Starting phenix.real_space_refine on Mon Sep 23 12:02:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrf_11380/09_2024/6zrf_11380.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrf_11380/09_2024/6zrf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrf_11380/09_2024/6zrf_11380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrf_11380/09_2024/6zrf_11380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrf_11380/09_2024/6zrf_11380.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrf_11380/09_2024/6zrf_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-5461/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: 1.52, per 1000 atoms: 0.68 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: 0.90 Conformation dependent library (CDL) restraints added in 254.3 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: 1.65 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: 0.99 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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: 0.360 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: 0.010 Set scattering table: 0.030 Process input model: 11.610 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.234 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: 0.0603 time to fit residues: 4.1455 Evaluate side-chains 21 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.249 Fit side-chains REVERT: E 20 SER cc_start: 0.8213 (p) cc_final: 0.7980 (t) REVERT: E 27 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8293 (tt) REVERT: G 34 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.7771 (m) REVERT: I 27 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7881 (tt) REVERT: D 27 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8153 (tt) REVERT: H 34 SER cc_start: 0.8224 (p) cc_final: 0.7434 (m) outliers start: 9 outliers final: 1 residues processed: 58 average time/residue: 0.0533 time to fit residues: 4.4751 Evaluate side-chains 51 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 19 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.024 2256 Z= 0.268 Angle : 0.699 5.963 3072 Z= 0.359 Chirality : 0.042 0.125 360 Planarity : 0.002 0.011 408 Dihedral : 7.757 21.071 372 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % 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: -5.86 (0.34), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.46 (0.26), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 18 PHE 0.015 0.004 PHE A 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 44 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.251 Fit side-chains REVERT: L 30 THR cc_start: 0.8333 (t) cc_final: 0.8052 (m) outliers start: 8 outliers final: 3 residues processed: 39 average time/residue: 0.0413 time to fit residues: 2.5791 Evaluate side-chains 37 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain I residue 34 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** C 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2958 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= 0.141 Angle : 0.597 5.616 3072 Z= 0.299 Chirality : 0.042 0.123 360 Planarity : 0.002 0.007 408 Dihedral : 6.538 18.281 372 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.75 % Allowed : 27.08 % 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: -5.76 (0.35), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 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 48 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.244 Fit side-chains REVERT: E 20 SER cc_start: 0.8499 (t) cc_final: 0.8087 (p) REVERT: E 27 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8307 (tt) REVERT: I 27 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7996 (tt) REVERT: D 27 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8238 (tt) REVERT: L 30 THR cc_start: 0.8507 (t) cc_final: 0.8231 (m) REVERT: L 34 SER cc_start: 0.8740 (p) cc_final: 0.8389 (m) outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 0.0491 time to fit residues: 3.3602 Evaluate side-chains 47 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 K residue 27 LEU Chi-restraints excluded: chain K residue 34 SER 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 20 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2256 Z= 0.295 Angle : 0.669 4.673 3072 Z= 0.345 Chirality : 0.042 0.125 360 Planarity : 0.002 0.010 408 Dihedral : 7.821 22.129 372 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 24.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 4.17 % Allowed : 26.67 % 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 A 18 PHE 0.014 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 40 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 30 time to evaluate : 0.264 Fit side-chains REVERT: E 27 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8510 (tt) REVERT: I 27 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8207 (tt) REVERT: D 27 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8544 (tt) REVERT: H 27 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8363 (tt) REVERT: L 30 THR cc_start: 0.8439 (t) cc_final: 0.8153 (m) REVERT: L 34 SER cc_start: 0.8732 (p) cc_final: 0.8349 (m) outliers start: 10 outliers final: 6 residues processed: 38 average time/residue: 0.0509 time to fit residues: 3.0153 Evaluate side-chains 37 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 27 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2256 Z= 0.191 Angle : 0.617 5.506 3072 Z= 0.307 Chirality : 0.042 0.127 360 Planarity : 0.002 0.007 408 Dihedral : 6.966 18.988 372 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 5.00 % Allowed : 25.83 % 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: -5.81 (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 0.011 0.002 PHE D 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 47 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 35 time to evaluate : 0.244 Fit side-chains REVERT: E 27 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8321 (tt) REVERT: I 27 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8070 (tt) REVERT: D 27 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8325 (tt) REVERT: H 27 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8163 (tt) REVERT: L 30 THR cc_start: 0.8499 (t) cc_final: 0.8243 (m) REVERT: L 34 SER cc_start: 0.8711 (p) cc_final: 0.8373 (m) outliers start: 12 outliers final: 7 residues processed: 44 average time/residue: 0.0497 time to fit residues: 3.3066 Evaluate side-chains 44 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 G residue 36 THR Chi-restraints excluded: chain I 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3255 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= 0.137 Angle : 0.561 5.449 3072 Z= 0.278 Chirality : 0.042 0.122 360 Planarity : 0.001 0.006 408 Dihedral : 6.051 17.063 372 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 5.00 % Allowed : 26.67 % 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: -5.85 (0.35), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 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 49 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.241 Fit side-chains REVERT: E 27 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8289 (tt) REVERT: I 27 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.7991 (tt) REVERT: D 27 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8233 (tt) REVERT: H 27 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8097 (tt) REVERT: L 27 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8216 (tt) REVERT: L 30 THR cc_start: 0.8514 (t) cc_final: 0.8262 (m) REVERT: L 34 SER cc_start: 0.8720 (p) cc_final: 0.8408 (m) outliers start: 12 outliers final: 5 residues processed: 47 average time/residue: 0.0508 time to fit residues: 3.5810 Evaluate side-chains 42 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 28 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain I 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 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 6 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.0570 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2256 Z= 0.104 Angle : 0.525 5.913 3072 Z= 0.260 Chirality : 0.042 0.120 360 Planarity : 0.001 0.005 408 Dihedral : 5.281 15.139 372 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.42 % Allowed : 26.25 % 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 (0.35), 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 0.003 0.001 HIS E 18 PHE 0.007 0.001 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 58 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.313 Fit side-chains REVERT: A 23 PHE cc_start: 0.8330 (m-80) cc_final: 0.8019 (m-10) REVERT: E 20 SER cc_start: 0.8541 (t) cc_final: 0.8029 (p) REVERT: E 27 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8298 (tt) REVERT: I 27 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.7982 (tt) REVERT: D 27 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8142 (tt) REVERT: H 27 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.7986 (tt) REVERT: J 20 SER cc_start: 0.8362 (t) cc_final: 0.8084 (p) REVERT: L 23 PHE cc_start: 0.8787 (m-80) cc_final: 0.8584 (m-10) REVERT: L 27 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8221 (tt) REVERT: L 30 THR cc_start: 0.8596 (t) cc_final: 0.8312 (m) REVERT: L 34 SER cc_start: 0.8755 (p) cc_final: 0.8438 (m) outliers start: 13 outliers final: 7 residues processed: 55 average time/residue: 0.0583 time to fit residues: 4.6896 Evaluate side-chains 53 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 22 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3235 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= 0.285 Angle : 0.649 4.940 3072 Z= 0.329 Chirality : 0.042 0.126 360 Planarity : 0.002 0.010 408 Dihedral : 7.349 21.880 372 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 4.17 % Allowed : 27.50 % 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: -5.86 (0.36), 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 0.002 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 38 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 28 time to evaluate : 0.247 Fit side-chains REVERT: E 27 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8488 (tt) REVERT: E 28 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8076 (t) REVERT: H 27 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8370 (tt) REVERT: L 30 THR cc_start: 0.8435 (t) cc_final: 0.8160 (m) REVERT: L 34 SER cc_start: 0.8764 (p) cc_final: 0.8381 (m) outliers start: 10 outliers final: 6 residues processed: 37 average time/residue: 0.0508 time to fit residues: 2.9395 Evaluate side-chains 37 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 28 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 G residue 34 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain H residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2256 Z= 0.121 Angle : 0.566 6.970 3072 Z= 0.274 Chirality : 0.042 0.127 360 Planarity : 0.001 0.005 408 Dihedral : 5.811 16.255 372 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 4.58 % Allowed : 27.92 % Favored : 67.50 % 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 : -4.46 (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 51 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.258 Fit side-chains REVERT: E 27 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8185 (tt) REVERT: E 28 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7889 (t) REVERT: I 27 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8025 (tt) REVERT: D 27 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8133 (tt) REVERT: H 27 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.7971 (tt) REVERT: J 20 SER cc_start: 0.8414 (t) cc_final: 0.8132 (p) REVERT: L 30 THR cc_start: 0.8515 (t) cc_final: 0.8271 (m) REVERT: L 34 SER cc_start: 0.8766 (p) cc_final: 0.8456 (m) outliers start: 11 outliers final: 6 residues processed: 48 average time/residue: 0.0514 time to fit residues: 3.7030 Evaluate side-chains 49 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.130647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.112805 restraints weight = 3825.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.115776 restraints weight = 2249.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.117789 restraints weight = 1582.977| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2256 Z= 0.200 Angle : 0.612 6.050 3072 Z= 0.301 Chirality : 0.042 0.128 360 Planarity : 0.002 0.007 408 Dihedral : 6.537 18.285 372 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % 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: -5.83 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.44 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.010 0.002 PHE K 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 930.39 seconds wall clock time: 17 minutes 45.57 seconds (1065.57 seconds total)