdb=" CA TYR R 280 " pdb=" N TYR R 280 " pdb=" C TYR R 280 " pdb=" CB TYR R 280 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.83e-01 ... (remaining 337 not shown) Planarity restraints: 329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO L 15 " -0.013 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" C PRO L 15 " 0.042 2.00e-02 2.50e+03 pdb=" O PRO L 15 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN L 16 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 64 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO R 65 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO R 65 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 65 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 193 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C ILE R 193 " 0.020 2.00e-02 2.50e+03 pdb=" O ILE R 193 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU R 194 " -0.007 2.00e-02 2.50e+03 ... (remaining 326 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 339 2.75 - 3.29: 1987 3.29 - 3.83: 3570 3.83 - 4.36: 3833 4.36 - 4.90: 7038 Nonbonded interactions: 16767 Sorted by model distance: nonbonded pdb=" OH TYR R 116 " pdb=" O ALA R 241 " model vdw 2.218 3.040 nonbonded pdb=" OE2 GLU R 167 " pdb=" NH2 ARG R 245 " model vdw 2.372 3.120 nonbonded pdb=" O LEU R 97 " pdb=" ND1 HIS R 101 " model vdw 2.499 3.120 nonbonded pdb=" O PHE L 13 " pdb=" N GLN L 16 " model vdw 2.522 3.120 nonbonded pdb=" C ASN R 272 " pdb=" OD1 ASN R 272 " model vdw 2.543 3.270 ... (remaining 16762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.090 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: 0.000 Process input model: 4.020 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.004 0.092 2073 Z= 0.206 Angle : 0.862 34.147 2827 Z= 0.403 Chirality : 0.038 0.156 340 Planarity : 0.004 0.033 329 Dihedral : 13.259 59.185 709 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.44 % Allowed : 11.89 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.53 (0.55), residues: 239 helix: 3.18 (0.35), residues: 201 sheet: None (None), residues: 0 loop : -2.90 (0.97), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 63 TYR 0.011 0.002 TYR R 248 PHE 0.014 0.001 PHE R 114 TRP 0.006 0.001 TRP R 255 HIS 0.002 0.001 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 2073) covalent geometry : angle 0.86237 ( 2827) hydrogen bonds : bond 0.07665 ( 164) hydrogen bonds : angle 4.67835 ( 492) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.080 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 0.4050 time to fit residues: 12.5060 Evaluate side-chains 28 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 263 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.0070 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 36 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.164600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.137411 restraints weight = 2028.624| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.51 r_work: 0.3205 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2073 Z= 0.141 Angle : 0.566 6.769 2827 Z= 0.294 Chirality : 0.039 0.124 340 Planarity : 0.004 0.042 329 Dihedral : 5.233 49.862 270 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.32 % Allowed : 9.69 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.37 (0.53), residues: 239 helix: 3.02 (0.33), residues: 201 sheet: None (None), residues: 0 loop : -2.58 (0.95), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 185 TYR 0.010 0.001 TYR R 227 PHE 0.016 0.002 PHE L 13 TRP 0.006 0.001 TRP R 37 HIS 0.002 0.001 HIS R 36 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 2073) covalent geometry : angle 0.56566 ( 2827) hydrogen bonds : bond 0.04726 ( 164) hydrogen bonds : angle 4.30117 ( 492) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.058 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.3642 time to fit residues: 12.3578 Evaluate side-chains 29 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 263 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.161823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.134958 restraints weight = 2038.832| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.43 r_work: 0.3199 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2073 Z= 0.142 Angle : 0.568 7.058 2827 Z= 0.294 Chirality : 0.039 0.123 340 Planarity : 0.005 0.044 329 Dihedral : 5.264 52.146 270 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.76 % Allowed : 7.49 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.26 (0.53), residues: 239 helix: 2.93 (0.34), residues: 201 sheet: None (None), residues: 0 loop : -2.50 (0.94), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 185 TYR 0.010 0.001 TYR R 280 PHE 0.016 0.002 PHE L 13 TRP 0.006 0.001 TRP R 139 HIS 0.003 0.001 HIS R 36 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 2073) covalent geometry : angle 0.56819 ( 2827) hydrogen bonds : bond 0.04838 ( 164) hydrogen bonds : angle 4.34664 ( 492) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.076 Fit side-chains REVERT: R 170 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.6710 (mpp) REVERT: R 261 LEU cc_start: 0.7664 (mt) cc_final: 0.7426 (mm) outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.4467 time to fit residues: 12.8655 Evaluate side-chains 29 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 166 MET Chi-restraints excluded: chain R residue 170 MET Chi-restraints excluded: chain R residue 263 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.160788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.130155 restraints weight = 2008.402| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.23 r_work: 0.3239 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2073 Z= 0.141 Angle : 0.570 7.156 2827 Z= 0.294 Chirality : 0.039 0.124 340 Planarity : 0.005 0.046 329 Dihedral : 5.314 53.573 270 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.20 % Allowed : 8.37 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.53), residues: 239 helix: 2.86 (0.34), residues: 201 sheet: None (None), residues: 0 loop : -2.58 (0.89), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 185 TYR 0.010 0.001 TYR R 227 PHE 0.015 0.002 PHE L 13 TRP 0.006 0.001 TRP R 37 HIS 0.003 0.001 HIS R 36 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 2073) covalent geometry : angle 0.57016 ( 2827) hydrogen bonds : bond 0.04821 ( 164) hydrogen bonds : angle 4.35417 ( 492) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.061 Fit side-chains REVERT: R 170 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.6595 (mpp) outliers start: 5 outliers final: 2 residues processed: 29 average time/residue: 0.4419 time to fit residues: 13.1516 Evaluate side-chains 29 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 170 MET Chi-restraints excluded: chain R residue 263 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.161118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.130716 restraints weight = 2050.334| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.24 r_work: 0.3224 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2073 Z= 0.137 Angle : 0.562 6.928 2827 Z= 0.288 Chirality : 0.039 0.123 340 Planarity : 0.005 0.047 329 Dihedral : 5.311 54.456 270 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.76 % Allowed : 8.81 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.53), residues: 239 helix: 2.89 (0.34), residues: 201 sheet: None (None), residues: 0 loop : -2.57 (0.87), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 245 TYR 0.009 0.001 TYR R 227 PHE 0.014 0.001 PHE L 13 TRP 0.006 0.001 TRP R 37 HIS 0.003 0.001 HIS R 36 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2073) covalent geometry : angle 0.56208 ( 2827) hydrogen bonds : bond 0.04708 ( 164) hydrogen bonds : angle 4.32196 ( 492) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.119 Fit side-chains REVERT: R 170 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.6633 (mpp) outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 0.4731 time to fit residues: 13.6413 Evaluate side-chains 28 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 170 MET Chi-restraints excluded: chain R residue 263 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 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 = 0.3739 r_free = 0.3739 target = 0.160899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.134769 restraints weight = 1986.018| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.49 r_work: 0.3171 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2073 Z= 0.155 Angle : 0.593 7.128 2827 Z= 0.303 Chirality : 0.040 0.125 340 Planarity : 0.005 0.048 329 Dihedral : 5.360 54.043 270 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.76 % Allowed : 7.93 % Favored : 90.31 % 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 are not related in a simple way. whole: 3.00 (0.53), residues: 239 helix: 2.76 (0.34), residues: 201 sheet: None (None), residues: 0 loop : -2.66 (0.85), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 245 TYR 0.010 0.002 TYR R 227 PHE 0.015 0.002 PHE L 13 TRP 0.007 0.001 TRP R 37 HIS 0.004 0.001 HIS R 36 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 2073) covalent geometry : angle 0.59286 ( 2827) hydrogen bonds : bond 0.05069 ( 164) hydrogen bonds : angle 4.39434 ( 492) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.070 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 0.4388 time to fit residues: 12.6062 Evaluate side-chains 27 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 263 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.159145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.128866 restraints weight = 2028.106| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.22 r_work: 0.3231 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2073 Z= 0.136 Angle : 0.564 7.096 2827 Z= 0.288 Chirality : 0.039 0.122 340 Planarity : 0.005 0.048 329 Dihedral : 5.320 55.272 270 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.32 % Allowed : 8.81 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.53), residues: 239 helix: 2.86 (0.34), residues: 201 sheet: None (None), residues: 0 loop : -2.66 (0.85), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 245 TYR 0.008 0.001 TYR R 280 PHE 0.013 0.001 PHE L 13 TRP 0.006 0.001 TRP R 37 HIS 0.006 0.001 HIS R 36 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2073) covalent geometry : angle 0.56416 ( 2827) hydrogen bonds : bond 0.04636 ( 164) hydrogen bonds : angle 4.31020 ( 492) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.080 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.4422 time to fit residues: 13.6437 Evaluate side-chains 27 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 263 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.0270 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.159794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.135444 restraints weight = 1996.032| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.37 r_work: 0.3222 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2073 Z= 0.142 Angle : 0.576 7.226 2827 Z= 0.296 Chirality : 0.039 0.123 340 Planarity : 0.005 0.048 329 Dihedral : 5.325 55.298 270 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.88 % Allowed : 9.25 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.53), residues: 239 helix: 2.84 (0.34), residues: 201 sheet: None (None), residues: 0 loop : -2.70 (0.85), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 245 TYR 0.009 0.001 TYR R 280 PHE 0.014 0.001 PHE L 13 TRP 0.006 0.001 TRP R 37 HIS 0.005 0.001 HIS R 36 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 2073) covalent geometry : angle 0.57594 ( 2827) hydrogen bonds : bond 0.04726 ( 164) hydrogen bonds : angle 4.33816 ( 492) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.089 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 27 average time/residue: 0.4526 time to fit residues: 12.5446 Evaluate side-chains 26 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 263 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.159874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.137075 restraints weight = 1983.405| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.32 r_work: 0.3227 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2073 Z= 0.141 Angle : 0.578 7.099 2827 Z= 0.296 Chirality : 0.039 0.122 340 Planarity : 0.005 0.048 329 Dihedral : 5.317 55.494 270 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.32 % Allowed : 8.81 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.53), residues: 239 helix: 2.85 (0.34), residues: 201 sheet: None (None), residues: 0 loop : -2.65 (0.85), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 245 TYR 0.009 0.001 TYR R 280 PHE 0.013 0.001 PHE L 13 TRP 0.006 0.001 TRP R 37 HIS 0.004 0.001 HIS R 36 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2073) covalent geometry : angle 0.57801 ( 2827) hydrogen bonds : bond 0.04658 ( 164) hydrogen bonds : angle 4.34296 ( 492) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.087 Fit side-chains REVERT: R 261 LEU cc_start: 0.7767 (mt) cc_final: 0.7483 (mm) outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.4671 time to fit residues: 12.4924 Evaluate side-chains 25 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 263 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.159557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.136435 restraints weight = 2013.876| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.43 r_work: 0.3209 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2073 Z= 0.142 Angle : 0.579 7.086 2827 Z= 0.297 Chirality : 0.039 0.122 340 Planarity : 0.005 0.048 329 Dihedral : 5.303 55.512 270 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.88 % Allowed : 9.25 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.52), residues: 239 helix: 2.83 (0.34), residues: 201 sheet: None (None), residues: 0 loop : -2.62 (0.85), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 245 TYR 0.009 0.001 TYR R 227 PHE 0.013 0.001 PHE L 13 TRP 0.006 0.001 TRP R 37 HIS 0.004 0.001 HIS R 36 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 2073) covalent geometry : angle 0.57932 ( 2827) hydrogen bonds : bond 0.04671 ( 164) hydrogen bonds : angle 4.34359 ( 492) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.074 Fit side-chains REVERT: R 261 LEU cc_start: 0.7805 (mt) cc_final: 0.7520 (mm) outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.3796 time to fit residues: 10.1816 Evaluate side-chains 25 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 263 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.159977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.136790 restraints weight = 2030.259| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.44 r_work: 0.3212 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2073 Z= 0.138 Angle : 0.574 7.186 2827 Z= 0.294 Chirality : 0.039 0.122 340 Planarity : 0.005 0.048 329 Dihedral : 5.286 55.814 270 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.32 % Allowed : 9.25 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.52), residues: 239 helix: 2.85 (0.34), residues: 201 sheet: None (None), residues: 0 loop : -2.54 (0.87), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 245 TYR 0.009 0.001 TYR R 227 PHE 0.012 0.001 PHE L 13 TRP 0.006 0.001 TRP R 37 HIS 0.004 0.001 HIS R 36 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 2073) covalent geometry : angle 0.57385 ( 2827) hydrogen bonds : bond 0.04570 ( 164) hydrogen bonds : angle 4.34205 ( 492) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 863.77 seconds wall clock time: 15 minutes 28.64 seconds (928.64 seconds total)