Starting phenix.real_space_refine on Mon Feb 10 20:10:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zrf_11380/02_2025/6zrf_11380.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zrf_11380/02_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_11380/02_2025/6zrf_11380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zrf_11380/02_2025/6zrf_11380.map" model { file = "/net/cci-nas-00/data/ceres_data/6zrf_11380/02_2025/6zrf_11380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zrf_11380/02_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-5592/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: 1.77, 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: 0.55 Conformation dependent library (CDL) restraints added in 237.7 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: 0.51 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: 0.64 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.790 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:2.830 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.200 ------------------------------------------------------------------------------- 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 : 0.227 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: 0.0589 time to fit residues: 4.0341 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 : 0.249 ------------------------------------------------------------------------------- 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: 0.6980 chunk 23 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** 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** ** 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 = 0.4211 r_free = 0.4211 target = 0.186728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.137786 restraints weight = 3661.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.141431 restraints weight = 1953.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.143778 restraints weight = 1309.375| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2256 Z= 0.137 Angle : 0.670 6.763 3072 Z= 0.338 Chirality : 0.044 0.128 360 Planarity : 0.002 0.006 408 Dihedral : 6.679 18.449 372 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.75 % Allowed : 10.83 % Favored : 85.42 % 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: -5.92 (0.34), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.50 (0.26), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 18 PHE 0.011 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 61 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.271 Fit side-chains REVERT: E 20 SER cc_start: 0.8387 (p) cc_final: 0.8130 (t) REVERT: E 27 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8387 (tt) REVERT: G 34 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.7871 (m) REVERT: I 27 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7974 (tt) REVERT: D 27 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8289 (tt) REVERT: H 34 SER cc_start: 0.8352 (p) cc_final: 0.7634 (m) outliers start: 9 outliers final: 1 residues processed: 58 average time/residue: 0.0596 time to fit residues: 4.9819 Evaluate side-chains 51 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** ** 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 = 0.4141 r_free = 0.4141 target = 0.134688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.117625 restraints weight = 3828.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.120506 restraints weight = 2181.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.122599 restraints weight = 1520.085| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2256 Z= 0.186 Angle : 0.637 6.241 3072 Z= 0.324 Chirality : 0.041 0.125 360 Planarity : 0.002 0.010 408 Dihedral : 6.972 17.700 372 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 3.33 % Allowed : 23.33 % Favored : 73.33 % 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 (0.34), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.43 (0.26), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 18 PHE 0.013 0.003 PHE K 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 49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.270 Fit side-chains REVERT: E 27 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8471 (tt) REVERT: L 30 THR cc_start: 0.8352 (t) cc_final: 0.8134 (m) REVERT: L 34 SER cc_start: 0.8539 (p) cc_final: 0.8290 (m) outliers start: 8 outliers final: 2 residues processed: 45 average time/residue: 0.0496 time to fit residues: 3.4445 Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 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 18 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.156828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.127752 restraints weight = 3722.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.131092 restraints weight = 2007.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.133180 restraints weight = 1350.203| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 2256 Z= 0.289 Angle : 0.686 4.611 3072 Z= 0.353 Chirality : 0.042 0.132 360 Planarity : 0.002 0.011 408 Dihedral : 7.965 22.391 372 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 24.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 3.75 % Allowed : 27.50 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 : -4.43 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.015 0.003 PHE A 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 43 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.235 Fit side-chains REVERT: I 27 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8225 (tt) REVERT: D 27 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8643 (tt) REVERT: L 30 THR cc_start: 0.8454 (t) cc_final: 0.8217 (m) REVERT: L 34 SER cc_start: 0.8754 (p) cc_final: 0.8425 (m) outliers start: 9 outliers final: 5 residues processed: 41 average time/residue: 0.0516 time to fit residues: 3.2712 Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain G residue 34 SER 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 36 THR Chi-restraints excluded: chain D 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: 4.9990 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** H 18 HIS ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.118328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.099985 restraints weight = 4192.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.102914 restraints weight = 2342.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.104908 restraints weight = 1609.935| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 2256 Z= 0.345 Angle : 0.739 6.185 3072 Z= 0.376 Chirality : 0.044 0.130 360 Planarity : 0.002 0.011 408 Dihedral : 8.303 24.167 372 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 26.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 4.58 % Allowed : 26.67 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.89 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.48 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.016 0.004 PHE K 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 37 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.197 Fit side-chains REVERT: E 27 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8585 (tt) REVERT: I 27 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8246 (tt) REVERT: D 27 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8675 (tt) REVERT: H 27 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8449 (tt) REVERT: L 30 THR cc_start: 0.8478 (t) cc_final: 0.8224 (m) REVERT: L 34 SER cc_start: 0.8754 (p) cc_final: 0.8360 (m) outliers start: 11 outliers final: 6 residues processed: 36 average time/residue: 0.0502 time to fit residues: 2.7592 Evaluate side-chains 35 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 36 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain H 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: 3.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 18 HIS ** K 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.199527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.167508 restraints weight = 3890.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.170115 restraints weight = 2363.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.171816 restraints weight = 1631.763| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2256 Z= 0.117 Angle : 0.571 5.551 3072 Z= 0.282 Chirality : 0.043 0.123 360 Planarity : 0.001 0.005 408 Dihedral : 6.146 18.429 372 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.58 % Allowed : 27.08 % Favored : 68.33 % 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 I 18 PHE 0.008 0.002 PHE G 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 52 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.251 Fit side-chains REVERT: E 27 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8337 (tt) REVERT: I 27 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8007 (tt) REVERT: D 27 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8323 (tt) REVERT: H 27 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.7997 (tt) REVERT: J 20 SER cc_start: 0.8767 (t) cc_final: 0.8299 (p) REVERT: L 30 THR cc_start: 0.8466 (t) cc_final: 0.8264 (m) REVERT: L 34 SER cc_start: 0.8728 (p) cc_final: 0.8522 (m) outliers start: 11 outliers final: 6 residues processed: 49 average time/residue: 0.0564 time to fit residues: 4.0490 Evaluate side-chains 43 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 36 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 28 SER 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: 4.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 18 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.159241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.132096 restraints weight = 3760.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.135673 restraints weight = 1992.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.138063 restraints weight = 1313.447| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 2256 Z= 0.194 Angle : 0.597 5.061 3072 Z= 0.302 Chirality : 0.042 0.125 360 Planarity : 0.002 0.007 408 Dihedral : 6.681 17.986 372 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 7.08 % Allowed : 25.00 % Favored : 67.92 % 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: -5.87 (0.35), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.47 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 18 PHE 0.010 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 51 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.222 Fit side-chains REVERT: E 27 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8408 (tt) REVERT: I 27 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8137 (tt) REVERT: D 27 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8499 (tt) REVERT: H 27 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8352 (tt) REVERT: L 27 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8370 (tt) REVERT: L 30 THR cc_start: 0.8490 (t) cc_final: 0.8273 (m) REVERT: L 34 SER cc_start: 0.8780 (p) cc_final: 0.8507 (m) outliers start: 17 outliers final: 8 residues processed: 47 average time/residue: 0.0607 time to fit residues: 4.2146 Evaluate side-chains 44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 18 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.185642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.137684 restraints weight = 3686.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.141428 restraints weight = 1887.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.143965 restraints weight = 1216.780| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2256 Z= 0.112 Angle : 0.537 5.888 3072 Z= 0.269 Chirality : 0.042 0.121 360 Planarity : 0.001 0.005 408 Dihedral : 5.632 16.714 372 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 5.00 % Allowed : 27.08 % Favored : 67.92 % 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: -5.86 (0.35), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.46 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS I 18 PHE 0.008 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 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.251 Fit side-chains REVERT: E 20 SER cc_start: 0.8686 (t) cc_final: 0.8132 (p) REVERT: E 27 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8340 (tt) REVERT: I 27 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8033 (tt) REVERT: D 27 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8328 (tt) REVERT: H 27 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8082 (tt) REVERT: J 20 SER cc_start: 0.8726 (t) cc_final: 0.8292 (p) REVERT: L 27 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8382 (tt) REVERT: L 30 THR cc_start: 0.8475 (t) cc_final: 0.8268 (m) REVERT: L 34 SER cc_start: 0.8809 (p) cc_final: 0.8588 (m) outliers start: 12 outliers final: 6 residues processed: 52 average time/residue: 0.0569 time to fit residues: 4.3358 Evaluate side-chains 50 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 0.0570 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.0060 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.5114 ------------------------------------------------------------------------------- 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** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.167574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.143862 restraints weight = 3569.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.147625 restraints weight = 1795.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.150197 restraints weight = 1143.727| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2256 Z= 0.092 Angle : 0.519 6.147 3072 Z= 0.258 Chirality : 0.042 0.120 360 Planarity : 0.001 0.005 408 Dihedral : 4.970 14.191 372 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 5.00 % Allowed : 26.25 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.35), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.41 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS I 18 PHE 0.007 0.001 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 66 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.232 Fit side-chains REVERT: A 23 PHE cc_start: 0.8213 (m-80) cc_final: 0.7926 (m-10) REVERT: E 20 SER cc_start: 0.8688 (t) cc_final: 0.8139 (p) REVERT: E 27 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8372 (tt) REVERT: E 28 SER cc_start: 0.8243 (OUTLIER) cc_final: 0.7993 (t) REVERT: I 27 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7994 (tt) REVERT: D 27 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8285 (tt) REVERT: H 27 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8025 (tt) REVERT: J 20 SER cc_start: 0.8688 (t) cc_final: 0.8392 (p) REVERT: L 27 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8419 (tt) REVERT: L 30 THR cc_start: 0.8538 (t) cc_final: 0.8303 (m) REVERT: L 34 SER cc_start: 0.8802 (p) cc_final: 0.8601 (m) outliers start: 12 outliers final: 5 residues processed: 63 average time/residue: 0.0640 time to fit residues: 5.5936 Evaluate side-chains 63 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 E residue 28 SER Chi-restraints excluded: chain G residue 27 LEU 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 4 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 18 HIS ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.120687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.101871 restraints weight = 4003.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.104861 restraints weight = 2249.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.106896 restraints weight = 1560.878| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.030 2256 Z= 0.372 Angle : 0.714 4.794 3072 Z= 0.366 Chirality : 0.043 0.128 360 Planarity : 0.002 0.012 408 Dihedral : 7.941 24.007 372 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 25.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 3.33 % Allowed : 27.50 % 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: -5.85 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.28), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.015 0.003 PHE L 15 ********************** 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 41 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.241 Fit side-chains REVERT: E 27 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8540 (tt) REVERT: E 28 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8229 (t) REVERT: K 18 HIS cc_start: 0.7571 (OUTLIER) cc_final: 0.7060 (t-90) REVERT: L 30 THR cc_start: 0.8474 (t) cc_final: 0.8198 (m) REVERT: L 34 SER cc_start: 0.8870 (p) cc_final: 0.8515 (m) outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 0.0523 time to fit residues: 3.1946 Evaluate side-chains 37 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 E residue 28 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain K residue 18 HIS Chi-restraints excluded: chain K residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.133162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.115210 restraints weight = 3705.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.118247 restraints weight = 2172.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.120199 restraints weight = 1522.541| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3555 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= 0.125 Angle : 0.585 6.786 3072 Z= 0.285 Chirality : 0.043 0.128 360 Planarity : 0.001 0.005 408 Dihedral : 6.133 17.481 372 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.58 % Allowed : 27.08 % Favored : 68.33 % 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: -5.87 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.47 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS K 18 PHE 0.008 0.002 PHE K 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1089.15 seconds wall clock time: 20 minutes 12.52 seconds (1212.52 seconds total)