Starting phenix.real_space_refine on Fri Mar 15 09:44:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3l_3741/03_2024/5o3l_3741.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3l_3741/03_2024/5o3l_3741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3l_3741/03_2024/5o3l_3741.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3l_3741/03_2024/5o3l_3741.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3l_3741/03_2024/5o3l_3741.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3l_3741/03_2024/5o3l_3741.pdb" } resolution = 3.4 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: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 3510 2.51 5 N 1010 2.21 5 O 1040 1.98 5 H 5790 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11360 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "G" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "H" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "I" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "J" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 5.28, per 1000 atoms: 0.46 Number of scatterers: 11360 At special positions: 0 Unit cell: (126.88, 104, 56.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 1040 8.00 N 1010 7.00 C 3510 6.00 H 5790 1.00 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 - 3.50 Amino acid : False - 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: 8.77 Conformation dependent library (CDL) restraints added in 1.3 seconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 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: 1.23 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: 9.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5780 1.03 - 1.22: 10 1.22 - 1.41: 2142 1.41 - 1.60: 3508 1.60 - 1.79: 10 Bond restraints: 11450 Sorted by residual: bond pdb=" CA HIS G 329 " pdb=" CB HIS G 329 " ideal model delta sigma weight residual 1.535 1.496 0.040 2.09e-02 2.29e+03 3.57e+00 bond pdb=" CA HIS C 329 " pdb=" CB HIS C 329 " ideal model delta sigma weight residual 1.535 1.496 0.039 2.09e-02 2.29e+03 3.55e+00 bond pdb=" CA HIS D 329 " pdb=" CB HIS D 329 " ideal model delta sigma weight residual 1.535 1.496 0.039 2.09e-02 2.29e+03 3.49e+00 bond pdb=" CA HIS H 329 " pdb=" CB HIS H 329 " ideal model delta sigma weight residual 1.535 1.497 0.039 2.09e-02 2.29e+03 3.44e+00 bond pdb=" CA HIS I 329 " pdb=" CB HIS I 329 " ideal model delta sigma weight residual 1.535 1.497 0.039 2.09e-02 2.29e+03 3.44e+00 ... (remaining 11445 not shown) Histogram of bond angle deviations from ideal: 102.38 - 108.21: 2511 108.21 - 114.04: 12568 114.04 - 119.87: 1906 119.87 - 125.70: 3683 125.70 - 131.53: 232 Bond angle restraints: 20900 Sorted by residual: angle pdb=" N GLY I 326 " pdb=" CA GLY I 326 " pdb=" C GLY I 326 " ideal model delta sigma weight residual 111.21 113.90 -2.69 1.04e+00 9.25e-01 6.67e+00 angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 111.21 113.87 -2.66 1.04e+00 9.25e-01 6.54e+00 angle pdb=" N GLY G 326 " pdb=" CA GLY G 326 " pdb=" C GLY G 326 " ideal model delta sigma weight residual 111.21 113.86 -2.65 1.04e+00 9.25e-01 6.49e+00 angle pdb=" N GLY J 326 " pdb=" CA GLY J 326 " pdb=" C GLY J 326 " ideal model delta sigma weight residual 111.21 113.86 -2.65 1.04e+00 9.25e-01 6.47e+00 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 111.21 113.86 -2.65 1.04e+00 9.25e-01 6.47e+00 ... (remaining 20895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.38: 4790 15.38 - 30.75: 325 30.75 - 46.13: 85 46.13 - 61.50: 65 61.50 - 76.88: 5 Dihedral angle restraints: 5270 sinusoidal: 3000 harmonic: 2270 Sorted by residual: dihedral pdb=" CA ILE C 360 " pdb=" C ILE C 360 " pdb=" N THR C 361 " pdb=" CA THR C 361 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA ILE D 360 " pdb=" C ILE D 360 " pdb=" N THR D 361 " pdb=" CA THR D 361 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA ILE B 360 " pdb=" C ILE B 360 " pdb=" N THR B 361 " pdb=" CA THR B 361 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 5267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 371 0.031 - 0.061: 241 0.061 - 0.091: 125 0.091 - 0.122: 108 0.122 - 0.152: 15 Chirality restraints: 860 Sorted by residual: chirality pdb=" CB VAL F 363 " pdb=" CA VAL F 363 " pdb=" CG1 VAL F 363 " pdb=" CG2 VAL F 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CB VAL D 363 " pdb=" CA VAL D 363 " pdb=" CG1 VAL D 363 " pdb=" CG2 VAL D 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CB VAL B 363 " pdb=" CA VAL B 363 " pdb=" CG1 VAL B 363 " pdb=" CG2 VAL B 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 857 not shown) Planarity restraints: 1650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 378 " -0.007 2.00e-02 2.50e+03 1.69e-02 8.58e+00 pdb=" CG PHE E 378 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE E 378 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE E 378 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 378 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE E 378 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE E 378 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE E 378 " 0.034 2.00e-02 2.50e+03 pdb=" HD2 PHE E 378 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE E 378 " -0.034 2.00e-02 2.50e+03 pdb=" HE2 PHE E 378 " -0.006 2.00e-02 2.50e+03 pdb=" HZ PHE E 378 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 378 " -0.007 2.00e-02 2.50e+03 1.69e-02 8.56e+00 pdb=" CG PHE I 378 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE I 378 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE I 378 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE I 378 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE I 378 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE I 378 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE I 378 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE I 378 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE I 378 " -0.034 2.00e-02 2.50e+03 pdb=" HE2 PHE I 378 " -0.007 2.00e-02 2.50e+03 pdb=" HZ PHE I 378 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 378 " -0.007 2.00e-02 2.50e+03 1.69e-02 8.53e+00 pdb=" CG PHE C 378 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE C 378 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 378 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 378 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE C 378 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 378 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE C 378 " 0.034 2.00e-02 2.50e+03 pdb=" HD2 PHE C 378 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE C 378 " -0.034 2.00e-02 2.50e+03 pdb=" HE2 PHE C 378 " -0.006 2.00e-02 2.50e+03 pdb=" HZ PHE C 378 " 0.024 2.00e-02 2.50e+03 ... (remaining 1647 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 306 2.05 - 2.69: 19958 2.69 - 3.33: 31993 3.33 - 3.96: 42915 3.96 - 4.60: 64842 Nonbonded interactions: 160014 Sorted by model distance: nonbonded pdb=" O SER D 316 " pdb=" HG SER F 316 " model vdw 1.419 1.850 nonbonded pdb=" O SER H 316 " pdb=" HG SER J 316 " model vdw 1.419 1.850 nonbonded pdb=" O SER B 316 " pdb=" HG SER D 316 " model vdw 1.419 1.850 nonbonded pdb=" O SER F 316 " pdb=" HG SER H 316 " model vdw 1.420 1.850 nonbonded pdb=" HG SER F 320 " pdb=" OD1 ASN F 368 " model vdw 1.420 1.850 ... (remaining 160009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 4.490 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 34.550 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 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 : 0.012 0.086 5660 Z= 0.511 Angle : 1.034 6.304 7580 Z= 0.537 Chirality : 0.057 0.152 860 Planarity : 0.010 0.055 960 Dihedral : 8.970 44.911 2160 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.39 % Favored : 77.61 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: -6.67 (0.16), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.08 (0.12), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS G 329 PHE 0.013 0.005 PHE I 346 TYR 0.009 0.003 TYR F 310 ARG 0.006 0.003 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ILE cc_start: 0.7973 (mp) cc_final: 0.7769 (mt) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.5511 time to fit residues: 199.7166 Evaluate side-chains 221 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN D 359 ASN E 336 GLN E 359 ASN ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS ** J 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5660 Z= 0.162 Angle : 0.761 6.734 7580 Z= 0.372 Chirality : 0.052 0.131 860 Planarity : 0.007 0.049 960 Dihedral : 6.890 19.071 740 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.14 % Favored : 79.86 % Rotamer: Outliers : 3.44 % Allowed : 16.88 % Favored : 79.69 % 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: -6.39 (0.16), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.87 (0.12), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 330 PHE 0.010 0.001 PHE F 378 TYR 0.016 0.002 TYR C 310 ARG 0.005 0.000 ARG J 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 246 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 358 ASP cc_start: 0.6437 (p0) cc_final: 0.6214 (p0) outliers start: 22 outliers final: 14 residues processed: 258 average time/residue: 0.4775 time to fit residues: 149.8809 Evaluate side-chains 231 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 217 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 359 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 5660 Z= 0.183 Angle : 0.715 5.471 7580 Z= 0.359 Chirality : 0.050 0.194 860 Planarity : 0.007 0.048 960 Dihedral : 6.481 17.229 740 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.03 % Favored : 81.97 % Rotamer: Outliers : 3.91 % Allowed : 16.25 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.31 (0.16), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.81 (0.12), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 362 PHE 0.005 0.001 PHE H 378 TYR 0.010 0.002 TYR A 310 ARG 0.003 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 233 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.6733 (mtp180) cc_final: 0.6458 (mtp180) REVERT: B 358 ASP cc_start: 0.6772 (p0) cc_final: 0.6453 (p0) REVERT: G 314 ASP cc_start: 0.6083 (OUTLIER) cc_final: 0.5584 (p0) outliers start: 25 outliers final: 19 residues processed: 249 average time/residue: 0.4859 time to fit residues: 148.5864 Evaluate side-chains 238 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 218 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain G residue 314 ASP Chi-restraints excluded: chain H residue 314 ASP Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 359 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.6461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5660 Z= 0.174 Angle : 0.693 4.784 7580 Z= 0.343 Chirality : 0.049 0.137 860 Planarity : 0.006 0.051 960 Dihedral : 6.088 16.522 740 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.58 % Favored : 80.42 % Rotamer: Outliers : 5.16 % Allowed : 15.78 % Favored : 79.06 % 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: -6.13 (0.16), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.66 (0.12), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 362 PHE 0.005 0.001 PHE B 346 TYR 0.009 0.002 TYR E 310 ARG 0.007 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 234 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.6737 (mtp180) cc_final: 0.6513 (mtp180) REVERT: B 358 ASP cc_start: 0.6794 (p0) cc_final: 0.6385 (p0) REVERT: D 325 LEU cc_start: 0.5287 (mt) cc_final: 0.4705 (mt) REVERT: G 314 ASP cc_start: 0.5878 (OUTLIER) cc_final: 0.5333 (p0) REVERT: I 314 ASP cc_start: 0.5845 (p0) cc_final: 0.5499 (p0) outliers start: 33 outliers final: 24 residues processed: 252 average time/residue: 0.4368 time to fit residues: 136.8547 Evaluate side-chains 245 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 314 ASP Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain H residue 314 ASP Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain I residue 359 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 ASN J 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.6841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5660 Z= 0.217 Angle : 0.702 7.660 7580 Z= 0.346 Chirality : 0.049 0.189 860 Planarity : 0.007 0.063 960 Dihedral : 5.981 16.537 740 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.03 % Favored : 81.97 % Rotamer: Outliers : 5.31 % Allowed : 17.34 % Favored : 77.34 % 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: -5.95 (0.17), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.53 (0.13), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 362 PHE 0.005 0.001 PHE B 346 TYR 0.012 0.002 TYR F 310 ARG 0.007 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 235 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 358 ASP cc_start: 0.6775 (p0) cc_final: 0.6384 (p0) REVERT: D 325 LEU cc_start: 0.5280 (mt) cc_final: 0.4655 (mt) REVERT: E 358 ASP cc_start: 0.6568 (p0) cc_final: 0.6191 (p0) REVERT: G 314 ASP cc_start: 0.6055 (OUTLIER) cc_final: 0.5439 (p0) outliers start: 34 outliers final: 25 residues processed: 253 average time/residue: 0.4206 time to fit residues: 132.9485 Evaluate side-chains 245 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 219 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain G residue 314 ASP Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain H residue 314 ASP Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 348 ASP Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 359 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.0970 chunk 67 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.7087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5660 Z= 0.117 Angle : 0.648 4.651 7580 Z= 0.317 Chirality : 0.048 0.131 860 Planarity : 0.007 0.054 960 Dihedral : 5.533 15.627 740 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.04 % Favored : 82.96 % Rotamer: Outliers : 4.53 % Allowed : 20.31 % Favored : 75.16 % 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: -5.71 (0.18), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.35 (0.13), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 330 PHE 0.004 0.001 PHE J 346 TYR 0.011 0.002 TYR A 310 ARG 0.004 0.001 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 243 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 358 ASP cc_start: 0.6644 (p0) cc_final: 0.6353 (p0) REVERT: D 325 LEU cc_start: 0.5249 (mt) cc_final: 0.4606 (mt) REVERT: E 358 ASP cc_start: 0.6475 (p0) cc_final: 0.6116 (p0) REVERT: G 314 ASP cc_start: 0.5948 (OUTLIER) cc_final: 0.5313 (p0) outliers start: 29 outliers final: 25 residues processed: 261 average time/residue: 0.4312 time to fit residues: 139.9398 Evaluate side-chains 247 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 221 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 314 ASP Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain H residue 314 ASP Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 348 ASP Chi-restraints excluded: chain I residue 359 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.7357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5660 Z= 0.169 Angle : 0.663 5.819 7580 Z= 0.323 Chirality : 0.047 0.145 860 Planarity : 0.006 0.056 960 Dihedral : 5.575 17.039 740 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.93 % Favored : 85.07 % Rotamer: Outliers : 4.69 % Allowed : 20.16 % Favored : 75.16 % 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: -5.61 (0.18), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.27 (0.14), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 362 PHE 0.006 0.001 PHE B 346 TYR 0.012 0.002 TYR A 310 ARG 0.003 0.001 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 228 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 358 ASP cc_start: 0.6642 (p0) cc_final: 0.6351 (p0) REVERT: C 307 GLN cc_start: 0.5387 (mp10) cc_final: 0.5165 (mp10) REVERT: D 325 LEU cc_start: 0.5285 (mt) cc_final: 0.4638 (mt) REVERT: E 358 ASP cc_start: 0.6649 (p0) cc_final: 0.6280 (p0) REVERT: G 314 ASP cc_start: 0.6047 (OUTLIER) cc_final: 0.5484 (p0) outliers start: 30 outliers final: 26 residues processed: 245 average time/residue: 0.4081 time to fit residues: 125.9329 Evaluate side-chains 248 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 221 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain G residue 314 ASP Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 314 ASP Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain J residue 314 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.7542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5660 Z= 0.127 Angle : 0.642 4.906 7580 Z= 0.312 Chirality : 0.048 0.135 860 Planarity : 0.006 0.060 960 Dihedral : 5.381 18.724 740 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.21 % Favored : 84.79 % Rotamer: Outliers : 5.00 % Allowed : 21.41 % Favored : 73.59 % 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: -5.46 (0.19), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.14), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 330 PHE 0.004 0.001 PHE B 378 TYR 0.011 0.002 TYR A 310 ARG 0.004 0.001 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 231 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 358 ASP cc_start: 0.6613 (p0) cc_final: 0.6333 (p0) REVERT: C 307 GLN cc_start: 0.5507 (mp10) cc_final: 0.5297 (mp10) REVERT: D 325 LEU cc_start: 0.5180 (mt) cc_final: 0.4563 (mt) REVERT: E 358 ASP cc_start: 0.6727 (p0) cc_final: 0.6351 (p0) REVERT: G 314 ASP cc_start: 0.6061 (OUTLIER) cc_final: 0.5487 (p0) REVERT: G 344 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7294 (mt) outliers start: 32 outliers final: 30 residues processed: 246 average time/residue: 0.4223 time to fit residues: 132.2556 Evaluate side-chains 257 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 225 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain G residue 314 ASP Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 314 ASP Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 348 ASP Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain J residue 314 ASP Chi-restraints excluded: chain J residue 344 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.7707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5660 Z= 0.156 Angle : 0.637 5.125 7580 Z= 0.310 Chirality : 0.047 0.130 860 Planarity : 0.006 0.060 960 Dihedral : 5.414 18.929 740 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % Rotamer: Outliers : 5.31 % Allowed : 21.41 % Favored : 73.28 % 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: -5.39 (0.19), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 330 PHE 0.004 0.001 PHE J 378 TYR 0.013 0.002 TYR D 310 ARG 0.004 0.001 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 225 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 358 ASP cc_start: 0.6627 (p0) cc_final: 0.6341 (p0) REVERT: D 325 LEU cc_start: 0.5401 (mt) cc_final: 0.4772 (mt) REVERT: E 358 ASP cc_start: 0.6802 (p0) cc_final: 0.6433 (p0) REVERT: G 314 ASP cc_start: 0.6041 (OUTLIER) cc_final: 0.5506 (p0) REVERT: G 344 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7402 (mt) REVERT: G 358 ASP cc_start: 0.6679 (p0) cc_final: 0.6463 (p0) REVERT: J 311 LYS cc_start: 0.5039 (tppt) cc_final: 0.4671 (tppt) outliers start: 34 outliers final: 31 residues processed: 241 average time/residue: 0.4110 time to fit residues: 124.5777 Evaluate side-chains 258 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 225 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain G residue 314 ASP Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 314 ASP Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 314 ASP Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain J residue 314 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.7865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5660 Z= 0.145 Angle : 0.634 5.049 7580 Z= 0.307 Chirality : 0.047 0.124 860 Planarity : 0.006 0.057 960 Dihedral : 5.334 17.691 740 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Rotamer: Outliers : 5.62 % Allowed : 22.19 % Favored : 72.19 % 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: -5.29 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 362 PHE 0.004 0.001 PHE H 346 TYR 0.014 0.002 TYR D 310 ARG 0.005 0.001 ARG H 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 229 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 358 ASP cc_start: 0.6620 (p0) cc_final: 0.6284 (p0) REVERT: D 325 LEU cc_start: 0.5465 (mt) cc_final: 0.4822 (mt) REVERT: E 358 ASP cc_start: 0.6817 (p0) cc_final: 0.6443 (p0) REVERT: G 314 ASP cc_start: 0.5974 (OUTLIER) cc_final: 0.5481 (p0) REVERT: G 358 ASP cc_start: 0.6675 (p0) cc_final: 0.6466 (p0) REVERT: J 311 LYS cc_start: 0.5132 (tppt) cc_final: 0.4782 (tppt) outliers start: 36 outliers final: 33 residues processed: 247 average time/residue: 0.4216 time to fit residues: 131.1969 Evaluate side-chains 256 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 222 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain E residue 307 GLN Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain G residue 314 ASP Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain H residue 311 LYS Chi-restraints excluded: chain H residue 314 ASP Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 314 ASP Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain J residue 314 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 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 = 0.4713 r_free = 0.4713 target = 0.158815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.139346 restraints weight = 26929.682| |-----------------------------------------------------------------------------| r_work (start): 0.4498 rms_B_bonded: 3.15 r_work: 0.4484 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4377 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.7983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5660 Z= 0.123 Angle : 0.614 4.744 7580 Z= 0.297 Chirality : 0.046 0.121 860 Planarity : 0.006 0.059 960 Dihedral : 5.234 17.705 740 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 4.84 % Allowed : 22.81 % Favored : 72.34 % 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: -5.16 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 330 PHE 0.004 0.001 PHE H 346 TYR 0.011 0.002 TYR D 310 ARG 0.011 0.001 ARG F 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4513.62 seconds wall clock time: 80 minutes 5.55 seconds (4805.55 seconds total)