Starting phenix.real_space_refine on Wed Mar 5 15:06:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zrf_11380/03_2025/6zrf_11380.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zrf_11380/03_2025/6zrf_11380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zrf_11380/03_2025/6zrf_11380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zrf_11380/03_2025/6zrf_11380.map" model { file = "/net/cci-nas-00/data/ceres_data/6zrf_11380/03_2025/6zrf_11380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zrf_11380/03_2025/6zrf_11380.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 3 Type Number sf(0) Gaussians C 1368 2.51 5 N 396 2.21 5 O 456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2220 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "E" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "G" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "I" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "K" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "B" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "F" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "H" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "J" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "L" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Time building chain proxies: 1.78, per 1000 atoms: 0.80 Number of scatterers: 2220 At special positions: 0 Unit cell: (64.965, 47.925, 47.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 456 8.00 N 396 7.00 C 1368 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: 0.61 Conformation dependent library (CDL) restraints added in 262.5 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 552 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 360 1.28 - 1.34: 384 1.34 - 1.41: 276 1.41 - 1.47: 373 1.47 - 1.54: 863 Bond restraints: 2256 Sorted by residual: bond pdb=" CA TYC F 37 " pdb=" C TYC F 37 " ideal model delta sigma weight residual 1.525 1.486 0.039 2.10e-02 2.27e+03 3.38e+00 bond pdb=" CA TYC B 37 " pdb=" C TYC B 37 " ideal model delta sigma weight residual 1.525 1.487 0.038 2.10e-02 2.27e+03 3.32e+00 bond pdb=" CA TYC I 37 " pdb=" C TYC I 37 " ideal model delta sigma weight residual 1.525 1.487 0.038 2.10e-02 2.27e+03 3.26e+00 bond pdb=" CA TYC C 37 " pdb=" C TYC C 37 " ideal model delta sigma weight residual 1.525 1.487 0.038 2.10e-02 2.27e+03 3.25e+00 bond pdb=" CA TYC G 37 " pdb=" C TYC G 37 " ideal model delta sigma weight residual 1.525 1.487 0.038 2.10e-02 2.27e+03 3.21e+00 ... (remaining 2251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 2723 1.54 - 3.07: 277 3.07 - 4.61: 60 4.61 - 6.14: 1 6.14 - 7.68: 11 Bond angle restraints: 3072 Sorted by residual: angle pdb=" C PHE J 23 " pdb=" CA PHE J 23 " pdb=" CB PHE J 23 " ideal model delta sigma weight residual 110.65 102.97 7.68 1.95e+00 2.63e-01 1.55e+01 angle pdb=" C PHE B 23 " pdb=" CA PHE B 23 " pdb=" CB PHE B 23 " ideal model delta sigma weight residual 110.65 103.84 6.81 1.95e+00 2.63e-01 1.22e+01 angle pdb=" C PHE I 23 " pdb=" CA PHE I 23 " pdb=" CB PHE I 23 " ideal model delta sigma weight residual 110.65 103.84 6.81 1.95e+00 2.63e-01 1.22e+01 angle pdb=" C PHE A 23 " pdb=" CA PHE A 23 " pdb=" CB PHE A 23 " ideal model delta sigma weight residual 110.65 103.86 6.79 1.95e+00 2.63e-01 1.21e+01 angle pdb=" C PHE K 23 " pdb=" CA PHE K 23 " pdb=" CB PHE K 23 " ideal model delta sigma weight residual 110.65 103.86 6.79 1.95e+00 2.63e-01 1.21e+01 ... (remaining 3067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.60: 876 6.60 - 13.20: 170 13.20 - 19.80: 143 19.80 - 26.40: 35 26.40 - 33.00: 72 Dihedral angle restraints: 1296 sinusoidal: 456 harmonic: 840 Sorted by residual: dihedral pdb=" CA ALA F 25 " pdb=" C ALA F 25 " pdb=" N ILE F 26 " pdb=" CA ILE F 26 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ALA A 25 " pdb=" C ALA A 25 " pdb=" N ILE A 26 " pdb=" CA ILE A 26 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ALA D 25 " pdb=" C ALA D 25 " pdb=" N ILE D 26 " pdb=" CA ILE D 26 " ideal model delta harmonic sigma weight residual 180.00 161.99 18.01 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 1293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 149 0.026 - 0.051: 172 0.051 - 0.077: 15 0.077 - 0.102: 12 0.102 - 0.128: 12 Chirality restraints: 360 Sorted by residual: chirality pdb=" CA ILE F 26 " pdb=" N ILE F 26 " pdb=" C ILE F 26 " pdb=" CB ILE F 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE G 26 " pdb=" N ILE G 26 " pdb=" C ILE G 26 " pdb=" CB ILE G 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE E 26 " pdb=" N ILE E 26 " pdb=" C ILE E 26 " pdb=" CB ILE E 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 357 not shown) Planarity restraints: 408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 23 " 0.012 2.00e-02 2.50e+03 1.04e-02 1.90e+00 pdb=" CG PHE C 23 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE C 23 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 23 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 23 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 23 " 0.012 2.00e-02 2.50e+03 1.04e-02 1.89e+00 pdb=" CG PHE B 23 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE B 23 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 23 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 23 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 23 " 0.012 2.00e-02 2.50e+03 1.04e-02 1.88e+00 pdb=" CG PHE I 23 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE I 23 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE I 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE I 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE I 23 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE I 23 " 0.002 2.00e-02 2.50e+03 ... (remaining 405 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 78 2.57 - 3.16: 2248 3.16 - 3.74: 3211 3.74 - 4.32: 4612 4.32 - 4.90: 8142 Nonbonded interactions: 18291 Sorted by model distance: nonbonded pdb=" O SER H 20 " pdb=" OG SER J 20 " model vdw 1.993 3.040 nonbonded pdb=" ND2 ASN C 31 " pdb=" OD1 ASN C 35 " model vdw 2.148 3.120 nonbonded pdb=" ND2 ASN B 31 " pdb=" OD1 ASN B 35 " model vdw 2.148 3.120 nonbonded pdb=" ND2 ASN E 31 " pdb=" OD1 ASN E 35 " model vdw 2.148 3.120 nonbonded pdb=" ND2 ASN G 31 " pdb=" OD1 ASN G 35 " model vdw 2.148 3.120 ... (remaining 18286 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.120 Find NCS groups from input model: 0.060 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.010 0.039 2256 Z= 0.494 Angle : 1.065 7.678 3072 Z= 0.555 Chirality : 0.041 0.128 360 Planarity : 0.003 0.010 408 Dihedral : 13.340 33.000 744 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 42.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.22 (0.32), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.73 (0.24), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 18 PHE 0.024 0.005 PHE C 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.262 Fit side-chains REVERT: A 35 ASN cc_start: 0.7912 (m110) cc_final: 0.7708 (m110) REVERT: F 27 LEU cc_start: 0.9119 (tt) cc_final: 0.8909 (tt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0619 time to fit residues: 4.2055 Evaluate side-chains 21 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.135667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.117758 restraints weight = 3759.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.120880 restraints weight = 2068.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.123032 restraints weight = 1415.536| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2256 Z= 0.151 Angle : 0.675 6.728 3072 Z= 0.343 Chirality : 0.044 0.130 360 Planarity : 0.002 0.007 408 Dihedral : 6.920 18.698 372 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.75 % Allowed : 13.33 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.94 (0.33), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.25), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 18 PHE 0.012 0.002 PHE I 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.241 Fit side-chains REVERT: E 20 SER cc_start: 0.8344 (p) cc_final: 0.8074 (t) REVERT: E 27 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8392 (tt) REVERT: I 27 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8035 (tt) REVERT: B 30 THR cc_start: 0.8441 (t) cc_final: 0.8211 (m) REVERT: D 27 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8343 (tt) REVERT: H 34 SER cc_start: 0.8322 (p) cc_final: 0.7538 (m) outliers start: 9 outliers final: 2 residues processed: 56 average time/residue: 0.0585 time to fit residues: 4.6913 Evaluate side-chains 44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain D residue 27 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.131778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.114455 restraints weight = 3855.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.117390 restraints weight = 2212.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.119480 restraints weight = 1541.794| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2256 Z= 0.237 Angle : 0.672 6.067 3072 Z= 0.342 Chirality : 0.042 0.131 360 Planarity : 0.002 0.010 408 Dihedral : 7.506 19.673 372 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 3.33 % Allowed : 24.58 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.85 (0.34), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.26), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 18 PHE 0.014 0.003 PHE F 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.262 Fit side-chains REVERT: L 30 THR cc_start: 0.8293 (t) cc_final: 0.8079 (m) outliers start: 8 outliers final: 2 residues processed: 39 average time/residue: 0.0506 time to fit residues: 3.1101 Evaluate side-chains 37 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain G residue 27 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.0040 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.162777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.136777 restraints weight = 3674.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.140331 restraints weight = 1977.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.142702 restraints weight = 1300.214| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2256 Z= 0.143 Angle : 0.583 5.866 3072 Z= 0.294 Chirality : 0.042 0.123 360 Planarity : 0.002 0.007 408 Dihedral : 6.421 17.800 372 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.58 % Allowed : 25.42 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.74 (0.35), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 18 PHE 0.010 0.002 PHE K 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.259 Fit side-chains REVERT: E 20 SER cc_start: 0.8640 (t) cc_final: 0.8213 (p) REVERT: E 27 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8364 (tt) REVERT: I 27 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8047 (tt) REVERT: D 27 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8367 (tt) REVERT: H 27 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8159 (tt) REVERT: L 30 THR cc_start: 0.8508 (t) cc_final: 0.8272 (m) REVERT: L 34 SER cc_start: 0.8742 (p) cc_final: 0.8483 (m) outliers start: 11 outliers final: 6 residues processed: 48 average time/residue: 0.0493 time to fit residues: 3.5983 Evaluate side-chains 49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain H residue 27 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.158904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.131331 restraints weight = 3748.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.134864 restraints weight = 1986.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.137213 restraints weight = 1314.679| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2256 Z= 0.204 Angle : 0.594 4.719 3072 Z= 0.305 Chirality : 0.042 0.124 360 Planarity : 0.002 0.008 408 Dihedral : 6.930 17.910 372 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 3.75 % Allowed : 25.00 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.75 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.011 0.003 PHE A 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.257 Fit side-chains REVERT: E 27 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8380 (tt) REVERT: I 27 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8181 (tt) REVERT: D 27 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8509 (tt) REVERT: L 30 THR cc_start: 0.8434 (t) cc_final: 0.8192 (m) REVERT: L 34 SER cc_start: 0.8747 (p) cc_final: 0.8496 (m) outliers start: 9 outliers final: 6 residues processed: 40 average time/residue: 0.0522 time to fit residues: 3.2075 Evaluate side-chains 43 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain D residue 27 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.182630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.134057 restraints weight = 3628.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.137715 restraints weight = 1922.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.140100 restraints weight = 1266.864| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2256 Z= 0.148 Angle : 0.559 5.250 3072 Z= 0.281 Chirality : 0.042 0.123 360 Planarity : 0.001 0.006 408 Dihedral : 6.244 17.143 372 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.58 % Allowed : 25.42 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.77 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.39 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 18 PHE 0.009 0.002 PHE K 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.221 Fit side-chains REVERT: E 27 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8356 (tt) REVERT: I 27 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8037 (tt) REVERT: D 27 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8354 (tt) REVERT: H 27 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8179 (tt) REVERT: L 30 THR cc_start: 0.8466 (t) cc_final: 0.8244 (m) REVERT: L 34 SER cc_start: 0.8730 (p) cc_final: 0.8495 (m) outliers start: 11 outliers final: 6 residues processed: 46 average time/residue: 0.0525 time to fit residues: 3.6360 Evaluate side-chains 45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain H residue 27 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.182562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.134901 restraints weight = 3723.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.138688 restraints weight = 1936.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.140957 restraints weight = 1263.288| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2256 Z= 0.142 Angle : 0.537 5.372 3072 Z= 0.271 Chirality : 0.042 0.122 360 Planarity : 0.001 0.006 408 Dihedral : 5.935 16.034 372 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 5.42 % Allowed : 25.00 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.81 (0.35), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.42 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.009 0.002 PHE K 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.261 Fit side-chains REVERT: E 27 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8289 (tt) REVERT: I 27 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8009 (tt) REVERT: D 27 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8303 (tt) REVERT: H 27 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8192 (tt) REVERT: J 20 SER cc_start: 0.8656 (t) cc_final: 0.8229 (p) REVERT: L 27 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8398 (tt) REVERT: L 30 THR cc_start: 0.8446 (t) cc_final: 0.8200 (m) REVERT: L 34 SER cc_start: 0.8730 (p) cc_final: 0.8474 (m) outliers start: 13 outliers final: 7 residues processed: 44 average time/residue: 0.0502 time to fit residues: 3.3656 Evaluate side-chains 45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.163026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.137249 restraints weight = 3719.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.141021 restraints weight = 1920.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.143510 restraints weight = 1248.262| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2256 Z= 0.139 Angle : 0.528 5.680 3072 Z= 0.266 Chirality : 0.042 0.122 360 Planarity : 0.001 0.006 408 Dihedral : 5.754 15.255 372 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 5.42 % Allowed : 25.42 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.80 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.42 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 18 PHE 0.009 0.002 PHE K 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.244 Fit side-chains REVERT: E 20 SER cc_start: 0.8656 (t) cc_final: 0.8142 (p) REVERT: E 27 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8316 (tt) REVERT: I 27 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8065 (tt) REVERT: D 27 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8310 (tt) REVERT: H 27 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8193 (tt) REVERT: J 20 SER cc_start: 0.8679 (t) cc_final: 0.8272 (p) REVERT: L 27 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8402 (tt) REVERT: L 30 THR cc_start: 0.8431 (t) cc_final: 0.8197 (m) REVERT: L 34 SER cc_start: 0.8742 (p) cc_final: 0.8512 (m) outliers start: 13 outliers final: 7 residues processed: 46 average time/residue: 0.0521 time to fit residues: 3.6537 Evaluate side-chains 46 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.123119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.104162 restraints weight = 3904.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.107112 restraints weight = 2230.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.109180 restraints weight = 1564.465| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.023 2256 Z= 0.284 Angle : 0.638 4.987 3072 Z= 0.325 Chirality : 0.042 0.130 360 Planarity : 0.002 0.009 408 Dihedral : 7.354 21.706 372 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 5.83 % Allowed : 24.58 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.82 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.43 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.013 0.003 PHE K 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.246 Fit side-chains REVERT: E 27 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8555 (tt) REVERT: I 27 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8199 (tt) REVERT: H 27 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8430 (tt) REVERT: L 27 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8415 (tt) REVERT: L 30 THR cc_start: 0.8431 (t) cc_final: 0.8170 (m) REVERT: L 34 SER cc_start: 0.8831 (p) cc_final: 0.8512 (m) outliers start: 14 outliers final: 7 residues processed: 43 average time/residue: 0.0502 time to fit residues: 3.3011 Evaluate side-chains 41 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.184005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.135906 restraints weight = 3644.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.139613 restraints weight = 1877.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.142110 restraints weight = 1216.352| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2256 Z= 0.128 Angle : 0.562 6.959 3072 Z= 0.273 Chirality : 0.042 0.127 360 Planarity : 0.001 0.005 408 Dihedral : 5.868 16.146 372 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.58 % Allowed : 25.42 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.82 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.43 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 18 PHE 0.008 0.002 PHE K 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.246 Fit side-chains REVERT: E 20 SER cc_start: 0.8728 (t) cc_final: 0.8195 (p) REVERT: E 27 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8363 (tt) REVERT: I 27 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8066 (tt) REVERT: D 27 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8371 (tt) REVERT: H 27 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8125 (tt) REVERT: J 20 SER cc_start: 0.8770 (t) cc_final: 0.8374 (p) REVERT: L 27 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8407 (tt) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.0587 time to fit residues: 4.3478 Evaluate side-chains 48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.185395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.134636 restraints weight = 3607.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.138423 restraints weight = 2013.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.140800 restraints weight = 1358.070| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2256 Z= 0.160 Angle : 0.579 6.023 3072 Z= 0.285 Chirality : 0.042 0.127 360 Planarity : 0.001 0.005 408 Dihedral : 5.995 15.911 372 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 4.58 % Allowed : 25.42 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.80 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.42 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.009 0.002 PHE K 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1173.32 seconds wall clock time: 21 minutes 17.94 seconds (1277.94 seconds total)